Research Highlights

Dynamic Regulation of Histone Chaperone Nucleoplasmin May 3, 2018
Small-angle X-ray scattering (SAXS) analysis of nucleoplasmin (Npm) Core+A2 truncation (1-145) bound to five H2A/H2B dimers. (Top) SAXs envelope of the pentameric complex (pink) with the best nuclear magnetic resonance (NMR)–restrained SAXS hybrid model inside. (Bottom) SAXS curve of the complex (purple dots). Simulated SAXS curve (black line) from the best-scoring structural model. [From Warren, C., et al. “Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.” Nat. Commun. 8, 2215 (2017). DOI:10.1038/s41467-017-02308-3. Reused under a Creative Commons license (CC BY 4.0,​).]
Histones are eukaryotic cell nuclei proteins that package and order DNA into structural units called nucleosomes. Chromatin is the complex of DNA and proteins comprising the genome’s physiological form. As chromatin’s chief protein components, histones act as spools around which DNA winds, playing a role in gene regulation. A chaperone protein assists in the folding and unfolding of macromolecules, such as in the assembly of nucleosomes from folded histones and DNA. Nucleoplasmin (Npm) is a highly conserved embryonic histone chaperone, responsible for the maternal storage and zygotic release of histones H2A and H2B. Npm contains a pentameric N-terminal Core domain and an intrinsically disordered C-terminal Tail domain. Although intrinsically disordered regions are common among histone chaperones, their roles in histone binding and chaperoning have remained unclear.

This study, using the Xenopus laevis Npm Tail domain, unveils the architecture of the Npm histone complex and a mechanism of histone chaperone regulation. It demonstrates that intramolecular regulation of the histone chaperone Npm controls histone binding and release—a key process in the earliest stages of embryonic development. Structural analyses enabled model constructions of both the Npm Tail domain and the pentameric complex, revealing that the Tail domain controls the binding of histones through specific, electrostatic interactions. Functional analyses demonstrated that these competitive interactions negatively regulate Npm histone chaperone activity in vitro. Data from these studies establish a potentially generalizable mechanism of histone chaperone regulation via dynamic and specific intramolecular shielding of histone interaction sites.

Warren, C., et al. “Dynamic intramolecular regulation of the histone chaperone nucleoplasmin controls histone binding and release.” Nat. Commun. 8, 2215 (2017). DOI:10.1038/s41467-017-02308-3.

Instruments and Facilities Used: Bruker 600 nuclear magnetic resonance (NMR) and Inova 600 NMR instruments in the Albert Einstein College of Medicine (AECM) Einstein Structural NMR Resource; and bio–small-angle X-ray scattering (bio-SAXS) beamline 4-2, SLAC National Accelerator Laboratory’s Stanford Synchrotron Radiation Lightsource (SSRL).

“Zip-code” Mechanism for Hormone Signaling Revealed January 25, 2018
Crystal structure of multikinase inhibitor sKLB bound to fibroblast growth factor (FGF) FGF21CT reveals two distinct binding sites. Structure of extracellular domain of β-Klotho “longevity” protein (green ribbons) bound to FGF21 hormone (salmon ball-and-stick) unveils critical molecular interactions required for hormone binding and cell activation. Yellow sticks denote nitrogen (N)-linked glycans. Grey dashed lines denote regions that do not exhibit significant electron density. About 30 angsroms (Å) apart, the FGF binding sites on the β-Klotho D1 and D2 domains are located on the opposite side of the molecule from the flexible linker that connects the two glycosidase domains and may contribute to the interdomain dynamic properties that enable complex formation with ligands and FGF receptors (FGFRs). [Reprinted by permission from Springer Nature: Lee, S., et al. “Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signaling.” Nature 553, 501–505 (2018). DOI:10.1038/nature25010. Copyright 2018]
Named after the Greek goddess who spun the thread of life, Klotho proteins play an important role in the regulation of longevity and metabolism. Alpha-Klotho is a membrane-spanning protein expressed predominantly in the kidney, as well as in the brain. Mice lacking α-klotho exhibit a range of signs associated with aging and have elevated blood phosphate levels. Like α-klotho, β-klotho functions as a co-receptor for endocrine fibroblast growth factors (FGFs). FGF21 is secreted from the liver following fasting, acting in fat cells and the brain to induce metabolic adaptation to fasting and responses to stress. Although FGF receptors (FGFRs) are expressed in a wide range of tissues, expression of the β-klotho “longevity” protein in the liver, fat, and brain restricts the target organs of these endocrine FGFs.

In a recent Yale Medical School–led study, researchers revealed the three-dimensional (3D), high-resolution structure of β-Klotho, illuminating its intricate mechanism and potential for antiaging therapeutics, as well as for treating a wide range of medical conditions. X-ray crystallography data revealed critical molecular interactions required for hormone binding and cell activation. The specific “zip-code”–like interactions of β-klotho receptors appear to regulate critical metabolic processes in the liver, kidneys, and brain, among other organs. Analysis yielded several insights, including that β-Klotho is the primary receptor that binds to FGF21, a key hormone that stimulates insulin sensitivity and glucose metabolism, causing weight loss. The researchers believe this new understanding can guide the development of therapies by improving the biological activity of FGF21. Also found were a new variant of FGF21 that has 10 times higher potency and cellular activity and the evidence of how a structurally related enzyme (glycosidase) that breaks down sugars evolved into a receptor for a hormone that lowers blood sugar. Researchers believe the untangled β-Klotho structure presents a platform for exploring and developing agents that either enhance or block the pathway, enabling therapies for conditions such as liver cancer and bone diseases.

Lee, S., et al. “Structures of β-klotho reveal a ‘zip code’-like mechanism for endocrine FGF signaling.” Nature 553, 501–505 (2018). DOI:10.1038/nature25010.

Instruments and Facilities Used: X-ray data were collected from β-klotho–receptor crystals at Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, beamline 14-1 as part of the program to aid National Synchrotron Light Source (NSLS) users prior to NSLS-II operations.

Structure of a Flavoenzyme Assembly Intermediate January 18, 2018
(a) The structure of the FrdA-SdhE flavoenzyme assembly intermediate: flavoprotein subunit FrdA (cyan), assembly factor SdhE (green), flavin adenine dinucleotide FAD (orange sticks), and malonate (yellow sticks). The boxed region highlights the covalent interaction between the FAD and the enzyme. (b) Overlay of the flavin-binding domains of the FrdA subunit from the FrdA-SdhE intermediate (cyan) and the FrdA subunit from the mature assembled FrdABCD complex (gray). A rotation of 10.8° is observed in the capping domain of the assembly intermediate when compared to assembled FrdABCD. [From Sharma, P., et al. “Crystal structure of an assembly intermediate of respiratory Complex II,” Nat. Commun. 9, 274 (2018). DOI:10.1038/s41467-017-02713-8. Reused under a Creative Commons license (CC BY 4.0,​.)]
Enzymes frequently depend on an electron transport cofactor for executing catalytic functions such as reduction-oxidation (redox) reactions. For flavoenzymes, the cofactor is flavin adenine dinucleotide (FAD), whose binding type with the enzyme impacts the redox potential and thus reaction chemistry, such as for metabolism and detoxification. Researchers in this study discovered that the structure of an assembled flavoenzyme intermediate reveals the mechanism of covalent flavin binding in respiration. Assembly factors include SdhAF2 in humans, SdhE in Escherichia coli, and Sdh5 in yeast. Other revelations include that mitochondrial flavoenzymes drive both noncovalent and covalent redox reactions and that the assembly factor (SdhE, a small protein of ~90 to 140 amino acids, conserved in all kingdoms) in the structure of the SdhE:FrdA complex with covalent FAD stabilizes a conformation of the flavoprotein subunit FrdA that favors succinate oxidation.

Researchers fixed the E. coli FrdA-SdhE intermediate via site-specific crosslinking, resolving the structure to 2.6 angstroms (Å). This study identified that SdhE stabilizes an FrdA conformation that likely enables the mechanism of autocatalytic covalent flavinylation. FrdA’s FAD-binding domain and capping domain both interact with SdhE, but structural data revealed a 10.8° difference in their angles. The investigators believe that domain rotation affects flavinylation, showing that enzymes are tuned to catalyze reactions in different ways and that conformational diversity can directly relate to catalytic mechanism diversity.

Sharma, P., et al. “Crystal structure of an assembly intermediate of respiratory Complex II.” Nat. Commun. 9, 274 (2018). DOI:10.1038/s41467-017-02713-8.

Instruments and Facilities Used: Small angle X-ray scattering (SAXS) and diffraction and mass spectrometry analysis using beamline 9-2 at Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory (SLAC).

A Regional Model for Uranium Redox and Mobility December 15, 2017
Anoxic organic-enriched sediments strongly accumulate uranium as U(IV), sulfide, and other reduced species. Seasonal reduction-oxidation (redox) cycling triggered by changing water tables can intermittently mobilize these species. [Courtesy Vincent Noël and John Bargar, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory]
Uranium (U) contamination stubbornly persists as a challenging and costly water quality concern at former uranium ore processing sites across the Upper Colorado River Basin (UCRB). Plumes at these sites are not self-attenuating via natural flushing by groundwater as originally expected. Recent studies at the Rifle, Colo., legacy site suggest that organic-enriched anoxic sediments create conditions that promote reduction of U(VI) to relatively immobile U(IV), causing it to accumulate locally under persistently saturated and anoxic conditions. However, incursion of oxidants into reduced sediments could transform contaminants, allowing these sediments to act as secondary sources of uranium. Oxidant incursions take place during periods of changing water tables, which occur in UCRB throughout the year. If these sediments were regionally common in the UCRB and exposed to varying reduction-oxidation (redox) conditions, then they could contribute to maintaining the longevity of regional uranium plumes.

To investigate these issues, researchers examined the occurrence and distribution of reduced and oxidized iron (Fe), sulfur (S), and U species in sediment cores spanning dry and oxic to wet and reduced conditions at three different UCRB sites. Detailed molecular characterization involved chemical extractions, X-ray absorption spectroscopy (XAS), Mössbauer spectroscopy, and X-ray microspectroscopy. This work demonstrates that anoxic organic-enriched sediments occur at all sites, strongly accumulate sulfides and U, and are exposed to strong seasonal redox cycles. Uranium was found to be present as U(IV) complexed to sediment-associated organic carbon and possibly to mineral surfaces. This finding is significant because complexed U(IV) is relatively susceptible to oxidative mobilization. Sediment particle size, organic carbon content, and pore saturation control redox conditions in sediments and thus strongly influence Fe, S, and U biogeochemistry. These findings help to illuminate the mechanistic linkages between hydrology, sediment texture, and biogeochemistry. They further provide enhanced contextual and conceptual underpinnings to support reactive transport modeling of uranium, other contaminants, and nutrients in redox-variable floodplains—a subject of importance to BER research missions. Cyclic redox variability has major implications for mobility of carbon (C), nitrogen (N), and metal contaminants in groundwater and surface waters. Redox-variable, organic-enriched sediments mediate the mobility of C, N, Fe, S, U, and metal contaminants regionally in the UCRB. Organic-enriched sediments were established to regionally mediate groundwater quality within the UCRB.

Noël, V., et al. “Understanding controls on redox processes in floodplain sediments of the Upper Colorado River Basin.” Sci. Total Environ. 603–604, 663–675 (2017). DOI:10.1016/j.scitotenv.2017.01.109.

Noël, V., et al. “Redox constraints over U(IV) mobility in the floodplains of Upper Colorado River Basin.” Environ. Sci. Technol. 51(19), 10954–10964 (2017). DOI:10.1021/acs.est.7b02203.

Instruments and Facilities Used: X-ray absorption spectroscopy and X-ray microprobe mapping at Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory (SLAC), and Mössbauer spectroscopy at Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL).

Cyanobacterial Studies Examine Cellular Structure During Nitrogen Starvation November 15, 2017
Researchers from Washington University in St. Louis and Oak Ridge National Laboratory (ORNL) are using neutrons to study what happens when cyanobacteria cell samples (pictured) are starved for nitrogen. They are especially interested in how this process affects phycobilisomes, large antenna protein complexes in the cells that harvest light for photosynthesis. A better understanding of this natural phenomenon could lead to improvements in artificial resources like solar panels. [Courtesy ORNL]
Using nondestructive neutron scattering techniques, scientists are examining how single-celled organisms called cyanobacteria produce oxygen and obtain energy through photosynthesis. Collaborators are conducting a series of experiments to study the behavior of phycobilisomes—large antenna protein complexes in cyanobacteria cells. Phycobilisomes harvest light to initiate photosynthesis, and a better understanding of this process could help researchers design more efficient solar panels and other artificial structures that mimic natural systems. Neutrons can analyze these delicate structures without damaging or killing the cyanobacteria and with more spatial accuracy than other techniques like microscopy. Bio-SANS allows observing what’s happening at the nanoscale level in real time in a living cell.

Phycobilisomes attach to cellular membranes where the light-dependent reactions of photosynthesis take place. Changing the antenna complexes of the phycobilisomes can have dramatic and far-reaching consequences in cyanobacteria. Artificially modifying phycobilisomes by deleting certain genes in the cells caused structural defects in the cellular membranes and other cell physiology, allowing scientists to observe the resulting structural changes.

Starving the cyanobacteria for nitrogen naturally modifies the antenna complexes, causing the antenna to decrease in size and leading to significant cellular membrane modifications, because the cells break down the phycobilisomes and use them as an alternative nitrogen source to survive. By determining the extent of these changes, the team hopes to better understand the structure-function relationship between cellular organization and natural modification. These processes can be immediately reversed by restoring nitrogen to the cells. The researchers plan to compare these results to those recorded from their genetic studies to explore the differences between artificial and natural modifications and their effects on the intracellular makeup of cyanobacteria.

Instruments and Facilities Used: Photosynthetic Antenna Research Center (PARC), a DOE-funded Energy Frontier Research Center based at Washington University. Small angle neutron scattering (SANS) Bio-SANS instrument, beamline CG‑3, at Oak Ridge National Laboratory’s High Flux Isotope Reactor.

Precise Control of Neutron Contrast in Surfactant Micelles Provides Platform for Membrane Structure Studies September 29, 2017
Detergent Micelles
The scattering collected for detergent at its solution match point, where contrast still persists between core and shell, produces a non-flat scattering profile (red). Incorporating the non-ionic detergent DDM with deuterium-labelled chains allows matching of the core and shell contrast, producing the flat scattering profile shown in blue. [Reprinted with permission from Oliver, R. C., S. V. Pingali, and V. S. Urban. “Designing Mixed Detergent Micelles for Uniform Neutron Contrast.” J. Phys. Chem. Lett. 8, 5041–5046 (2017). [DOI: 10.1021/acs.jpclett.7b02149]. Copyright 2017 American Chemical Society.]
Scientists in this study have successfully demonstrated the ability to manipulate the neutron contrast of detergent micelles by incorporating a similar detergent with deuterium-labelled alkyl chains. The presence of excess detergent micelle scattering often has a detrimental influence on scattering data obtained for membrane protein–detergent complexes. Isolation of the scattering signal from the protein of interest can be accomplished by eliminating all scattering from the detergent. Using this approach enabled determination of the overall structure and oligomeric state of a small membrane protein enzyme.

Oliver, R. C., et al. “Designing Mixed Detergent Micelles for Uniform Neutron Contrast.” The Journal of Physical Chemistry Letters 8(20), 5041–5046 (2017). [DOI:10.1021/acs.jpclett.7b02149].

Instruments and Facilities Used: Small angle neutron scattering (SANS): Bio-SANS beamline (CG3) of the High-Flux Isotope Reactor at Oak Ridge National Laboratory (ORNL). Recorded scattering data using MantidPlot software. Neutron contrast studies: ModULes for the Analysis of Contrast (MULCh) Variation Data at University of Sydney (

Dynamics on Cellulose Show Two Important Populations from Neutron Scattering and Simulations September 19, 2017
Elastic Intensity Scans
Elastic intensity scans of dry and hydrated cellulose. Dashed lines denote inflection points in the curves at 220 and 260 K, the temperatures at which the surface water (nonfreezing) and interfibrillar water (freezing) become mobile in the hydrated cellulose sample, respectively. Inset illustration depicts water populations associated with cellulose. [Adapted from O’Neill, H., et al. “Dynamics of Water Bound to Crystalline Cellulose.” Sci. Rep. 7, 11840 (2017). [DOI:10.1038/s41598-017-12035-w]. Reused under a Creative Commons license (CC BY 4.0, Curve colors were modified, and additional labels and inset added.]
Biomass pretreatment is necessary to make cellulose accessible to hydrolysis for conversion to biofuels. Understanding water’s role in cellulose reactivity will aid discovery of the underlying processes that change biomass morphology and reactivity during different pretreatment regimes for biofuels production. In this study, cellulose-water interactions were examined using neutron scattering supported by molecular dynamics simulation. The data show two distinct populations of water molecules—one tightly “bound” to the surface and the other interfibrillar and translationally mobile. Accurate models of hydration water in the cell wall can address fundamental questions about cellulose-water interactions. The mobility of the interfibrillar water is also important to enzyme and chemical attack and is distinct from the bound and bulk water.

O’Neill, H. M., et al. “Dynamics of Water Bound to Crystalline Cellulose.” Sci. Rep. 7, Article 11840 (2017). [DOI:10.1038/s41598-017-12035-w].

Instruments and Facilities Used: Deuterium labeling, neutron scattering, and molecular dynamics simulation; quasi-elastic neutron scattering (QENS) using BASIS, the Backscattering Spectrometer, at Oak Ridge National Laboratory (ORNL) Spallation Neutron Source (SNS). Structural characterization using small-angle neutron scattering (SANS) CG-3 Bio-SANS instrument at High Flux Isotope Reactor (HFIR) facility of ORNL and X-ray diffraction (XRD) analysis combined with SANS. Wide-Angle X-ray Diffraction (WAXD) using theta-theta goniometer Bruker D5005 instrument; quasi-elastic neutron scattering (QENS) using BASIS, the Backscattering Spectrometer at ORNL SNS; Molecular Dynamics (MD) Simulations (GROMACS software and the CHARMM C36 carbohydrate force field); and TIP4P water model.

Measuring and Modeling Poplar Root Water Extraction After Drought Using Neutron Imaging September 9, 2017
 poplar seedling
Composite images of 16 radiographs of 11-week-old poplar seedling in sand. Intensity indicates water content. [Reprinted with permission of Springer from Dhiman, I., et al. “Quantifying Root Water Extraction After Drought Recovery Using Sub-mm In Situ Empirical Data.” Plant Soil 47, 1–17 (2017). [DOI:10.1007/s11104-017-3408-5]. © U.S. Government (outside the USA) 2017.]
Neutron radiography was used to measure soil water movement and water uptake by individual roots in situ. Root water uptake was linked to root traits; smaller-diameter roots had greater water uptake per unit surface area than larger-diameter roots. Model analysis based on root-free soil hydraulic properties indicated unreasonably large water fluxes among the vertical soil layers during the first 16 hours after wetting. These results suggest problems with common soil hydraulic or root surface area modeling approaches, indicating the need to further investigate and understand the impacts of roots on soil hydraulic properties. This work highlights the team’s ability to link root water uptake to characteristic root traits, thus enabling performance assessment of common water uptake models

Dhiman, I., et al. “Quantifying Root Water Extraction After Drought Recovery Using sub-mm In Situ Empirical Data.” Plant Soil 417, 1–17 (2017). [DOI:10.1007/s11104-017-3408-5].

Instruments and Facilities Used: Sequential neutron radiography using CG1-D beam line using cold neutrons, at High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Neutron attenuation by plant samples was detected with a 25-μm lithium fluoride / zinc sulfide (LiF/ ZnS) scintillator linked to a charge coupled detector (CCD) camera system (iKon – L 936, Andor Technology plc., Belfast, U.K.). Roots scanned and dimensions measured using WinRhizo software (Regent Instruments Inc., Quebec, Canada.

The Origins of Photosynthesis in a Sun-Loving Bacteria September 8, 2017
Crystallization to Structural Solution
Crystallization to Structural Solution: (a) Emerald-colored protein crystals used. (b) Representative diffraction pattern with spots highlighted in blue circles and resolution rings designated by dashed lines. (c) Artistic representation developed from these patterns of the resultant three-dimensional protein crystal structure of the heliobacterial reaction center. [Courtesy Christopher Gisriel, Arizona State University]
Reaction centers (RCs) are pigment-protein complexes that drive photosynthesis by converting light into chemical energy (electrons) to power the cell, possibly arising from a homodimeric protein. The symmetry of a homodimer is broken in heterodimeric rRC structures, while the 2.2-Angstrom resolution X-ray structure of the homodimeric RC-photosystem from the phototroph Heliobacterium modesticaldum exhibits perfect C2 symmetry. The core polypeptide dimer and two small subunits coordinate 54 bacteriochlorophylls and 2 carotenoids that capture and transfer energy to the electron-transfer chain at the center, which performs charge separation and comprises 6 (bacterio)chlorophylls and an iron-sulfur cluster; unlike other RCs, it lacks a bound quinone. This structure preserves characteristics of the ancestral reaction center, providing insight into the evolution of photosynthesis.

Enough sunlight hits the Earth to power the planet many times over—if energy capture were more efficient. Thus, scientists have looked at nature’s means to understand photosynthesis in a sun-loving, soil-dwelling bacterium. A team of scientists has gained a fundamental understanding of the inner workings of this vital process and how it differs among plant systems. Their discovery may provide a new template for beginning organic-based solar panel design (i.e., “artificial leaves”) or possibly renewable biofuel applications.

But the team’s structural biologists are capturing freeze-frame images of crystallized proteins throughout the whole process of the simplest form of photosynthesis, in the single-celled heliobacteria, which are fundamentally different than plants. Instead of using water like plants, for example, heliobacteria use hydrogen sulfide and grow without oxygen; after photosynthesis, they give off the foul-smelling sulfur gas in place of oxygen. The scientists grew the “perfect” X-ray diffracting crystal charge after many initial trials. In this breakthrough study, they found an almost perfect symmetry in the heliobacter RC, which helps it gather every available photon of near-infrared light to build chlorophylls.

Gisriel, C., et al. “Structure of a symmetric photosynthetic reaction center–photosystem,” Science 357(6355), 1021–1025 (2017). [DOI:10.1126/science.aan5611].

Instruments and Facilities Used: X-ray macromolecular crystallograpy at Biodesign Center for Applied Structural Discovery at Arizona State University. Advanced Light Source at Berkeley Center for Structural Biology at Lawrence Berkeley National Laboratory. Structural Biology Center–CAT beamline of the Advanced Photon Source at Argonne National Laboratory.

Exploring the Roots of Photosynthesis in a Soil-Dwelling Bacterium September 8, 2017
structure H. modesticaldum
Overall structure of the H. modesticaldum photosynthetic reaction center. The transmembrane helices are shown in gold and red. Light-harvesting “antenna” molecules are colored green, and the electron-transfer chain is colored blue. [From Gisriel, C., et al. “Structure of a Symmetric Photosynthetic Reaction Center–Photosystem,” Science 357(6355), 1021–1025 (2017). DOI:10.1126/science.aan5611. Reprinted with permission from AAAS.]
The simplest known bacterium able to drive photosynthesis is found in muddy soils near hot springs. Heliobacterium modesticaldum is a sun-loving, soil-dwelling, thermophilic bacterium that photosynthesizes near-infrared light, unlike plants, which use different parts of visible light. The photosynthesis reaction centers (RCs) of H. modesticaldum are thought to resemble the earliest common ancestor of all photosynthesis complexes, which evolved around three billion years ago. Thus, a clear, detailed picture of the H. modesticaldum RC would provide valuable insight into the early evolution of photosynthesis. However, successfully purifying an RC protein and growing the crystals needed for X-ray crystallography can be a lengthy, difficult process.

Researchers successfully capped 7 years of work by obtaining a high-resolution (2.2 Å) structure of the membrane protein at the heart of the photosynthetic RC of H. modesticaldum. The structure revealed details such as the interactions between light-harvesting “antenna” molecules and the electron-transfer chain, where the initial steps required to convert photon energy into chemical energy occurs. With this data, the research team was able to make comparisons to other types of RCs, gaining new perspectives on the early evolution of photosynthesis and how nature optimized light-driven energy collection. This work will help unlock the secrets of photosynthesis, possibly leading to the development of cleaner, solar-based renewable energy.

Gisriel, C., et al. “Structure of a Symmetric Photosynthetic Reaction Center–Photosystem.” Science 357(6355), 1021–1025 (2017). [DOI:10.1126/science.aan5611].

Instruments and Facilities: Beamline 8.2.1 at Advanced Light Source at Lawrence Berkeley National Laboratory; Advanced Photon Source at Argonne National Laboratory.

X-ray Footprinting Solves Mystery of Metal-Breathing Protein August 14, 2017
3D structural rendering of protein
Results from X-ray footprinting mass spectrometry (XFMS) experiments at Lawrence Berkeley National Laboratory’s (LBNL) Advanced Light Source, mapped out on these three-dimensional structural renderings of a protein, helped researchers identify where the protein binds with a mineral. Red areas indicate possible binding areas. [Reprinted with permission from Fukushima, T., et al. “The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface.” J. Am. Chem. Soc. 139(36), 12647–12654, (2017). [DOI:10.1021/jacs.7b06560]. Copyright (2017) American Chemical Society.]
Scientists have discovered the details of an unconventional coupling between a bacterial protein and a mineral that allows the bacterium to breathe when oxygen is not available. This research could lead to new innovations in linking proteins to other materials for bio-based electronic devices, such as sensors that can diagnose disease or detect contaminants. It also could help researchers to understand and control the chemical reactions sparked by these protein-material interactions and, eventually, how organisms remodel their environment and make biominerals.

Researchers relied on an X-ray-based technique known as “footprinting” to pinpoint the chemical connections between the bacterial protein and nanoparticles composed of iron and oxygen. The study identified a previously mapped, surprisingly small and weak binding site, but unknown was how the site bound to the metal-containing mineral because conventional techniques can’t see this binding process. Footprinting reveals interactions of proteins in a near-native environment. The protein selected for the study is from the metal-reducing bacterium Shewanella oneidensis, which “eats sugar and basically breathes minerals” when oxygen is unavailable. This study already is providing ideas on how to redesign these proteins to make better electronic connections and thus more sensitive bioelectronic sensors.

Fukushima, T., et al. “The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface.” J. Am. Chem. Soc. 139(36), 12647–12654, (2017). [DOI:10.1021/jacs.7b06560].

Instruments and Facilities Used: X-ray beamline 5.3.1 of the Advanced Light Source (ALS) to perform “footprinting” and mass spectrometry at the Biological Nanostructures Facility at the Molecular Foundry, both at Lawrence Berkeley National Laboratory (LBNL), and the LBNL-led DOE Joint BioEnergy Institute.

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Hacking the Bacterial Social Network August 11, 2017
structure of protein complex CdiA-Cdil-EF-Tu
Scientists have determined the molecular structure of this protein complex—an insight that could lead to new biomedical strategies for overcoming pathogenic bacteria that cause infectious diseases. This representation shows the neutralized complex of the CdiA toxin (purple and beige) with the CdiI immunity protein (orange and pink) and the elongation factor (EF)–Tu (grey and green). [Karolina Michalska, Argonne National Laboratory]
Scientists have determined the molecular structures of a highly specialized set of proteins that a strain of Escherichia coli bacteria use to communicate and defend their turf. Ironically, loads of bacteria cover the devices humans use to communicate—even more than on toilet seats, according to one study. Bacteria appear to have their own form of social network that allows these single-cell creatures to attract and repel one another. This insight stems from new research that could lead to new biomedical strategies for overcoming pathogenic bacteria that cause infectious diseases such as pneumonia and food-borne illnesses.

The work builds on the 2005 discovery that the bacteria produce toxic proteins, which they can transfer to their neighbors through direct contact to either kill or control them, possibly to gain better access to nutrients in densely populated microbial communities through a process called contact-dependent growth inhibition (CDI). Learning how the bacteria interact and communicate is helping to resolve the possibly different activities of the toxins, which “may affect different bacteria differently.” Found in soil and gut bacteria, as well as in human pathogens, some of these toxins of CDI systems are present, for example, in Pseudomonas aeruginosa, which is involved in lung disease.

The team obtained the molecular structures of proteins that belong to a three-part system of the NC101 strain of E. coli, which consists of the CDI toxin, its immunity protein, and its elongation factor (EF). The latter, known as EF-Tu, is a protein that plays a key role in protein synthesis. Knowing the protein structures of all three parts helps scientists understand their function. Discovery of the immunity protein has led scientists to suspect that the system’s purpose  includes competition and signaling (intracommunication), as well as killing and controlling other bacteria. Actually, only a few molecules of the toxin “get into the neighboring cell,” so perhaps the toxin is “not meant to kill, but rather to control and communicate.” It can act on the transfer ribonucleic acid (tRNA) only under highly specific circumstances, and it is the first case seen where the EF is “needed for the toxin to function.” Researchers used high-bright X-rays to characterize, or identify, biological proteins and inspect chemical processes at the nanoscale level (i.e., one billionth of a meter).

Michalska, K., et al. “Structure of a Novel Antibacterial Toxin That Exploits Elongation Factor Tu to Cleave Specific Transfer RNAs.” Nucleic Acids Res. 45(17), 10306–10320 (2017). [DOI:10.1093/nar/gkx700].

Instruments and Facilities Used: Advanced Photon Source 19-ID beamline and Advanced Protein Characterization Facility at Argonne National Laboratory.

New Chemical Strategy for Conversion of CO2 to Biomass August 3, 2017
acetone carboxylase
Upon nucleotide binding, acetone carboxylase undergoes conformational shifts, opening an internal solvent channel. (a) Ligand-free structure showing a substrate channel (grey) linking the nucleotide binding site to the outside solvent and allowing adenosine triphosphate (ATP) cofactor and carbon dioxide (CO2) substrate to enter. Access to the manganese (Mn) active site is closed by an α-helix in the path. (b) The adenosine monophosphate (AMP)–bound structure shows an opening of an internal channel (grey) linking the nucleotide binding site to the Mn active site. The blocking helix becomes a disordered loop when AMP is bound. [From Mus, F., et al. “Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation.” Nat. Sci. Rep. 7, Article 7234 (2017). DOI:10.1038/s41598-017-06973-8. Reused under a Creative Commons license (CC by 4.0,]
A research team has uncovered a new mechanism for enzyme-mediated carbon dioxide (CO2) capture and conversion. They have revealed new and unique elements of carboxylation chemistry (CC) that could be used in catalytic strategies for converting CO2 into chemical feedstock or biomass. The crystal structure of acetone carboxylase (AC; enzyme involved in biodegradation by bacteria) was solved using X-ray crystallographic data. The inactive, unbound (apo) structure shows a substrate channel blocked off from the manganese (Mn) active site where CO2 conversion takes place. An adenosine monophosphate (AMP)–bound structure contains large conformational changes that open the channel to the active site. Highly reactive intermediates in the channel are protected from outside solvent as they are transported to the Mn active site for CO2 conversion. Stepwise mechanisms of carboxylation reactions differ in essential ways with respect to co-substrate, co-factor, and metal requirements. Knowledge of these mechanisms provides the basis for an increased fundamental understanding of CC, contributing to future strategies for CO2 capture and conversion to biomass. These in turn may mitigate the effects of increasing concentrations of CO2 on the global climate.

Mus, F., et al. “Structural Basis for the Mechanism of ATP-Dependent Acetone Carboxylation.” Nat. Sci. Rep. 7, Article 7234 (2017). [DOI:10.1038/s41598-017-06973-8].

Instruments and Facilities Used: X-ray crystallographic data from the Stanford Synchrotron Lightsource (SSLS) at SLAC National Accelerator Laboratory (SLAC). Structural data from macromolecular crystallography were measured on SSLS beamline 12-2; Advanced Photon Source (APS) at Argonne National Laboratory (ANL); and the Diamond Light Source, Oxfordshire, United Kingdom.

The CRISPR Target-Recognition Mechanism July 20, 2017

Cas1-Cas2 complexSurface representation of the Cas1-Cas2 complex, consisting of four Cas1 proteins (light and dark green) and two Cas2 proteins (yellow). Donor DNA (brown) is being integrated into the target DNA (blue), at a precise location in the CRISPR array, following a short leader sequence (red). [From Wright, A. V., et al.  “Structures of the CRISPR Genome Integration Complex,” Science 357(6356), 1113–1118 (2017). [DOI:10.1126/science.aao0679. Reprinted with permission from AAAS*.]

* Readers may view, browse, and/or download material for temporary copying purposes only, provided these uses are for noncommercial personal purposes. Except as provided by law, this material may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed, published, or sold in whole or in part, without prior written permission from the publisher.



Bacterial DNA is characterized by regions of clustered regularly interspaced short palindromic repeats (CRISPRs) and associated Cas proteins (CRISPR-associated endonucleases). The CRISPR-Cas system has revolutionized gene editing by vastly simplifying the insertion of short snippets of new (“donor”) DNA into very specific locations of target DNA. Researchers in this study have discovered how Cas proteins recognize their target locations with such great specificity. They used x-ray crystallography to solve the structures of Cas1 and Cas2—responsible for DNA-snippet capture and integration—as the proteins were bound to synthesized DNA strands designed to mimic different stages of the process. The research also demonstrated how the system works in its native context as part of a bacterial immune system and how Cas proteins act as general-purpose molecular recording devices—tools for encoding information in genomes.

Cas1 appears to have evolved from a more “promiscuous” (less selective) type of enzyme that catalyzes the movement of DNA sequences from one position to another (a transposase). At some point, Cas1 acquired an unusual degree of specificity for a particular location in the bacterial genome, the CRISPR array. This specificity is critical to the bacteria, both for acquiring immunity and for avoiding genome damage caused by the insertion of viral fragments at the wrong location. The researchers wanted to learn how Cas1-Cas2 proteins recognize the target sequence to enable comparison with previously studied transposases and integrases (i.e., enzymes that catalyze the integration of donor DNA into target DNA) and to determine whether the proteins can be altered to recognize new sequences for custom applications.

The researchers crystallized Cas1-Cas2 in complex with preformed DNA strands that mimicked reaction intermediates and products. X-ray crystallography revealed that the structures showed substantial distortions in the target DNA, but there were surprisingly few sequence-specific contacts with the Cas1-Cas2 complex, and the DNA’s resulting flexibility produced disorder in the crystals. Attempts to model the DNA across the disordered sections showed that the DNA had to be even more distorted. Cryoelectron microscopy experiments, coupled with the crystallography data, confirmed that an accessor protein called the integration host factor (IHF) introduces an additional sharp bend in the DNA, bringing an upstream recognition sequence into contact with Cas1 to increase both the specificity and efficiency of integration. The architecture of the CRISPR integration complex suggests that subtle adjustment of the distance between Cas1 active sites could reprogram the system to recognize different target sites. Changes in its architecture could be exploited, thereby, for genome tagging applications and also may explain the natural divergence of CRISPR arrays in bacteria.

Wright, A. V., et al. “Structures of the CRISPR Genome Integration Complex,” Science 357(6356), 1113–1118 (2017). [DOI:10.1126/science.aao0679].

Instruments and Facilities Used: X-ray macromolecular crystallography; beamline 8.3.1; protein crystallography (PX); and scattering/diffraction at the Advanced Light Source at Lawrence Berkeley National Laboratory; Stanford Synchrotron Radiation Light Source 9-2 beamline.


Brown Rot Fungi Reveal a New Approach for Biomass Conversion to Fuels and Chemicals July 11, 2017
Brown rot fungi

(A) Brown rot fungi mushrooms, (B) SANS profiles, (C) SFG spectra of brown rot fungi–mediated cellulose deconstruction, and (D) AFM images of repolymerized lignin in brown rot cell walls. [(A) Wikimedia Commons, Zinnmann; (B) Authors; (C) and (D) From Goodell, B., et al. “Modification of the Nanostructure of Lignocellulose Cell walls via a Non-Enzymatic Lignocellulose Deconstruction System in Brown Rot Wood-Decay Fungi.” Biotechnol. Biofuels 10, 179 (2017). [DOI 10.1186/s13068-017-0865-2]. Reused under a Creative Commons license (CC BY 4.0,]
A multimodal approach used in this study examined wood decay by the brown rot fungi, Gloeophyllum trabeum or Rhodonia placenta, that degrade wood using a chelator-mediated Fenton (CMF) reaction. Small-angle neutron scattering (SANS) showed changes in microfibril bundling and lignin structure during biomass breakdown. Complementary approaches, sum frequency generation (SFG) spectroscopy, X-ray diffraction, atomic force microscopy (AFM), and transmission electron microscopy (TEM) also contributed information on nanoscale structural changes in wood over time. Woods studied were southern yellow pine (Pinus spp.) and birch (Betula verrucosa Ehr.). The data support a degradation mechanism in which sugars released by non-enzymatic action diffuse from the cell wall,  facilitated by increasing the porosity of the cell walls. This is a paradigm shift in understanding the mechanism of brown rot fungal degradation.

Goodell, B., et al. “Modification of the Nanostructure of Lignocellulose Cell Walls via a Non-Enzymatic Lignocellulose Deconstruction System in Brown Rot Wood-Decay Fungi.” Biotechnol. Biofuels 10(1), 179 (2017). [DOI:10.1186/s13068-017-0865-2].

Instruments and Facilities Used: Small angle neutron scattering (SANS) – Bio-SANS at High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). Sum frequency generation (SFG) spectroscopy, broadband SFG system. Chelator-mediated Fenton treatments (CMF) and cellulase treatment. X-ray diffraction analysis (XRD) – PANalytical Empyrean diffractometer, The Netherlands, equipped with a Cu X-ray source. Attenuated total reflectance Fourier transform infrared analysis (ATR-FTIR): Nicolet 8700 FTIR Spectrometer (Thermo Scientific) equipped with a smart iTR diamond ATR unit, a KBr beam splitter, and a deuterated triglycine sulfate (DTGS) detector. Atomic force microscopy (AFM) of brown-rotted wood surfaces. Nanoscope IIIa AFM-Digital Instruments, Santa Barbara, California with three 5 µm scans. Transmission electron microscopy (TEM) – Philips CM12 TEM instrument (Philips, Eindhoven, The Netherlands); images recorded on Kodak 4489 negative film and the films subsequently scanned using an Epson Perfection Pro 750 film scanner.

Novel Orange Carotenoid Proteins Shedding Light on Evolution of Cyanobacteria Photoprotection July 10, 2017
blue-green algae
Filamentous blue-green algae [Courtesy Landcare Research. Reused under a Creative Commons license (CC By 4.0,]
A research study has identified and characterized a new, functionally distinct member of the orange carotenoid protein (OCP) family. The OCP complex enables chromatically acclimating blue-green algae to avoid cellular damage and growth inhibition in conditions of high light or nutrient stress. In a recent bioinformatic analysis of all available cyanobacterial genomes, the group found that many of these ecophysiologically diverse organisms encode more than one copy of the full-length OCP. The study’s focus was the filamentous blue-green algae Tolypothrix, which encodes two OCPs.

One copy was determined to be functionally equivalent to the well-characterized OCP of Synechocystis cyanobacteria, dubbed OCP1. But the second, OCP2, was distinct in several key aspects. The researchers hypothesize that OCP2 and another bioinformatically identified protein, OCPx, reflect intermediate stages in the evolution of photoprotection in cyanobacteria.

Bao, H., et al. “Additional Families of Orange Carotenoid Proteins in the Photoprotective System of Cyanobacteria.” Nature Plants 3, Article 17089 (2017). [DOI:10.1038/nplants.2017.89].

Instruments and Facilities: X-ray macromolecular crystallography and diffraction at Advanced Light Source at Lawrence Berkeley National Laboratory.

Finding New Clues to a Common Respiratory Virus June 30, 2017
protein structure
Illustrated structure of a protein that helps a common respiratory virus evade the immune system. The structure was determined via X-ray crystallography at the Advanced Photon Source at Argonne National Laboratory. [Adapted by permission from Springer Nature: Chatterjee, S., et al. “Structural Basis for Human Respiratory Syncytial Virus NS1-Mediated Modulation of Host Responses.” Nat. Microbiol. 2, Article 17101 (2017). DOI:10.1038/nmicrobiol.2017.101. Copyright 2017.]
Each year in the United States, more than 57,000 children younger than 5 years old are hospitalized due to respiratory syncytial virus (RSV) infection, and about 14,000 adults older than 65 die from it. By age 2, most children have been infected with RSV, experiencing usually only mild cold symptoms. People with weakened immune systems, however, such as infants and the elderly, can face serious complications, including pneumonia and, in some cases, death. Now, scientists studying the virus using bright X-rays have found clues to how RSV causes disease. They mapped the molecular structure of an RSV protein that interferes with the body’s ability to fight off the virus. Knowing the structure of this protein will help them understand how the virus impedes immune response, potentially leading to a vaccine or treatment for this common infection.

With no approved vaccine and limited treatment for RSV, doctors prescribe the antiviral drug ribavirin only in the most severe cases because it is expensive and not very effective. Thus, most people with RSV receive only supportive care to make them more comfortable while their bodies fight off the virus. People with weakened immune systems face a tough fight with RSV. The researchers say that solving the structure of this elusive protein will enable them to see what the protein looks like and help them define what it does and how it does it. Ultimately, this capability and finding could lead to new targets for vaccine or drug development.

Scientists have long known that a nonstructural RSV protein (known as NS1) is key to the virus’s ability to evade the body’s immune response. However, its structure was unknown, so scientists were unable to determine exactly how the enigmatic NS1 interfered with the immune system. Using X-ray crystallography, the scientists determined the three-dimensional (3D) structure of NS1, and, in a detailed analysis of the structure, they identified a piece of the protein known as the alpha 3 helix, possibly critical for suppressing the immune response.

The researchers created different versions of this NS1 protein, with some having an intact and some with a mutated alpha 3 helix region. They tested the functional impact of helix 3 and created a set of viruses containing either the original or the mutant NS1 genes, measuring the effect on the immune response when they infected cells with these viruses. They found that viruses with the mutated helix region did not suppress the immune response, while the ones with the intact helix region did, globally modulating the immune response.

The findings also showed that the protein’s alpha 3 helix region was necessary for the virus to dial down the body’s immune response, giving the virus a better chance of surviving and multiplying—in other words, causing disease. Thus, a vaccine or treatment that targets the alpha 3 helix may supply what is needed to prevent immune suppression.

Chatterjee, S., et al. “Structural Basis for Human Respiratory Syncytial Virus NS1-Mediated Modulation of Host Responses.” Nat. Microbiol. 2, Article 17101 (2017). [DOI:10.1038/nmicrobiol.2017.101].

Instruments and Facilities Used: X-ray crystallography at the Advanced Photon Source at Argonne National Laboratory.

Pulling the Tablecloth Out from Under Essential Metabolism June 26, 2017
tomatoes peanuts soybeans
For the first time, scientists have caught a vital cell machinery molecule in the process of evolving. A key enzyme plants use to make tyrosine, an amino acid necessary for life, was thought to be conserved across the plant kingdom, but the scientists found a mutated form in legumes. In cherry tomatoes, the basic canonical form of the enzyme dominates; peanuts can switch hit; and some strains of soybeans (lumpy beans at right) have lost the canonical form. [Courtesy Jez laboratory, Washington University in St. Louis]
Plants caught in the act, changing chemistry thought to be immutable because necessary for life

Plants are the chemists of the living world, producing hundreds of thousands of small molecules that provide protection—to screen sunrays, to poison plant eaters, to scent the air, to color flowers, and for much other vegetative business.

Called “secondary metabolites,” these chemicals are distinguished from “primary metabolites,” which are the essential building blocks of proteins, fats, sugars, and DNA. Secondary metabolites just smooth the way in life, but failure to make primary metabolites correctly and efficiently is fatal. Genes for enzymes in the molecular assembly lines of primary metabolism have duplicates, allowing more tolerance of mutations that might have destabilized the primary pathways because the originals were still on the job. With evolutionary constraints thus relaxed, synthetic machinery was able to accumulate enough mutations to do new chemistry.

Widely conserved, primary metabolism it was thought to remain unchanged across many different groups of organisms because it operates correctly and efficiently and because its products are necessary for life. But now, a collaborative team of scientists has caught primary metabolism in the act of evolving. In a comprehensive study of a primary-metabolism assembly line in plants, they discovered a key enzyme evolving from a canonical form possessed by most plants, through noncanonical forms in tomatoes, to a switch-hitting form found in peanuts, and finally committing to the novel form in some strains of soybeans. This feat is comparable to pulling the tablecloth out from under the dishes without breaking any of them. A collaborative study of this biochemical pathway resulted in the crystallization of the soybean enzyme to reveal how nature changed the way the protein works, also capturing plants “building a pathway that links the primary to the secondary metabolism,” to reveal evolutionary machinery that creates new molecules.

A new pathway discovered for making tyrosine is much less constrained than the old one, raising the possibility that carbon flow could be directed away from lignin to increase the yields of drugs or nutrients to levels that would allow them to be produced in commercial quantities. Though the scientists have found two different assembly lines for tyrosine, they have not determined why except in general terms. This work is important because it demonstrates that primary metabolism does evolve.

Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants.” Nat. Chem. Biol. 13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].

Instruments and Facilities Used: X-ray macromolecular crystallography; diffraction data collected at beamline 19-ID of the Advanced Photon Source at Argonne National Laboratory Structural Biology Center.

Revealing a Peanut Family Secret for Making Chemical Building Blocks June 26, 2017
PDH enzyme 3D
The three-dimensional structure of the prephenate dehydrogenase (PDH) enzyme from the soybean legume. This structure helped show that only one mutation in PDH allowed legumes to evolve a new way to make the amino acid tyrosine. [Courtesy Cynthia Holland, Washington University in St. Louis]
Peanuts have a secret. It is a subtle one, but the peanut and its legume kin have not one, but two ways to make the tyrosine amino acid—one of 20 required to make all of this family’s proteins—an essential plant and human nutrient. Though a seemingly small feat, this unique way of making such an important chemical building block has been a mystery since its discovery in the 1960s. New research abetted by high-brightness X-ray beams is revealing how this second tyrosine pathway emerged in the legume family. Plant chemistry has evolved to make many different chemical compounds, many of which are important to human society, such as food, fiber, feed, fuel, and medicine. Starting from simpler compounds like tyrosine, these important molecules are precursors of countless interesting and useful chemicals such as morphine. The recently determined structure of the new plant enzyme could be a useful tool for biotechnologists trying to control the production of tyrosine and its derivatives. The team has tied this major evolutionary change in plant metabolism to a single mutation in the new enzyme.

In the 1960s and 1970s, scientists observed that plants used one pathway, known as arogenate dehydrogenase (ADH), to make tyrosine. They found that the legume family (i.e., peas, beans, and peanuts), however, had uniquely added a second, called prephenate dehydrogenase (PDH), previously known to be only in microbes. Two years ago, part of this team discovered the genes responsible for making tyrosine, learning that before peanuts and peas evolved into separate lineages, the legumes had evolved PDH enzymes from their existing ADH ones. These sister enzymes are very similar, so only a small number of changes could account for how ADH enzymes evolved into PDH ones. But there were still too many changes to test. The international collaborating teams purified the PDH enzyme of the soybean legume and determined its three-dimensional (3D) structure, which revealed that only a couple of mutations had occurred at the site where the chemical reactions take place. Instead of dozens of possible mutations, there were only two. Thus, changing a single amino acid in the center of the enzyme largely converted the soybean PDH enzyme back into its ancestor ADH enzyme, and this crucial switch also worked in reverse and for enzymes from multiple species. The scientists believe the legume PDH insensitivity to tyrosine could help to produce more tyrosine, and its useful derivatives, in systems like yeast or engineered plants.

Schenck, C. A., et al. “Molecular Basis of the Evolution of Alternative Tyrosine Biosynthetic Routes in Plants,” Nat. Chem. Biol. 13, 1029–1035 (2017). [DOI:10.1038/nchembio.2414].

Instruments and Facilities Used: Structural Biology Center (SBC)–CAT beam 19-ID of the Advanced Photon Source at Argonne National Laboratory.

Revealing How Bacterial Organelles Assemble June 23, 2017
Kerfeld and Sutter

Cheryl Kerfeld and Markus Sutter handle crystallized proteins at Berkeley National Laboratory’s Advanced Light Source. [Image courtesy Marilyn Chung, Lawrence Berkeley National Laboratory]
Structure of microcompartment’s protein shell could help research in bioenergy, pathogenesis, and biotechnology

Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing the structure and assembly of the organelle’s protein shell at atomic-level resolution. They studied the “photogenic” organelle shell of an ocean-dwelling slime bacteria Haliangium ochraceum. Providing the first view of the shell of an intact bacterial organelle membrane, this full structural view can help provide important information for beneficial use in fighting pathogens or bioengineering bacterial organelles. The research team said these organelles, or bacterial microcompartments (BMCs), are used by some bacteria to fix carbon dioxide. Thus, understanding how the microcompartment membrane is assembled, as well as how it lets some compounds pass through while impeding others, could contribute to research in enhancing carbon fixation and, more broadly, bioenergy. This class of organelles also helps many types of pathogenic bacteria metabolize compounds that are not available to normal, nonpathogenic microbes, giving the pathogens a competitive advantage.

Sutter, M., et al. “Assembly Principles and Structure of a 6.5-MDa Bacterial Microcompartment Shell.” Science 23(6344), 1293–1297 (2017). [DOI:10.1126/science.aan3289].

Instruments and Facilities Used: Michigan State University–DOE Plant Research Laboratory and the Molecular Biophysics and Integrated Bioimaging Division at Lawrence Berkeley National Laboratory; Stanford Synchrotron Radiation Lightsource.

Study on Human Skin Microbiome Finds Archaea Abundance Associated with Age June 22, 2017
archaeal cells
(Left, blue and green images) Fluorescence images of archaeal cells in skin wipe samples; the Advanced Light Source (ALS) at Argonne National Laboratory was used to measure infrared absorption spectra of different Archaea types. (Right, illustration) The hierachical chart of the human skin archaeome with Thaumarchaeota (red), Euryarchaeota (green), and Crenarchaeota (blue). [From Moissl-Eichinger, C., et al. “Human Age and Skin Physiology Shape Diversity and Abundance of Archaea on Skin.” Sci. Rep. 7, 4039 (2017). [DOI:10.1038/s41598-017-04197-4]. Reused under a Creative Commons license (CC BY 4.0,]
What’s on your skin? Your skin is crawling with single-celled microorganisms—and they’re not just bacteria. This study found that the skin microbiome also contains the extreme-loving archaea, and that the amount of these microbes varies with age. The microbiome forms a protective layer that protects the body from pathogens. Both genetic and chemical analyses of samples collected from human volunteers ranging in age from 1 to 75 showed that archaea were most abundant in subjects younger than 12 and older than 60. Before the study, the existence of archaea on human skin was unknown, but they are now known to play an important part. The international study also determined that gender was not a factor but that people with dry skin have more archaea. Results from genetic analysis and infrared spectroscopy imaging allowed scientists to link lower levels of oily secretion of sebaceous glands and with increased archaea, most of which have proven to be beneficial.

Moissl-Eichinger, C., et al. “Human Age and Skin Physiology Shape Diversity and Abundance of Archaea on Skin.” Sci. Rep. 7, 4039 (2017). [DOI:10.1038/s41598-017-04197-4].

Instruments and Facilities Used: Fluorescence in situ hybridization (FISH); quantitative polymerase chain reaction (PCR); next-generation sequencing; Fourier Transform infrared (FTIR) focal plan array (FPA) hyperspectral imaging. Facilities: Advanced Light Source at the Berkeley Synchrotron Infrared Structural Biology Imaging Project; BioTechMed-Graz, the Bavaria California Technology Center.

Engineering Better Plant Cultivars for Iron Uptake by Modifying the Fe Deficiency Response in Arabidopsis thaliana June 16, 2017
Root tip scans
(Left) Representative synchrotron X-ray fluorescent (SXRF) scans of root tips of plants grown for 7 days on B5 medium and then transferred to iron (Fe) medium for 3 days. (Middle) SXRF scan of leaves showing Fe (red). (Right) SXRF scan showing Fe (red), zinc (green), manganese (blue) localization in developed, green siliques. [Reproduced from Hindt, M. N., et al. “BRUTUS and Its Paralogs, BTS LIKE1 and BTS LIKE2, Encode Important Negative Regulators of the Iron Deficiency Response in Arabidopsis thaliana.” Metallomics 9(7), 876–890 (2017) with permission of The Royal Society of Chemistry. 10.1039/C7MT00152E]
Many populations in developing countries rely on plants for dietary iron (Fe)—essential for plant growth, crop yields, and human health, but, due to its low or limited solubility, Fe is sparingly available in neutral or basic soils and thus not readily accessible in the rhizosphere. Leading to a restricted Fe content in many plants, this low solubility is a major factor contributing to the widespread prevalence of Fe deficiency anemia in people with plant-based diets. Thus, increasing plant Fe acquisition and storage may have profound impacts on plant and human nutrition and can be achieved by manipulating genes and related mechanisms governing Fe homeostasis in plants. However, understanding the balance between positive and negative regulation of the Fe deficiency response is essential for efforts to engineer plants having a sufficient but not toxic level of Fe. Although plants often are challenged with Fe deficiency, no environment remains constant, making Fe availability in the rhizosphere dependent on many factors. When sufficient Fe is available, plants must effectively suppress Fe-deficiency response to avoid excessive uptake.

A research team has identified a novel Fe-binding domain allele called BTS in a mutagenesis screen for altered Fe accumulation (bts-3). Data showed that bts-3 is more tolerant than wild type to Fe-deficient conditions and that bts-3 is sensitive to Fe-sufficient conditions and accumulates excessive Fe. A triple mutant with loss of both BTS paralogs and a partial loss of BTS expression exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects, with the mutations also changing their uptake of important minerals such as zinc (Zn) and manganese (Mn). Genetic knockdowns and modifications of the proteins have been implicated in regulating plant uptake of Fe. This work will lead to greater understanding of plant Fe homeostasis to inform efforts for improved crops. Identifying natural variants of these genes in crop species may lead to traditional breeding efforts to generate higher-Fe cultivars.

Hindt, M. N., et al. “BRUTUS and its Paralogs, BTS LIKE1 and BTS LIKE2, Encode Important Negative Regulators of the Iron Deficiency Response in Arabidopsis thaliana.” Metallomics 9(7), 876–890 (2017). [DOI:10.1039/C7MT00152E].

Instruments and Facilities Used: PerkinElmer LAS Ltd, Seer Green, United Kingdom, and Elemental Scientific Inc., Omaha, Neb.; synchrotron X-ray fluorescence (SXRF) at National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory; Stanford Synchrotron Lightsource (SSLS) at SLAC National Accelerator Laboratory (SLAC); real-time quantitative PCR (Step One Plus Real Time PCR System using Applied Biosystems Version 2.2.3; Advanced Photon Source (APS) at Argonne National Laboratory (ANL); and Australian Synchrotron, Victoria. Two-dimensional SXRF analysis was performed at various X-ray microprobe beamlines: microarray analysis and X-ray fluorescence imaging (XFI) on SSLS beamline 2-3 at SLAC; X26A and X27A of NSLS; XFM beamline of the Australian Synchrotron; APS beamline 2-ID-D. Microarray analysis performed at Geisel School of Medicine in the Genomics Shared Resource at Dartmouth College. Elemental concentration analysis (inductively coupled plasma-mass spectrometry (ICP-MS, PerkinElmer NexION 300D equipped with Elemental Scientific Inc. autosampler and Apex HF sample introduction system at PerkinElmer LAS Ltd, Seer Green, U.K., and Elemental Scientific Inc., Omaha, Neb., respectively, in the standard mode.

Using Neutrons to Resolve Plasma Membrane Organization in Living Bacterial Cells May 23, 2017
Bacillus subtilis cell wall

(Left) The cell wall (greenish brown, at top) of Bacillus subtilis is shown, along with the bacterium’s plasma membrane (blue and red) and a portion of cytoplasm (rust, at bottom). (Right) SANS used in conjunction with selective hydrogen/deuterium labeling techniques revealed the structure of the plasma membrane, including nanoscale lipid domains, while blocking interfering signals from other cellular features. [From Nickels, J. D., et al. “The In Vivo Structure of Biological Membranes and Evidence for Lipid Domains.” PLOS Biology 15(5), e2002214 (2017). [DOI:10.1371/journal.pbio.2002214]. Reused under a Creative Commons license (CC BY 4.0,]
A new strategy devised by scientists at Oak Ridge National Laboratory used nondestructive small-angle neutron scattering (SANS) to reveal, for the first time, nanoscale membrane structures in living cells.

Neutron scattering spectra confirmed that the plasma membrane of the bacterium Bacillus subtilis is lamellar with an average hydrophobic thickness of 24 Ångstroms. The data also revealed that the membrane contains lipid features of approximately 40 nm or less in size, consistent with hypothesized “lipid rafts” in biological systems. The observation of lipid segregation in the plasma membrane of a bacterium is consistent with the notion of nanoscopic lipid assemblies, often described as lipid rafts in mammalian systems, implying that lipid domains are integral features of all biological membranes. Among their functions, lipid rafts are thought to play a vital role in cell signaling and facilitate movement of essential biomolecules in and out of the cell.

In addition to these scientific findings, the methods developed provide a new experimental platform for pursuing additional areas of inquiry (e.g., systematic in vivo investigations of cell membrane structure and response to diverse environmental stimuli). This new approach also may prove valuable, for example, in biomass feedstock and biofuel production, where bacterial cell membranes play important roles, and in biomedicine, where bacterial membrane domains affect antibiotic resistance. Furthermore, the strategy for “visualizing” the membrane can be used with other physical characterization techniques to examine additional cell structures such as the cell wall.

Nickels, J. D., et al. “The In Vivo Structure of Biological Membranes and Evidence for Lipid Domains.” PLOS Biology 15(5): e2002214 (2017). [DOI:10.1371/journal.pbio.2002214]

Instruments and Facilities Used: Small-angle neutron scattering (SANS) at the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). EQ-SANS at Spallation Neutron Source at ORNL. Oak Ridge Leadership Computing Facility at ORNL.

Related ORNL News Feature: Neutrons provide the first nanoscale look at a living cell membrane

DOE Highlight: First Look at a Living Cell Membrane

The work described in this highlight builds on previous work including:

  • Heberle, F.A., et al. “Bilayer Thickness Mismatch Controls Domain Size in Model Membranes.” Journal of the American Chemical Society 135, 6853-6859 (2013). [DOI: 10.1021/ja3113615]
  • Nickels, J.D. et al. “Mechanical Properties of Nanoscopic Lipid Domains.” Journal of the American Chemical Society 137, 15772-15780 (2015). [DOI: 10.1021/jacs.5b08894]
  • Nickels, J.D. et al. “Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes.” 192, 87-99 (2015). [DOI:10.1371/journal.pbio.2002214]
Probing S-layer Protein Structural Dynamics by SAXS May 9, 2017
Biophysical Journal Cover Image
Calcium mediates the structural state of the Caulobacter crescentus surface layer protein, RsaA. Image featured on the cover of Biophysical Journal.

All archaea, and many bacteria, possess a protein shell referred to as a surface layer (S-layer), which usually consist of a single protein that self-assembles into a two-dimensional (2D) crystal lattice.  Studies have revealed the structural dynamics of this S-layer protein from the model bacterium Caulobacter crescentus, called RsaA. Using small angle scattering and diffraction (SAXS/D) techniques, multiple structural states of RsaA were successfully characterized including monomeric, aggregated, and crystalline states (see figure), with only monomeric Rssa forming 2D crystals. Enabling differentiation of the discrete states, these results rationalize physiological data implicating RsaA as a player in environmental adaptation of C. crescentus. The findings also provide a biochemical and physiological basis for RsaA’s calcium (Ca)-binding behavior, which extends far beyond Ca’s usual role in S-layer biology of aiding biogenesis or oligomerization, and demonstrate a connection to cellular fitness. Further characterization using slow and fast time-resolved SAXS/D methods is ongoing.

SAXS/D data
Small angle X-ray scattering and diffraction (SAXS/D) data of five solutions with different concentrations of the Caulobacter crescentus S-layer protein, RsaA, in the presence of calcium (Ca). Scattering profiles indicate concentration-dependent crystallization. Automatic indexing of the numbered peaks yielded a hexagonal crystal lattice consistent with predictions and denoted by Miller indices. (Top) The diffraction pattern obtained for the highest concentration used (8 mg/ml) shows powder rings. (Bottom) Transmission electron microscopy of the 8 mg/ml RsaA in the presence of 10 millimole per Liter (mm/L) of calcium chloride (CaCl2) (scale bar 200 nm). [Reprinted from Herrmann, J., et al. “Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer.” Biophys. J. 112(9), 1841–1851 (2017). DOI:10.1016/j.bpj.2017.04.003. Copyright 2017, with permission from Elsevier.]
Herrmann, J., et al. “Environmental Calcium Controls Alternate Physical States of the Caulobacter Surface Layer,” Biophys. J. 112(9), 1841–1851 (2017). [DOI:10.1016/j.bpj.2017.04.003].

Instruments and Facilities Used: Stanford ChEM-H Macromolecular Structure Knowledge Center,  Stanford Department of Structural Biology Electron Microscopy Center, Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory (SLAC). Beamlines or instruments used: transmission electron microscopy (TEM) and small angle X-ray scattering and diffraction (SAXS/D) at SSRL beamline 4-2 at SLAC.

Could This Enzyme Help Turn Biofuel Waste into Something Useful? April 18, 2017
LigM Structure
The protein structure of LigM was determined using X-ray crystallography, revealing novel structural elements that are unique to LigM (red) in addition to a conserved tetrahydrofolate-binding domain (gray) that is found throughout life. LigM binds to its substrates (green) using internal binding cavities. [From Kohlera, A. C., et al. “Structure of Aryl O-Demethylase Offers Molecular Insight into a Catalytic Tyrosine-Dependent Mechanism.” PNAS 114(16), E3205–E3214 (2017). DOI:10.1073/pnas.1619263114.]
Joint BioEnergy Institute study targets LigM for its role in breaking down aromatic pollutants

A protein used by common soil bacteria is providing new clues in the effort to convert aryl compounds, a common waste product from industrial and agricultural practices, into something of value. The protein structure of the enzyme LigM was determined using X-ray crystallography, revealing novel structural elements (red in figure) and a conserved tetrahydrofolate-binding domain (gray), with LigM binding to its substrates (green) using internal binding cavities.

Researchers used have resolved the soil bacterium Sphingomonas to metabolize aryl compounds derived from lignin, the stiff, organic material that gives plants their structure. In biofuel production, aryl compounds are a byproduct of the breakdown of lignin, some pathways of which involve demethylation, an often critical precursor to additional modification steps of lignin-derived aryl compounds. The simple, single-enzyme system of LigM, as well as its functionality over a broad temperature range, makes it an attractive demethylase for use in aromatic conversion. Other findings included: half the LigM enzyme was homologous to known structures with a tetrahydrofolate-binding domain that is found in both simple and complex organisms; the other half of LigM’s structure is completely unique, providing a starting point for determining where its aryl substrate-binding site is located; and LigM is a tyrosine-dependent demethylase. This research provides groundwork needed to aid in developing an enzyme-based system for converting aromatic waste into useful products.

Kohlera, A. C., et al. “Structure of Aryl O-Demethylase Offers Molecular Insight into a Catalytic Tyrosine-Dependent Mechanism.” PNAS 114(16), E3205–E3214 (2017). [DOI:10.1073/pnas.1619263114].

Instruments and Facilities Used: Beam line 8.2.2 and X-ray macromolecular crystallography at Berkeley Center for Structural Biology Advanced Light Source at Lawrence Berkeley National Laboratory.

Sequencing of Green Alga Genome Provides Blueprint to Advance Clean Energy, Bioproducts April 12, 2017
Chromoshloris zofingiensis
Chromoshloris zofingiensis cell morphology. Cryo-soft X-ray tomography of a reconstructed cell with segmented nucleus (purple), chloroplast (green), mitochondria (red), lipids (yellow), and starch granules within the chloroplast (blue). (A) A representative orthoslice of the reconstructed cell. (B) Three-dimensional segmentation over two orthogonal orthoslices. (C) Segmented chloroplast and nucleus. (D) Fully segmented cell. [Reprinted with permission from Roth, M. S., et al. “Chromosome-Level Genome Assembly and Transcriptome of the Green Alga Chromochloris zofingiensis Illuminates Astaxanthin Production.” PNAS 114(21), E4296–E4305 (2017). [DOI:10.1073/pnas.1619928114]. Image credit Melissa S. Roth, HHMI/UC-Berkely and Andreas Walter, LBNL]
Microalgae have potential to help meet energy and food demands without exacerbating environmental problems. The unicellular green alga Chromochloris zofingiensis produces lipids for biofuels and a highly valuable carotenoid nutraceutical, astaxanthin. Thus advanced understanding of its biology is needed to facilitate commercial development. The assembly of the C. zofingiensis chromosome-level nuclear genome, organelle genomes, and transcriptome from diverse growth conditions was derived from a combination of short- and long-read sequencing in conjunction with optical mapping, revealing a compact genome of ∼58 Mbp distributed over 19 chromosomes containing 15,274 predicted protein-coding genes. Found in the genome were 2 genes encoding beta-ketolase (BKT), the key enzyme synthesizing astaxanthin, and both were up-regulated by high light. Isolation and molecular analysis of astaxanthin-deficient mutants. Moreover, the transcriptome under high light exposure revealed candidate genes that could be involved in critical yet missing steps of astaxanthin biosynthesis, including ABC transporters, cytochrome P450 enzymes, and an acyltransferase. The high-quality genome and transcriptome provide insight into the green algal lineage and carotenoid production. Microalgae are a promising source of sustainable bioproducts for the increasing demand for food and energy without exacerbating worsening environmental problems. The algae have potential for use as a biofuel feedstock and nutraceutical molecules, including the carotenoid astaxanthin. Analyses of the C. zofingiensis genome and transcriptome and experiments characterizing astaxanthin production advance understanding of algae and carotenoids  and enhance the commercial potential of C. zofingiensis.

Roth, M. S., et al.. “Chromosome-Level Genome Assembly and Transcriptome of the Green Alga Chromochloris zofingiensis Illuminates Astaxanthin Production.” PNAS 114(21), E4296–E4305 (2017). [DOI:10.1073/pnas.1619928114].

Instruments and Facilities Used: Soft X-ray tomography at National Center for X-ray Tomography (NCXT), operated jointly by Berkeley Lab (LBNL) and University of California, San Francisco, at LBNL’s Advanced Light Source. Other techniques: whole-genome optical mapping, high light RNA sequencing, transcriptome sequencing, and long read sequencing.

Direct Measurement of Protein Dynamics In Vivo April 7, 2017
quasi-elastic neutron scattering (QENS)
Labeling strategy for probing live cells using quasi-elastic neutron scattering (QENS). Graph: QENS spectra of uninduced cells (blue) and cells with expressed GroEL protein (red) in the deuterium oxide (D2O) buffer. [Reprinted with permission from Anunciado, D. B., et al. “In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale.” J. Phys. Chem. Lett. 8(8), 1899–1904 (2017). DOI: 10.1021/acs.jpclett.7b00399. Copyright 2017 American Chemical Society.]
Quasi-elastic neutron scattering was used to study the protein GroEL in vivo. Protiated GroEL was over-expressed in deuterated Escherichia coli cells by addition of protiated amino acids during induction of GroEL. The data showed retardation factors of ∼2 and ∼4 for the internal dynamics and global diffusion of the protein, compared to those of the protein in solution at the same concentration. Comparison with literature values suggests that the effective diffusivity of proteins depends on the length or time scale probed. Selective isotope labeling of biomolecules in cells opens up new lines of biological research using “in-cell neutron scattering” to extract information on dynamics of biomolecular systems that is unobtainable by other analysis techniques.

Anunciado, D. B., et al. “In Vivo Protein Dynamics on the Nanometer Length Scale and Nanosecond Time Scale.” J. Phys. Chem. Lett. 8(8), 1899–1904 (2017). [DOI:10.1021/acs.jpclett.7b00399].

Instruments and Facilities Used: Quasi-elastic neutron scattering, BASIS neutron backscattering spectrometer at Spallation Neutron Source at Oak Ridge National Laboratory.

Ebola Virus January 22, 2017

In the Ebola virus one of the proteins, VP40, has the ability to refold to achieve new functions;  three structural forms of VP40 have been determined, with each structure conferring a separate and essential function in the virus life cycle.  The image illustrates (top) a butterfly-shaped dimer critical for membrane trafficking; (middle) a rearranged hexameric structure essential for building and releasing nascent virions; (bottom) an RNA-binding octameric ring that controls transcription in infected cells

Bornholdt, T. Noda, D.M. Abelson, P. Halfmann, M.R. Wood, Y. Kawaoka, E. Ollmann Saphire, Cell 154, 763 (2013) [DOI: 10.1016/j.cell.2013.07.015]

Neutrons Identify Oxygen Activation in LPMOs December 22, 2016
Fungal lytic polysaccharide monooxygenases (LPMOs)
Scientists used neutrons to probe the structural details of the specialized LPMO fungal enzyme that relies on oxidation to digest molecules, aiming to improve the efficiency of enzymatic cellulose breakdown. [From O’Dell, W. B., P. K. Agarwal, and F. Meilleur. “Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase.” Angew. Chem. Int. Ed. 56, 767–770 (2017). [DOI:10.1002/anie.201610502]. ©2017 The Authors. Published by Wiley-VCH Verla GmbH & Co. KGaA, Weinheim.]
Fungal lytic polysaccharide monooxygenases (LPMOs) are known to enhance the efficiency of cellulose-hydrolyzing enzymes through oxidative cleavage of the glycosidic bonds. For this study, PMO-2 from Neurospora crassa was heterologously expressed from Pichia pastoris, purified, and crystallized for high-resolution X-ray crystal structures that revealed “prebound” molecular oxygen in the resting state and a dioxo species in complex with the catalytic copper (Cu2+) ion, which is the first structural description of molecular oxygen (O2) activation by a LPMO. In addition, neutron diffraction studies and density functional theory calculations have identified a role for a conserved histidine in promoting oxygen activation. Extension of these studies to the enzyme-substrate complex could provide a complete picture of the enzymatic mechanism for the potential benefit of applications such as bioethanol production.

O’Dell, W. B., et al. “Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase.” Angew. Chem. Int. Ed. 129(3), 785–788 (2017). [DOI:10.1002/anie.201610502].

Instruments and Facilities Used: Neutron crystallography. Joint X-ray/neutron refinement at Center for Structural Molecular Biology at Oak Ridge National Laboratory (ORNL). Diffraction data were collected at SER-CAT 22-ID at the Advanced Photon Source at Argonne National Laboratory and at CG-4D IMAGINE (NSF MRI 09229719) at the High Flux Isotope Reactor at ORNL.

Detailing the Molecular Roots of Alzheimer’s Disease December 20, 2016
TREM2 is a protein involved in Alzheimer’s disease and other neurodegenerative disorders. Its electrostatic surface structure, depicted here, was determined at the Structural Biology Center X-ray facility at the Advanced Photon Source at Argonne National Laboratory. [From Kober, D. L., et al. “Neurodegenerative Disease Mutations in TREM2 Reveal a Functional Surface and Distinct Loss-of-Function Mechanisms.” eLife 5, e20391 (2016). DOI:10.7554/eLife.20391. Reused under a Creative Commons license (CC BY 4.0,]
Scientists have captured the three-dimensional (3D) detail of the structure of a molecule implicated in Alzheimer’s disease. Knowing the shape of this molecule—and how that shape may be disrupted by certain genetic mutations—can help in understanding how Alzheimer’s and other neurodegenerative diseases develop and how to prevent and treat them.

From past studies, scientists think that the molecule TREM2 possibly is involved in cognitive decline, the hallmark of neurodegenerative diseases, because certain mutations that alter the structure of TREM2 are associated with an increased risk of developing late-onset Alzheimer’s, frontal temporal dementia, Parkinson’s disease, and sporadic amyotrophic lateral sclerosis (ALS). Other TREM2 mutations are linked to Nasu-Hakola disease, a rare inherited condition that causes progressive dementia and death in most patients by age 50.Although its exact contribution is unknown, dysfunctional TREM2 does relate to neurodegeneration, and “inflammation is the common thread in all these conditions.” The scientists investigated what TREM2 mutations do to the structure of the protein itself to impact its function, so ways can be found to correct it.

Structural analysis of TREM2 revealed that the mutations associated with Alzheimer’s alter the surface of the protein, while those linked to Nasu-Hakola influence the “guts” of the protein. The difference in location could explain the severity of Nasu-Hakula, in which signs of dementia begin in young adulthood. The internal mutations totally disrupt the structure of TREM2, resulting in fewer TREM2 molecules. The surface mutations, in contrast, leave TREM2 intact but likely make it harder for the molecule to connect to proteins or send signals as normal TREM2 molecules would.

TREM2 lies on the surface of immune cells called microglia, which are thought to be important “housekeeping” cells involved in, for example, maintaining healthy brain biology via a process called phagocytosis that cleans cellular waste, including the amyloid beta that is known to accumulate in Alzheimer’s disease. If the microglia lack TREM2 or the TREM2 is dysfunctional, these cellular housekeepers can’t perform their cleanup tasks. Though the exact function of TREM2 is still unknown, mice without TREM2 have defects in their microglia. With these structural data, scientists can study how TREM2 works, or doesn’t work, in these neurodegenerative diseases, as well as other inflammatory conditions including chronic obstructive pulmonary disease and stroke. The structure of TREM2 could be important for understanding many chronic and degenerative diseases.

Kober, D. L., et al. “Neurodegenerative Disease Mutations in TREM2 Reveal a Functional Surface and Distinct Loss-of-Function Mechanisms,” eLife 5, e20391 (2016). [DOI:10.7554/eLife.20391].

Instruments and Facilities Used: X-ray Facility at the Advanced Photon Source (APS) at Argonne National Laboratory

Hollow Pyramid Unlocks Principles of Protein Architecture December 14, 2016
symmetric crystal structure
Designed and observed cage symmetry. (A) Left: Schematic diagram of the symmetry principles used to design the 12-subunit tetrahedral cage by fusing two oligomeric domains (green and orange) by a semirigid linker (magenta). Right: Single point mutation distinguishing our PCtrip construct from PCquad replaces tyrosine (black sticks) with alanine in the trimeric domain that makes contact with the linker. (B) Side-by-side view of the theoretically designed (perfectly symmetric) model of the protein cage (left) and the most symmetric crystal structure obtained in this work for the PCquad variant (right). (C) Walleyed stereo view of three crystal structures of PCquad (yellow, magenta, and blue) overlaid on the ideal model (green ribbon), showing the agreement of the observed structures and the design. [[From Lai, Y.-T., et al., “Designing and Defining Dynamic Protein Cage Nanoassemblies in Solution.” Sci. Adv. 2(12), e1501855 (2016). DOI:10.1126/sciadv.1501855. Reused under a Creative Commons license (CC BY NC-4.0,]
Large biological macromolecules (up to 10,000 atoms) can catalyze chemical reactions in ways that are difficult to replicate inorganically. Their size allows for the complexity needed to perform such functions, but it also makes them more susceptible to misfolding and aggregating—thus, the importance of understanding the fundamental architectural principles that cause large proteins to favor specific conformations. At the nanoscale, where organic chemical groups interact with solvent water molecules, these principles are very different from the ones used to build houses and cars. To investigate these principles, a group of researchers designed a protein that would self-assemble into a hollow pyramid (or tetrahedron). Upon crystallizing the macromolecule, the group found that they had indeed been successful in creating the assembly, but it was unexpectedly warped and collapsed in an asymmetric manner, with some edges bent inward—an asymmetric tetrahedron. To ensure that this was not an artifact of crystallization, they investigated the protein’s behavior in solution using small-angle x-ray scattering (SAXS), which showed that the collapse could be controlled by adjusting the solution’s salt concentration; the structure was disassembled by varying the pH.

The flexibility of this macromolecule suggests that it could be useful for the controlled capture and release of smaller compounds. Overall, the researchers expect that, with the tools and techniques developed here, the combination of SAXS with crystallography or electron microscopy could be increasingly useful in analyzing and optimizing designed protein assemblies and understanding their behavior in solution.

Lai, Y.-T., et al. “Designing and Defining Dynamic Protein Cage Nanoassemblies in Solution.” Sci. Adv. 2(12), e1501855 (2016). [DOI:10.1126/sciadv.1501855].

Instruments and Facilities Used: Small-angle X-ray scattering (SAXS) at Advanced Light Source (ALS) with SIBYLS Beamline 12.3.1 (a joint crystallography and SAXS beamline) at Lawrence Berkeley National Laboratory.

Crystal Structure of NOV1 December 12, 2016

The crystal structure of NOV1, a stilbene cleaving oxygenase, shows the features of this enzyme at atomic resolution. This protein fold view highlights the placement of an iron (orange), dioxygen (red), and resveratrol, a representative substrate (blue) in the active site of the enzyme.  Enzymes such as NOV1 could be of value in the biological production of important molecular fragments derived from lignin. (Image courtesy of Ryan McAndrew/JBEI and Berkeley Lab)

LBNL Article

McAndrew, R.P., N. Sathitsuksanoh, M.M. Mbughuni, R.A. Heins, J.H. Pereira, A. George, K.L. Sale, B.G. Fox, B.A. Simmons, and Paul D. Adams. 2016. “Structure and mechanism of NOV1, a resveratrol-cleaving dioxygenase” PNAS 113 (50) 14324-14329. doi:10.1073/pnas.1608917113

Designing Cyclic Oligomers: Greater than the Sum of Their Parts December 5, 2016
Computational oligomer design.
Computational oligomer design. Scientists used small angle solution studies and X-ray scattering to prove that synthetic design matched the computational design. [Reprinted by permission from Springer Nature: Fallas, J. A., et al. “Computational Design of Self-Assembling Cyclic Protein Homo-Oligomers.” Nat. Chem. 9, 353–360 (2017). DOI:10.1038/nchem.2673. Copyright 2017.]
Cyclic proteins that assemble from multiple identical subunits (homo-oligomers) play key roles in many biological processes, including enzymatic catalysis and function and cell signaling. Researchers in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division worked with University of Washington’s David Baker, who led a team to design in silico and crystallize self-assembling cyclic homo-oligomer proteins.

A strategy was developed that designs interfaces onto idealized proteins aimed to direct their assembly into multimeric complexes. Researchers used structural characterization, both X-ray crystallography and small angle X-ray scattering (SAXS), to show that many of the designs adopted the target oligomerization state and predicted structure. Not only does the work demonstrate that scientists have a basic understanding of what determines oligomerization, but that they could design proteins with tunable shape, size, and symmetry for a variety of biological applications.

Fallas, J. A., et al.Computational Design of Self-Assembling Cyclic Protein Homo-Oligomers.” Nat. Chem. 9, 353–360 (2017). [DOI:10.1038/nchem.2673].

Instruments and Facilities Used: Crystallography Collective program; beamline 5.0.2; small angle X-ray scattering (SAXS) on the SIBYLS BL12.3.1 beamline. Advanced Photon Source synchrotron beamline 24-ID-C at Berkeley Center for Structural Biology and Advanced Light Source at Lawrence Berkeley National Laboratory (LBNL).

Mapping the Migration of Genetic Material November 15, 2016
skeletonized structure of heterochromatin
This computer rendering shows the skeletonized structure of heterochromatin (red represents a thin region while white represents a thick region), a tightly packed form of DNA surrounding another form of DNA-carrying material known as euchromatin (dark blue represents a thin region and yellow represent the thickest) in a mouse’s mature nerve cell. [Courtesy Lawrence Berkeley National Laboratory and University of California, San Francisco]
Researchers have used a powerful soft X-ray microscope to capture tomographic images of the genetic material in the nuclei of nerve cells at different stages of maturity. This first quantitative analysis of nuclear organization in intact mammalian cells has generated detailed three-dimensional (3D) visualizations that show an unexpected connectivity in the genetic material, called chromatin. The results could aid in understanding how the patterning and reorganization of chromatin relate to the specialization of a stem cell’s function as specific genes are activated or silenced.

Understanding the logic of nuclear architecture and how it contributes to stem-cell differentiation remains challenging. Until now, imaging the nucleus was possible only indirectly, by staining it, hopefully with even distribution. In this work, researchers used soft X-ray microtomography to record a series of images from mouse olfactory nerve cells in three separate stages of development. This unique technique provides a new way of looking at the nucleus without the need to chemically treat the cell, allowing visualization of intact cells in a near-native state at a resolution of about 50 nanometers.

After imaging frozen cells at each stage from dozens of different angles, the researchers used each set of 2D images to calculate a 3D reconstruction detailing the changing chromatin formations in the nucleus, collecting the images using soft X-rays within the “water window” [i.e., 284 to 543 electron electronvolts (eV)]. The absorption of X-rays by biomolecules is linear with biochemical composition and concentration, generating a unique X-ray linear absorption coefficient measurement for each voxel (3D pixel analog). Thus, the researchers were able to visually distinguish between different types of chromatin—heterochromatin, due to an increased biomolecular concentration, appears darker than euchromatin in computer-generated tomographic orthoslices (virtual sections) through the nucleus.

The results showed that chromatin compaction increases as the cell matures, and that condensed chromatin moves to the nuclear core during differentiation. Though the chromatin was thought to exist as a series of disconnected islands, the results showed how it was compartmentalized into two distinct regions of “crowding” that form a continuous network throughout the nucleus. Also, based on comparison of these results to those of similar cells in which the gene for a heterochromatin binding protein had been inactivated (“knocked out”), the researchers concluded that it regulates the reorganization of chromatin in mature neurons.

Soft x-ray tomography provides a powerful method to study chromatin and nuclear architecture in vivo. There is no need for chemical fixation and sectioning, preventing a plethora of artifacts introduced either by fixatives or by visualization of only thin sections. The researchers believe performing statistical analyses is now possible to based on large collections of cell nuclei images sorted by different stages of development.

Le Gros, M. A., et al. “Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization During Neurogenesis In Vivo,” Cell Reports 17(8), 2125–2136 (2016). [DOI:10.1016/j.celrep.2016.10.060].

Instruments and Facilities Used: Soft X-ray tomography (beamline 2.1) of the Advanced Light Source at the National Center for X-Ray Tomography at Lawrence Berkeley National Laboratory.

Investigating Ptychography of a Bacterium’s Inner Compass November 15, 2016
Magnetovibrio blakemorei
(Left) Schematic of the pathway of magnetosome biomineralization for Magnetovibrio blakemorei strain MV-1. (Center) Ptychography absorption image of a single MV-1 cell (average of 76 images from 700 to 732 eV). Four spatial regions are identified: (A) gap in the magnetosome chain, (B) precursor region, (C) immature magnetosome, and (D) mature magnetosome. (Right) Fe L3 spectra from regions A through D. [Left image courtesy Xiaohui Zhu; Middle and right images from Zhu, X., et al. “Measuring Spectroscopy and Magnetism of Extracted and Intracellular Magnetosomes Using Soft X-Ray Ptychography,” PNAS 113, E8219 (2016). DOI:10.1073/pnas.1610260114.]
Magnetotactic bacteria (MTB) synthesize chains of magnetic nanocrystals (magnetosomes) that interact with the Earth’s magnetic field like an inner compass needle, simplifying their search for optimum environments. Some studies investigating how these magnetosomes form suggest that hematite or amorphous ferrihydrite act as precursors, while others posit that they are formed directly from solution-phase Fe(II) and Fe(III). Thus, identifying the chemical states of precursors would be a good way to differentiate among competing models.

Ptychography is a coherent diffractive imaging technique with high resolution (7 nm in this work) and excellent chemical-state sensitivity. Researchers obtained ptychographic absorption and phase spectra of magnetosomes from a marine MTB (Magnetovibrio blakemorei strain MV-1). The data, obtained from mature magnetosomes, immature magnetosomes, precursor regions, and the gaps between magnetosome chains, indicated that different iron species can coexist in a single cell. Based on the results, the researchers proposed a model in which soluble Fe(II) is taken up from the environment and partially oxidized to Fe(III), which in turn is then oxidized and transformed into hematite and ultimately into magnetite.

Researchers also used ptychography to measure the X-ray magnetic circular dichroism (XMCD) spectra of both extracellular and intracellular magnetosomes. XMCD probes the magnetism of a crystal in a site-specific manner, showing that absorption and XMCD ptychography signals provide complementary information. These experiments demonstrate that ptychography, which combines high spatial resolution, high-sensitivity chemical speciation, and site-specific magnetic information, offers a powerful probe for biomineralization studies.

Zhu, X., et al. “Measuring Spectroscopy and Magnetism of Extracted and Intracellular Magnetosomes Using Soft X-Ray Ptychography,” PNAS 113, E8219 (2016). [DOI:10.1073/pnas.1610260114].

Instruments and Facilities Used: Scanning transmission X-ray microscope (STXM) on beamline 10ID1 of Canadian Light Source at University of Saskatchewan and the Advanced Light Source Beamlines and 11.0.2 at Lawrence Berkeley National Laboratory.

Description of Hydration Water in Green Fluorescent Protein Solution October 6, 2016
green fluorescent protein
Graphic representation of hydration water surrounding green fluorescent protein. [Reprinted with permission from Perticaroli, S., et al. “Description of Hydration Water in Protein (Green Fluorescent Protein) Solution.” J. Am. Chem. Soc. 139(3), 1098–1105 (2017). [DOI:10.1021/jacs.6b08845]. Copyright 2016 American Chemical Society.]
Many unanswered questions remain about how macromolecules in solution perturb the water molecules in which they are immersed. Scientists used neutron scattering to provide an experimental description of the dynamical perturbation of water molecules surrounding proteins in solution, which play an important role in protein function and stability. Quantifying the magnitude of the perturbation of water around the green fluorescent protein (GFP), they found a systematic length-scale dependence of the dynamical retardation factor compared to the perturbation of bulk water. The findings deepen the understanding of water perturbation, which is of practical interest to researchers in food science, personal care, pharmaceutics, and protein dynamics.

Perticaroli, S., et al. “Description of Hydration Water in Protein (Green Fluorescent Protein) Solution.” J. Am. Chem. Soc. 139(3), 1098–1105 (2017). [DOI:10.1021/jacs.6b08845].

Instruments and Facilities Used: Neutron scattering at Center for Structural Molecular Biology and Spallation Neutron Source at Oak Ridge National Laboratory.

How Your Body Transports Zinc to Protect Your Health August 15, 2016
zinc serum albumin
Illustration of the way zinc binds with serum albumin to be transported around the human body. [From Handing, K. B., et al. “Circulatory Zinc Transport Is Controlled by Distinct Interdomain Sites on Mammalian Albumins.” Chem. Sci. 7, 6635 (2016). DOI:10.1039/c6sc02267g. Published by The Royal Society of Chemistry and reused under a Creative Commons license (CC by 3.0,]
Zinc is essential for wound healing, vision, DNA creation, the senses of taste and smell, and even for sexual health. But despite its importance, scientists have never fully understood the mechanism that moves the mineral through the body—until now. An international collaboration of researchers have, for the first time, created detailed blueprints of the molecular “moving vans” that ferry this important mineral through the blood everywhere it is needed. The finding gives scientists new insights into this important process and a deeper understanding of the critical role it plays in maintaining good health.

Zinc is carried through the body by a protein known as serum albumin. Scientists proved the location of the primary site where serum albumin binds with zinc, but the team also found several more secondary binding sites, revealing a more complex interaction than anticipated.

While computer models previously had been used to predict how serum albumin picks up zinc, the team used X-ray macromolecular crystallography to obtain data-based images of protein crystals showing how zinc actually bound to serum albumin. The technique allowed them to pinpoint the location of each particular zinc atom, though it was a challenging task. The schematics produced allow scientists to see, for the first time, exactly how serum albumin and zinc come together. Serum albumin also transports many other things, such as hormones and fatty acids.

Too much zinc is toxic to the body, so it must make zinc available where it is needed, but prevent harmful, excessive buildup. The study’s findings could help shed light on why certain drugs affect some patients differently than others.

Handing, K. B., et al. “Circulatory Zinc Transport is Controlled by Distinct Interdomain Sites on Mammalian Albumins.” Chem. Sci. 7, 6635 (2016). [DOI:10.1039/c6sc02267g].

Instruments and Facilities Used: X-ray macromolecular crystallography; Life Sciences Collaborative Access Team (LS-CAT) 21-ID-F and 21-ID-G X-ray beamlines and Structural Biology Center (SBC)-CAT 19-BM-D X-ray beamline, all at the Advanced Photon Source at Argonne National Laboratory

Cellulose Synthesis Complex January 12, 2016

The plant cellulose synthesis complex is a large multi-subunit transmembrane protein complex responsible for synthesis of cellulose chains and their assembly into microfibrils. The image shows ab initio structures of CESA trimers calculated from small-angle scattering data represented by semi-transparent grey surface envelopes, superposed with the computational atomic models in orange. Image credits: Thomas Splettstoesser,, Berlin Germany

Vandavasi, V.G., D.K. Putnam, Q. Zhang, L. Petridis, W.T. Heller, B.T. Nixon, C.H. Haigler, U. Kalluri, L. Coates, and P. Langan. 2016. “A structural study of CESA1 catalytic domain of Arabidopsis cellulose synthesis complex: evidence for CESA trimers.” Plant physiology  170(1):123-35.  [DOI: 10.1104/pp.15.01356]

Finding Manganese Reduction-Oxidation Drives Plant Debris Decomposition September 22, 2015
cross-sectioned Douglas-fir needle
Fluorescence microscope image showing a cross-sectioned Douglas-fir needle prepared for this work and analyzed using ALS beamlines 1.4.3, 10.3.2 and 9.0.2. [Courtesy Marco Keiluwit]
Microbial decomposition of plant debris (“litter”) regulates nutrient availability, ecosystem productivity, and carbon (C) cycling. Historically, scientists thought climate (primarily temperature and precipitation) regulated the rate of litter decomposition, which then influenced the rate at which nutrients become available and C contained in the litter was released back into the atmosphere as the greenhouse gas carbon dioxide (CO2). Recently, evidence has shown that geochemical factors also influence litter decomposition rates. A research team has shown that long-term litter decomposition rates in forest ecosystems are closely related to the process of manganese (Mn) reduction-oxidation (redox) in a variety of forest ecosystems. A strong correlation had been observed previously between litter Mn content and decomposition rates, but the underlying mechanisms were not well understood. In redox cycling, redox governs Mn reactions, frequently mediated by microbes, which accumulate and oxidize Mn in the litter, then using the oxidized Mn species to break down plant cells.

By pairing high-resolution chemical imaging analysis with a long-term litter decomposition experiment under field conditions, the researchers discovered that litter decomposition is tightly coupled to redox cycling of Mn. The researchers discovered why Mn exerts such a strong control on litter decomposition rates and the mechanism of the underlying biogeochemical process, observing molecular changes within the litter as it decomposed over the years and probing structural changes within the very large biomolecules present in litter that frequently are not directly detectable by other means. This tunable technique also allowed the scientists to selectively ionize different biopolymers present in the litter, such as lignin, which is an important biopolymer because it lends rigidity to plant cell walls and protects litter from microbial decay.

In microenvironments within the litter, microbes actively cycle Mn as they colonize and break down the litter, and research indicates that biogeochemical constraints on bioavailability, mobility, and Mn reactivity in the plant-soil system may have a profound impact on litter decomposition rates. Understanding more about the mobility and reactivity of Mn in the plant-soil system also helps researchers improve their ability to accurately predict carbon cycling trends in ecosystems, contributing to greater insights into climate change patterns.

Keiluweit, M.. et al. “Long-Term Litter Decomposition Controlled by Manganese Redox Cycling,” PNAS 12(38), E5253–E5260 (2015). [DOI:10.1073/pnas.1508945112].

Instruments and Facilities Used: Beamlines 10.3.2 (X-ray microprobe capabilities) and 1.4.3 (Fourier transform infrared spectromicroscopy) at Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory; beamline 4-3 at Stanford Synchrotron Radiation Light Source (SSRLS).

Modular Construction on a Biomolecular Scale August 25, 2015

The spherical protein ferritin was used to synthesize a porous 3-D crystalline framework material, and further engineered to have metal hubs on its surface.  Organic molecules bridge these hubs, and in a controlled way create a porous material with potential uses from efficient fuel storage to carbon capture and conversion.  The study shows the great potential for proteins as building blocks with exquisite properties of electron transfer and bioinspired catalysis.

A. Sontz, J. B. Bailey, S. Ahn and F. A. Tezcan, “A Metal Organic Framework with Spherical Protein Nodes: Rational Chemical Design of 3D Protein Crystals”, J. Am. Chem. Soc. 137, 11598 (2015), doi: 10.1021/jacs.5b07463

BAP Protein June 10, 2015

Closer look at microorganism provides insight on carbon cycling

The research team reconstructed the crystal structure of BAP, a protein involved in the process by which marine archaea release carbon, to determine how it functioned, as well as its larger role in carbon cycling in marine sediments.
ANL Article

Karolina Michalska, Andrew D. Steen, Gekleng Chhor, Michael Endres, Austen T. Webber, Jordan Bird, Karen G. Lloyd, and Andrzej Joachimiak. “New aminopeptidase from ‘microbial dark matter’ archaeon” The FASEB Journal doi: 10.1096/fj.15-272906. Published online June 10, 2015.


Protein Cage November 19, 2014

Using Small-angle X-ray scattering (SAXS) to efficiently and quickly image large protein molecular assemblies, scientists have designed a hollow, cube-shaped protein cage that has the potential for delivering proteins or other chemicals to specific locations for medical, energy, and other applications. The nanocage crystal structure was optimized at the Advanced Light Source (Image courtesy of Greg Hura, LBNL).

Lai, Y.T., E. Reading, G.L. Hura, K.L.Tsai, A. Laganowsky, F.J. Asturias,  J.A. Tainer, C.V. Robinson, and T.O. Yeates. 2014.“Structure of a Designed Protein Cage that Self-Assembles into a Highly Porous Cube,” Nature Chemistry 6, 1065–1071. doi:10.1038/nchem.2107

Feature Article at LBNL


Understanding Nitrogen Fixation in Bacteria September 26, 2014


Nitrogen fixation is required for all forms of life, being essential for the biosynthesis of molecules that are used in creating plants and organisms.  Nitrogenase is the only known enzyme capable of performing this multi-electron reduction, and understanding how it does this conversion is of high importance also for the production of ammonia (as fertilizer), for energy efficiency (as industrial processes to produce ammonia consumes enormous amounts of energy), and for global warming (capturing N2).  The structure of the CO inhibitor bound to the FeMo-cofactor active site in nitrogenase at high resolution provides insight into a catalytic competent state, establishes the importance of a bridging S atom, and indicates how N2 might bind during turn-over. Stanford Synchrotron Radiation Lightsource.

Spatzal, K.A. Perez, O. Einsle, J.B. Howard, D.C. Rees, “Ligand binding to the FeMo-cofactor: Structures of CO-bound and reactivated nitrogenase” Science 345, 1620-1623 (2014), doi: 10.1126/science.1256679

SSRL Highlight

Biomass Deconstruction January 12, 2014

Illustration of structural rearrangement of cellulose and matrix copolymers during thermochemical pretreatment of lignocellulose biomass. Image credits: Thomas Splettstoesser,, Berlin Germany

Langan, P., L. Petridis, H.M. O’Neill, S.V. Pingali, M. Foston, Y. Nishiyama, et al. 2014. “Common processes drive the thermochemical pretreatment of lignocellulosic biomass.” Green Chem. 16(1):63-8. [DOI:10.1039/C3GC41962B]

Spatial Organization of Lipid Domains in a Biomimetic Four-Lipid System May 8, 2013

Floating freely in cell membranes, lipid rafts are organizing centers for membrane-mediated processes. Neutron scattering techniques were used to characterize lipid domain size transitions from nanometers to micrometers in a four-component biomimetic lipid mixture.  Results suggest that reversible changes in lipid composition may regulate the size of functional domains in lipid rafts. The BioSANS instrument at the ORNL Center for Structural Molecular Biology and the EQ-SANS instrument (BER) at the ORNL Spallation Neutron Source (BES) were used in this study.

Heberle F.A., Petruzielo R.S., Pan J., Drazba P., Kucerka N., Standaert R.F., Feigenson G.W., Katsaras J., “Bilayer thickness mismatch controls domain size in model membranes”, Journal of the American Chemical Society, 135, 18, 6853-6859 (2013). DOI: 10.1021/ja3113615

Major Scaffold Component in Nuclear Pore Complex April 2, 2013

The Nuclear Pore Complex (NPC) is a 50 MDa macromolecular assembly solely responsible for the transport of macromolecules across the nuclear membrane within the eukaryotic cell. The core structure of the NPC (shown as a wire-mesh) is made up of two outer rings, two inner rings and a membrane ring. A hybrid method approach was used to determine the detailed architecture of the NPC combining structural data from crystallography, small-angle x-ray scattering, normal mode analysis, molecular dynamics simulation and electron microscopy as well as information from functional and biochemical studies.

Sampathkumar, S. J. Kim, P. Upla, W. J. Rice, J. Phillips, B. L. Timney, U. Pieper, J. B. Bonanno, J. Fernandez-Martinez, Z. Hakhverdyan, N. E. Ketaren, T. Matsui, T. M. Weiss, D. L. Stokes, J. M. Sauder, S. K. Burley, A. Sali, M. P. Rout and S. C. Almo, “Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex”, Structure 21, 560 (2013) doi: 10.1016/j.str.2013.02.005

X-rays and Protein Crystal Samples January 3, 2013

Lessening X-ray damage is healthy for protein discovery data too

Protein crystal samples are placed on a small metal tip so x-rays from the adjacent beam pipe can pass through them and diffract off the atoms inside the crystal. Using computational methods, scientists interpret the scattered light patterns recorded by detectors to create an image of how the atoms are located inside the crystal.
ANL Article
Image credit: Wayne Anderson, Northwestern University.

Karolina Michalska, Kemin Tan, Hui Li, Catherine Hatzos-Skintges, Jessica Bearden, Gyorgy Babnigg, and Andrzej Joachimiak. “GH1-family 6-P-β-glucosidases from human microbiome lactic acid bacteria”Acta Cryst. (2013). D69, 451-463. DOI: 10.1107/s0907444912049608

Watching the Evolution of a Protein’s Function December 9, 2012

A major challenge in research to enable large-scale biofuels production is developing enzymes that are highly efficient in converting biomass components into usable fuels.  Using directed evolution (i.e., a technique for modifying protein function), researchers have determined the structural basis for converting a noncatalytic small protein into an effective enzyme for for linking RNA molecules.  Extended x-ray absorption fine structure (EXAFS) was used to determine the Zn-containing active-site structure of this RNA ligase, synthesized through in-vitro directed evolution.

F.-A. Chao, A. Morelli, J. C. Haugner, III, L. Churchfield, L. N. Hagmann, L. Shi, L. R. Masterson, R. Sarangi, G. Veglia and B. Seeling, “Structure and Dynamics of a Primordil Catalytic Fold Generated by in vitro Evolution”, Nat. Chem. Biol. 9, 81 (2013) doi: 10.1038/nchembio.1138

Comparison of GH3 Protein Binding Sites May 24, 2012

In plants, GH3 proteins act as molecular on/off switches that control bioactive plant hormone formation by catalyzing the addition of specific amino acids to jasmonic acid, auxin, and benzoates. X-ray structures of GH3 proteins reveal a common three-dimensional fold but variability in the hormone binding site. This figure shows the variation in the jasmonic acid binding site of Arabidopsis thaliana GH3.11/JAR1 (gold) and the salicylic acid binding site of A. thaliana GH3.12/PBS3 (green).
BER Highlight

Westfall, C. S., et al. 2012. “Structural Basis for Prereceptor Modulation of Plant Hormones by GH3 Proteins,” Science 336, 1708–11. DOI: 10.1126/science.1221863