Dynamic Regulation of Histone Chaperone Nucleoplasmin

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, https://creativecommons.org/licenses/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).

X-Ray Footprinting Solves Mystery of Metal-Breathing Protein

Participants in protein-wiring study, LBNL
Participants in a protein-wiring study at Lawrence Berkeley National Laboratory included (from left): Jose Cornejo, Corie Ralston, Caroline Ajo-Franklin, Sayan Gupta, and Behzad Rad. Not pictured: Tatsuya Fukushima, Christopher Petzold, Leanne Chan, and Rena Mizrahi. [Courtesy Paul Mueller, Lawrence Berkeley National Laboratory]
Caroline Ajo-Franklin, a staff scientist in the Biological Nanostructures Facility at Lawrence Berkeley National Laboratory’s (LBNL) Molecular Foundry (one of the Nanoscale Science Research Centers supported by DOE’s Office of Basic Energy Sciences), teamed up with Corie Ralston to use X-ray mass spectrometry footprinting at LBNL’s Advanced Light Source. Ralston, who works in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, uses the X-ray mass spectrometry footprinting technique to precisely probe proteins and their surroundings at the Advanced Light Source. Ajo-Franklin and Ralston saw that they could use footprinting to answer a long-standing question in microbiology: how do bacterial proteins interact directly with minerals to transfer electrons and allow the microbe to live?

“Understanding what these interactions between proteins and materials look like can help us design them better,” Ajo-Franklin said, “and give us insight on how to connect living cells with devices.”

Surprisingly, “the biggest finding … was that our proteins bind relatively weakly,” Ajo-Franklin noted. “Most proteins that interface with materials bind really tightly,” changing shape as they form the connection. This particular protein does not appear to change shape at all and only interacts with the mineral in a small area, requiring about five times less binding energy, by comparison, than typical proteins that form biominerals. This finding makes a lot of sense, Ajo-Franklin, because this protein’s job “is to transfer electrons to the mineral, so it doesn’t have to be in contact for very long.”

Beamline contact:
Corie Ralston
Advanced Light Source

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What’s on Your Skin? Archaea, That’s What

Hoi-Ying Holman, Advanced Light Source, LBNL
As director of the Berkeley Synchrotron Infrared Structural Biology Imaging Program at the Advanced Light Source, Hoi-Ying Holman focuses on developing and providing research communities with new synchrotron infrared technologies for deciphering the relationship between genome and functional processes and identifying the connection between the genome and natural environments. [Courtesy Marilyn Chung, Lawrence Berkeley National Laboratory]
To characterize microbes on human skin, researchers from Austria, including Christine Moissl-Eichinger, collaborated with Hoi-Ying Holman and other scientists at the Berkeley Synchrotron Infrared Structural Biology Imaging Program, a BER-supported infrared beamline at the Advanced Light Source at Lawrence Berkeley National Laboratory. The research stemmed from a joint project between the National Aeronautics and Space Administration and the European Space Agency.

“We were checking spacecraft and their clean rooms for the presence of archaea, as they are suspected to be possible critical contaminants during space exploration,” Moissl-Eichinger said. “Certain methane-producing archaea, the so-called methanogens, could possibly survive on Mars. We did not find many signatures from methanogens, but we found loads of Thaumarchaeota, a very different type of archaea that survives with oxygen.”

This finding led to the discovery that these archaea are present on people’s skin. The infrared beamline was used to rapidly and precisely characterize samples from humans and determine the levels and types of microbes present, based on the chemical specificity of infrared spectroscopy. This analysis could then be linked back to the genomic data collected by the Austrian team. The detected archaea are probably involved in nitrogen turnover on skin and are capable of lowering skin pH, supporting the suppression of pathogens. The researchers found that because of changes in skin moisture, these microbes are most abundant in subjects younger than 12 and older than 60.

Beamline contact:
Hoi-Ying Holman
Berkeley Synchrotron Infrared Structural Biology Imaging Program
Advanced Light Source

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“Zip-code” Mechanism for Hormone Signaling Revealed

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

(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, https://creativecommons.org/licenses/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).

Biological Small Angle Scattering: Techniques, Strategies and Tips

“Biological Small Angle Scattering: Techniques, Strategies and Tips” edited by B Chaudhuri, IG Muñoz, S Qian, VS Urban was published by Springer (ISBN 978-981-10-6038-0) DOI: 10.1007/978-981-10-6038-0

Bio-SANS scientists S. Qian, V. Urban along with B. Chaudhuri (an early Bio-SANS user) and I. Munoz compiled the first introductory book on biological solution small angle scattering (SAS). Biological SAS has seen tremendous growth over the past decade because it is especially useful for studying proteins which in turn may have big implications for renewable energy, medical care and drug effectiveness. The chapters are written by international experts in solution SAS methodologies, many from US user facilities (SSRL, NCNR, LBNL). The carefully selected topics include techniques for improving data quality and analysis, as well as different scientific applications of SAS. The book includes the principles and theoretical background of various SAS techniques and practical aspects that range from sample preparation to data publication. It is a handbook for any researcher using X-ray/neutron small-angle scattering in biology.

Grand Challenges for Biological and Environmental Research: Progress and Future Vision

The Biological and Environmental Research (BER) program within the U.S. Department of Energy (DOE) Office of Science supports research focusing on the interconnections between energy production and the living environment. This fundamental research, conducted at universities, DOE national laboratories, and research institutions across the country, explores organisms and ecosystems that can influence the U.S. energy system and advances understanding of the relationships between energy and environment from local to global scales.

A report from the Biological and Environmental Research Advisory Committee

BER regularly solicits input from the scientific community to help guide its programs. The Biological and Environmental Research Advisory Committee (BERAC) is chartered under the Federal Advisory Committee Act to advise BER on its research portfolio and user facilities. To facilitate a synthesis of community input, the director of DOE’s Office of Science charged BERAC in March 2016 to review research progress and establish and deliver a revised long-term vision for BER by fall 2017. Questions considered during this process included:

  • To what extent has BER successfully met the challenges outlined in the 2010 report, Grand Challenges for Biological and Environmental Research: A Long-Term Vision?
  • What are the greatest scientific challenges that DOE faces in the long term (20-year horizon), and for which of these should BER take primary responsibility?
  • How should DOE position BER to address these challenges?
  • What new tools should be developed to integrate and analyze data from different disciplines?
  • What unique opportunities exist to partner with, or leverage assets from, other programs within the DOE Office of Science?
  • What scientific and technical advances are needed to train the future workforce in integrative science, including complex systems science?

Through a series of BERAC meetings, white papers, and a research community workshop, BERAC addressed these questions, identifying future grand challenges in five areas: biological systems, Earth and environmental systems, microbial to Earth system pathways, energy sustainability, and data analytics and computing. Providing critical support for these challenges are BER user facilities, research infrastructure, and emerging technologies. This report represents a synthesis of these grand challenges and the supporting facilities and technologies.

Publication date: November 2017

Suggested citation for this report: BERAC. 2017. Grand Challenges for Biological and Environmental Research: Progress and Future Vision; A Report from the Biological and Environmental Research Advisory Committee, DOE/SC–0190, BERAC Subcommittee on Grand Research Challenges for Biological and Environmental Research (science.energy.gov/~/media/ber/berac/pdf/Reports/BERAC-2017-Grand-Challenges-Report.pdf).

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A Regional Model for Uranium Redox and Mobility

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

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

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 (smb-research.smb.usyd.edu.au/NCVWeb/).