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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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2
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Zhao X, Gao Y, Gong Q, Zhang K, Li S. Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition. Nat Commun 2024; 15:6445. [PMID: 39085263 PMCID: PMC11292022 DOI: 10.1038/s41467-024-50722-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While studies have established the ATP-dependent formation of MuB filament as pivotal to this process, the high-resolution structure of a full-length MuB protomer and the underlying molecular mechanisms governing its oligomerization remain elusive. Here, we use cryo-EM to obtain a 3.4-Å resolution structure of the ATP(+)-DNA(+)-MuB helical filament, which encapsulates the DNA substrate within its axial channel. The structure categorizes MuB within the initiator clade of the AAA+ protein family and precisely locates the ATP and DNA binding sites. Further investigation into the oligomeric states of MuB show the existence of various forms of the filament. These findings lead to a mechanistic model where MuB forms opposite helical filaments along the DNA, exposing potential target sites on the bare DNA and then recruiting MuA, which stimulates MuB's ATPase activity and disrupts the previously formed helical structure. When this happens, MuB generates larger ring structures and dissociates from the DNA.
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Affiliation(s)
- Xiaolong Zhao
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yongxiang Gao
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qingguo Gong
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Kaiming Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Shanshan Li
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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3
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Xu XP, Cao W, Swift MF, Pandit NG, Huehn AE, Sindelar CV, De La Cruz EM, Hanein D, Volkmann N. High-resolution yeast actin structures indicate the molecular mechanism of actin filament stiffening by cations. Commun Chem 2024; 7:164. [PMID: 39079963 PMCID: PMC11289367 DOI: 10.1038/s42004-024-01243-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Actin filament assembly and the regulation of its mechanical properties are fundamental processes essential for eukaryotic cell function. Residue E167 in vertebrate actins forms an inter-subunit salt bridge with residue K61 of the adjacent subunit. Saccharomyces cerevisiae actin filaments are more flexible than vertebrate filaments and have an alanine at this position (A167). Substitution of this alanine for a glutamic acid (A167E) confers Saccharomyces cerevisiae actin filaments with salt-dependent stiffness similar to vertebrate actins. We developed an optimized cryogenic electron microscopy workflow refining sample preparation and vitrification to obtain near-atomic resolution structures of wild-type and A167E mutant Saccharomyces cerevisiae actin filaments. The difference between these structures allowed us to pinpoint the potential binding site of a filament-associated cation that controls the stiffness of the filaments in vertebrate and A167E Saccharomyces cerevisiae actins. Through an analysis of previously published high-resolution reconstructions of vertebrate actin filaments, along with a newly determined high-resolution vertebrate actin structure in the absence of potassium, we identified a unique peak near residue 167 consistent with the binding of a magnesium ion. Our findings show how magnesium can contribute to filament stiffening by directly bridging actin subunits and allosterically affecting the orientation of the DNase-I binding loop of actin, which plays a regulatory role in modulating actin filament stiffness and interactions with regulatory proteins.
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Affiliation(s)
- Xiao-Ping Xu
- Scintillon Institute, 6868 Nancy Ridge Drive, San Diego, CA, 92121, USA
| | - Wenxiang Cao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Mark F Swift
- Scintillon Institute, 6868 Nancy Ridge Drive, San Diego, CA, 92121, USA
| | - Nandan G Pandit
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Andrew E Huehn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Enrique M De La Cruz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Dorit Hanein
- Department of Chemistry and Biochemistry and Department of Biological Engineering, University of California, Santa Barbara, CA, 93106, USA.
| | - Niels Volkmann
- Department of Biological Engineering, Department of Electrical and Computer Engineering, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, 93106, USA.
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4
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Dubach VRA, San Segundo-Acosta P, Murphy BJ. Structural and mechanistic insights into Streptococcus pneumoniae NADPH oxidase. Nat Struct Mol Biol 2024:10.1038/s41594-024-01348-w. [PMID: 39039317 DOI: 10.1038/s41594-024-01348-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/06/2024] [Indexed: 07/24/2024]
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOXs) have a major role in the physiology of eukaryotic cells by mediating reactive oxygen species production. Evolutionarily distant proteins with the NOX catalytic core have been found in bacteria, including Streptococcus pneumoniae NOX (SpNOX), which is proposed as a model for studying NOXs because of its high activity and stability in detergent micelles. We present here cryo-electron microscopy structures of substrate-free and nicotinamide adenine dinucleotide (NADH)-bound SpNOX and of NADPH-bound wild-type and F397A SpNOX under turnover conditions. These high-resolution structures provide insights into the electron-transfer pathway and reveal a hydride-transfer mechanism regulated by the displacement of F397. We conducted structure-guided mutagenesis and biochemical analyses that explain the absence of substrate specificity toward NADPH and suggest the mechanism behind constitutive activity. Our study presents the structural basis underlying SpNOX enzymatic activity and sheds light on its potential in vivo function.
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Affiliation(s)
- Victor R A Dubach
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Redox and Metalloprotein Research Group, IMPRS on Cellular Biophysics, Frankfurt am Main, Germany
| | - Pablo San Segundo-Acosta
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Chronic Disease Programme, UFIEC, Carlos III Health Institute, Madrid, Spain.
| | - Bonnie J Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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5
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Carver A, Yu TY, Yates LA, White T, Wang R, Lister K, Jasin M, Zhang X. Molecular basis of FIGNL1 in dissociating RAD51 from DNA and chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603765. [PMID: 39071279 PMCID: PMC11275795 DOI: 10.1101/2024.07.16.603765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Maintaining genome integrity is an essential and challenging process. RAD51 recombinase, the central player of several crucial processes in repairing and protecting genome integrity, forms filaments on DNA. RAD51 filaments are tightly regulated. One of these regulators is FIGNL1, that prevents persistent RAD51 foci post-damage and genotoxic chromatin association in cells. The cryogenic electron microscopy structure of FIGNL1 in complex with RAD51 reveals that the FIGNL1 forms a non-planar hexamer and RAD51 N-terminus is enclosed in the FIGNL1 hexamer pore. Mutations in pore loop or catalytic residues of FIGNL1 render it defective in filament disassembly and are lethal in mouse embryonic stem cells. Our study reveals a unique mechanism for removing RAD51 from DNA and provides the molecular basis for FIGNL1 in maintaining genome stability.
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Affiliation(s)
- Alexander Carver
- DNA Processing Machines Laboratory, Francis Crick Institute, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
- These authors contributed equally to this study
| | - Tai-Yuan Yu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center
- These authors contributed equally to this study
| | - Luke A Yates
- DNA Processing Machines Laboratory, Francis Crick Institute, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Travis White
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center
| | - Raymond Wang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center
| | - Katie Lister
- DNA Processing Machines Laboratory, Francis Crick Institute, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center
| | - Xiaodong Zhang
- DNA Processing Machines Laboratory, Francis Crick Institute, London, UK
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, UK
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6
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Sibert BS, Kim JY, Yang JE, Ke Z, Stobart CC, Moore ML, Wright ER. Assembly of respiratory syncytial virus matrix protein lattice and its coordination with fusion glycoprotein trimers. Nat Commun 2024; 15:5923. [PMID: 39004634 PMCID: PMC11247094 DOI: 10.1038/s41467-024-50162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Respiratory syncytial virus (RSV) is an enveloped, filamentous, negative-strand RNA virus that causes significant respiratory illness worldwide. RSV vaccines are available, however there is still significant need for research to support the development of vaccines and therapeutics against RSV and related Mononegavirales viruses. Individual virions vary in size, with an average diameter of ~130 nm and ranging from ~500 nm to over 10 µm in length. Though the general arrangement of structural proteins in virions is known, we use cryo-electron tomography and sub-tomogram averaging to determine the molecular organization of RSV structural proteins. We show that the peripheral membrane-associated RSV matrix (M) protein is arranged in a packed helical-like lattice of M-dimers. We report that RSV F glycoprotein is frequently observed as pairs of trimers oriented in an anti-parallel conformation to support potential interactions between trimers. Our sub-tomogram averages indicate the positioning of F-trimer pairs is correlated with the underlying M lattice. These results provide insight into RSV virion organization and may aid in the development of RSV vaccines and anti-viral targets.
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Affiliation(s)
- Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Zunlong Ke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | | | | | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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7
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods 2024; 21:1340-1348. [PMID: 38918604 DOI: 10.1038/s41592-024-02321-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L Lawson
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | | | - Grigore D Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K Burley
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Vincent B Chen
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- , Berlin, Germany
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Protein Science, Septerna, South San Francisco, CA, USA
| | | | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Alexis L Rohou
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Benjamin D Sellers
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- Computational Chemistry, Vilya, South San Francisco, CA, USA
| | - Chenghua Shao
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Venkat Abbaraju
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - K D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- The Chinese University of Hong Kong, Hong Kong, China
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Robert A Nicholls
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Luisa U Schäfer
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature's Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
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8
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Yadav S, Vinothkumar KR. Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol 2024; 80:535-550. [PMID: 38935342 PMCID: PMC11220838 DOI: 10.1107/s2059798324005229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
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Affiliation(s)
- Swati Yadav
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
| | - Kutti R. Vinothkumar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
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9
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Hoff SE, Thomasen FE, Lindorff-Larsen K, Bonomi M. Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference. PLoS Comput Biol 2024; 20:e1012180. [PMID: 39008528 PMCID: PMC11271924 DOI: 10.1371/journal.pcbi.1012180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 07/25/2024] [Accepted: 05/20/2024] [Indexed: 07/17/2024] Open
Abstract
Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced models in which physico-chemical quality is sacrificed for excellent fit to the data. Furthermore, these techniques struggle to represent the conformational heterogeneity averaged out in low-resolution regions of density maps. Here we introduce EMMIVox, a Bayesian inference approach to determine single-structure models as well as structural ensembles from cryo-EM maps. EMMIVox automatically balances experimental information with accurate physico-chemical models of the system and the surrounding environment, including waters, lipids, and ions. Explicit treatment of data correlation and noise as well as inference of accurate B-factors enable determination of structural models and ensembles with both excellent fit to the data and high stereochemical quality, thus outperforming state-of-the-art refinement techniques. EMMIVox represents a flexible approach to determine high-quality structural models that will contribute to advancing our understanding of the molecular mechanisms underlying biological functions.
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Affiliation(s)
- Samuel E. Hoff
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France
| | - F. Emil Thomasen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Massimiliano Bonomi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France
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10
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Li HZ, Pike ACW, Lotsaris I, Chi G, Hansen JS, Lee SC, Rödström KEJ, Bushell SR, Speedman D, Evans A, Wang D, He D, Shrestha L, Nasrallah C, Burgess-Brown NA, Vandenberg RJ, Dafforn TR, Carpenter EP, Sauer DB. Structure and function of the SIT1 proline transporter in complex with the COVID-19 receptor ACE2. Nat Commun 2024; 15:5503. [PMID: 38951531 PMCID: PMC11217458 DOI: 10.1038/s41467-024-48921-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/16/2024] [Indexed: 07/03/2024] Open
Abstract
Proline is widely known as the only proteogenic amino acid with a secondary amine. In addition to its crucial role in protein structure, the secondary amino acid modulates neurotransmission and regulates the kinetics of signaling proteins. To understand the structural basis of proline import, we solved the structure of the proline transporter SIT1 in complex with the COVID-19 viral receptor ACE2 by cryo-electron microscopy. The structure of pipecolate-bound SIT1 reveals the specific sequence requirements for proline transport in the SLC6 family and how this protein excludes amino acids with extended side chains. By comparing apo and substrate-bound SIT1 states, we also identify the structural changes that link substrate release and opening of the cytoplasmic gate and provide an explanation for how a missense mutation in the transporter causes iminoglycinuria.
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Affiliation(s)
- Huanyu Z Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashley C W Pike
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Irina Lotsaris
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Karin E J Rödström
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Simon R Bushell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Speedman
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Evans
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dong Wang
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Didi He
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leela Shrestha
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chady Nasrallah
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Robert J Vandenberg
- Molecular Biomedicine Theme, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia.
| | | | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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11
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Han CW, Jeong MS, Jang SB. Influence of the interaction between p53 and ZNF568 on mitochondrial oxidative phosphorylation. Int J Biol Macromol 2024; 275:133314. [PMID: 38944084 DOI: 10.1016/j.ijbiomac.2024.133314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 07/01/2024]
Abstract
The tumor suppressor p53 plays important roles in suppressing the development and progression of cancer by responding to various stress signals. In addition, p53 can regulate the metabolic pathways of cancer cells by regulating energy metabolism and oxidative phosphorylation. Here, we present a mechanism for the interaction between p53 and ZNF568. Initially, we used X-ray crystallography to determine the irregular loop structure of the ZNF568 KRAB domain; this loop plays an important role in the interaction between p53 and ZNF568. In addition, Cryo-EM was used to examine how the p53 DBD and ZNF568 KRAB domains bind together. The function of ZNF568 on p53-mediated mitochondrial respiration was confirmed by measuring glucose consumption and lactate production. These findings show that ZNF568 can reduce p53-mediated mitochondrial respiratory activity by binding to p53 and inhibiting the transcription of SCO2. SIGNIFICANCE: ZNF568 can directly bind to the p53 DBD and transcriptionally regulate the SCO2 gene. SCO2 transcriptional regulation by interaction between ZNF568 and p53 may regulate the balance between mitochondrial respiration and glycolysis.
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Affiliation(s)
- Chang Woo Han
- Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Mi Suk Jeong
- Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Republic of Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Republic of Korea.
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12
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. J Struct Biol 2024; 216:108108. [PMID: 38944401 DOI: 10.1016/j.jsb.2024.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these energies, specifically a ∼ 4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope fitted with a non-standard SP-Twin lens. We also achieved a ∼ 3.2 Å resolution reconstruction of a 115 kDa asymmetric protein complex, proving Alpine's effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ∼ 3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hev Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States.
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States.
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13
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Chien CT, Puhl H, Vogel SS, Molloy JE, Chiu W, Khan S. Hub stability in the calcium calmodulin-dependent protein kinase II. Commun Biol 2024; 7:766. [PMID: 38918547 PMCID: PMC11199487 DOI: 10.1038/s42003-024-06423-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.
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Affiliation(s)
- Chih-Ta Chien
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Henry Puhl
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Steven S Vogel
- Laboratory of Biophotonics and Quantum Biology, National Institutes on Alcohol, Abuse and Alcoholism, National Institutes of Health, Rockville, MD, 208952, USA
| | - Justin E Molloy
- The Francis Crick Institute, London, UK
- CMCB, Warwick Medical School, Coventry, CV4 7AL, UK
| | - Wah Chiu
- Department of Bioengineering, and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Light source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
| | - Shahid Khan
- Molecular Biology Consortium @ Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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14
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Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Hogan DW, Flowers J, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 2024; 12:RP90606. [PMID: 38904665 PMCID: PMC11192534 DOI: 10.7554/elife.90606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift toward modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior Rfree and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g., Coot) and fit can be further improved by refinement using standard pipelines (e.g., Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.
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Affiliation(s)
- Stephanie A Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Ashraya Ravikumar
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Ph.D. Program in Biology, The Graduate Center, City University of New YorkNew YorkUnited States
| | - Blake Riley
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Akshay Raju
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
| | - Daniel W Hogan
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica Flowers
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
- Atomwise IncSan FranciscoUnited States
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research CenterNew YorkUnited States
- Department of Chemistry and Biochemistry, City College of New YorkNew YorkUnited States
- Ph.D. Programs in Biochemistry, Biology and Chemistry, The Graduate Center, City University of New YorkNew YorkUnited States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San FranciscoSan FranciscoUnited States
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15
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Handa S, Biswas T, Chakraborty J, Ghosh G, Paul BG, Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.23.563531. [PMID: 37961358 PMCID: PMC10634737 DOI: 10.1101/2023.10.23.563531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Diversity-generating retroelements (DGRs) create massive protein sequence variation in ecologically diverse microbes. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for cDNA synthesis by the reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Cryo-EM revealed that this RNA enveloped bRT and lay over barrel-shaped Avd, forming an intimate ribonucleoprotein (RNP). An abundance of essential interactions between RNA structural elements and bRT-Avd precisely positioned an RNA homoduplex for initiation of cDNA synthesis by cis -priming. Our results explain how the surrounding RNA primes cDNA synthesis, promotes processivity, terminates polymerization, and strictly limits mutagenesis to select proteins through mechanisms that are likely conserved in DGRs from distant taxa.
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16
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Lee J, Oldham ML, Manon V, Chen J. Principles of peptide selection by the transporter associated with antigen processing. Proc Natl Acad Sci U S A 2024; 121:e2320879121. [PMID: 38805290 PMCID: PMC11161800 DOI: 10.1073/pnas.2320879121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 05/30/2024] Open
Abstract
Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with antigen processing (TAP) transports nearly the entire repertoire of antigenic peptides into the endoplasmic reticulum for MHC-I loading. How TAP transports peptides specific for MHC-I is unclear. In this study, we used cryo-EM to determine a series of structures of human TAP, both in the absence and presence of peptides with various sequences and lengths. The structures revealed that peptides of eight or nine residues in length bind in a similarly extended conformation, despite having little sequence overlap. We also identified two peptide-anchoring pockets on either side of the transmembrane cavity, each engaging one end of a peptide with primarily main chain atoms. Occupation of both pockets results in a global conformational change in TAP, bringing the two halves of the transporter closer together to prime it for isomerization and ATP hydrolysis. Shorter peptides are able to bind to each pocket separately but are not long enough to bridge the cavity to bind to both simultaneously. Mutations that disrupt hydrogen bonds with the N and C termini of peptides almost abolish MHC-I surface expression. Our findings reveal that TAP functions as a molecular caliper that selects peptides according to length rather than sequence, providing antigen diversity for MHC-I presentation.
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Affiliation(s)
- James Lee
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Michael L. Oldham
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Victor Manon
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
| | - Jue Chen
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
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17
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Park J, Herrmann GK, Roy A, Shumate CK, Cisneros GA, Yin YW. An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol γ. SCIENCE ADVANCES 2024; 10:eadl3214. [PMID: 38787958 PMCID: PMC11122685 DOI: 10.1126/sciadv.adl3214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/18/2024] [Indexed: 05/26/2024]
Abstract
The replication accuracy of DNA polymerase gamma (Pol γ) is essential for mitochondrial genome integrity. Mutation of human Pol γ arginine-853 has been linked to neurological diseases. Although not a catalytic residue, Pol γ arginine-853 mutants are void of polymerase activity. To identify the structural basis for the disease, we determined a crystal structure of the Pol γ mutant ternary complex with correct incoming nucleotide 2'-deoxycytidine 5'-triphosphate (dCTP). Opposite to the wild type that undergoes open-to-closed conformational changes when bound to a correct nucleotide that is essential for forming a catalytically competent active site, the mutant complex failed to undergo the conformational change, and the dCTP did not base pair with its Watson-Crick complementary templating residue. Our studies revealed that arginine-853 coordinates an interaction network that aligns the 3'-end of primer and dCTP with the catalytic residues. Disruption of the network precludes the formation of Watson-Crick base pairing and closing of the active site, resulting in an inactive polymerase.
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Affiliation(s)
- Joon Park
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Arkanil Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Christie K. Shumate
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - G. Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Physics, University of Texas at Dallas, Richardson, TX 75080, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
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18
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Wakabayashi T, Oide M, Nakasako M. CryoEM-sampling of metastable conformations appearing in cofactor-ligand association and catalysis of glutamate dehydrogenase. Sci Rep 2024; 14:11165. [PMID: 38750092 PMCID: PMC11096400 DOI: 10.1038/s41598-024-61793-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/09/2024] [Indexed: 05/18/2024] Open
Abstract
Kinetic aspects of enzymatic reactions are described by equations based on the Michaelis-Menten theory for the initial stage. However, the kinetic parameters provide little information on the atomic mechanism of the reaction. In this study, we analyzed structures of glutamate dehydrogenase in the initial and steady stages of the reaction using cryoEM at near-atomic resolution. In the initial stage, four metastable conformations displayed different domain motions and cofactor/ligand association modes. The most striking finding was that the enzyme-cofactor-substrate complex, treated as a single state in the enzyme kinetic theory, comprised at least three different metastable conformations. In the steady stage, seven conformations, including derivatives from the four conformations in the initial stage, made the reaction pathway complicated. Based on the visualized conformations, we discussed stage-dependent pathways to illustrate the dynamics of the enzyme in action.
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Grants
- JPMJPR22E2 Japan Science and Technology Agency
- jp13480214 Japan Society for the Promotion of Science
- jp19204042 Japan Society for the Promotion of Science
- jp22244054 Japan Society for the Promotion of Science
- jp21H01050 Japan Society for the Promotion of Science
- jp26800227 Japan Society for the Promotion of Science
- 18J11653 Japan Society for the Promotion of Science
- jp15076210 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp20050030 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp22018027 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp23120525, jp25120725 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp15H01647 Ministry of Education, Culture, Sports, Science and Technology of Japan
- jp17H05891 Ministry of Education, Culture, Sports, Science and Technology of Japan
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Affiliation(s)
- Taiki Wakabayashi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan
| | - Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan
- PRESTO, Japan Science and Technology Agency, Chiyoda-Ku, Tokyo, 102-0076, Japan
- Protein Research Institute, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoko-Ku, Yokohama, Kanagawa, 223-8522, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-Cho, Sayo-Gun, Hyogo, 679-5148, Japan.
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19
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Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
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Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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20
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Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Flowers J, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546963. [PMID: 37425870 PMCID: PMC10327213 DOI: 10.1101/2023.06.28.546963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift towards modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior R f r e e and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g. Coot) and fit can be further improved by refinement using standard pipelines (e.g. Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.
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Affiliation(s)
- Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ashraya Ravikumar
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Ph.D. Program in Biology, The Graduate Center – City University of New York, New York, NY 10016
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Akshay Raju
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Jessica Flowers
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Hogan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Atomwise, Inc., San Francisco, CA, United States
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduate Center – City University of New York, New York, NY 10016
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
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21
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Hu W, Song A, Zheng H. Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2. Nat Commun 2024; 15:3616. [PMID: 38684689 PMCID: PMC11059360 DOI: 10.1038/s41467-024-48028-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.
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Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Alex Song
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, US.
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22
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Zerio CJ, Bai Y, Sosa-Alvarado BA, Guzi T, Lander GC. Human polymerase theta helicase positions DNA microhomologies for double-strand break repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591388. [PMID: 38712090 PMCID: PMC11071473 DOI: 10.1101/2024.04.26.591388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
DNA double-strand breaks occur in all human cells on a daily basis and must be repaired with high fidelity to minimize genomic instability1. Deficiencies in high-fidelity DNA repair by homologous recombination lead to dependence on DNA polymerase theta, which identifies DNA microhomologies in 3' single-stranded DNA overhangs and anneals them to initiate error-prone double-strand break repair. The resulting genomic instability is associated with numerous cancers, thereby making this polymerase an attractive therapeutic target2,3. However, despite the biomedical importance of polymerase theta, the molecular details of how it initiates DNA break repair remain unclear4,5. Here we present cryo-electron microscopy structures of the polymerase theta helicase domain bound to microhomology-containing DNA, revealing DNA-induced rearrangements of the helicase that enable DNA repair. Our structures show that DNA-bound helicase dimers facilitate a microhomology search that positions 3' single-stranded DNA ends in proximity to align complementary base pairs and anneal DNA microhomology. We define the molecular determinants that enable the polymerase theta helicase domain to identify and pair DNA microhomologies to initiate mutagenic DNA repair, providing mechanistic insights into therapeutic targeting of these interactions.
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Affiliation(s)
- Christopher J. Zerio
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | | | | | | | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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23
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Berkeley RF, Cook BD, Herzik MA. Machine learning approaches to cryoEM density modification differentially affect biomacromolecule and ligand density quality. Front Mol Biosci 2024; 11:1404885. [PMID: 38698773 PMCID: PMC11063317 DOI: 10.3389/fmolb.2024.1404885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/03/2024] [Indexed: 05/05/2024] Open
Abstract
The application of machine learning to cryogenic electron microscopy (cryoEM) data analysis has added a valuable set of tools to the cryoEM data processing pipeline. As these tools become more accessible and widely available, the implications of their use should be assessed. We noticed that machine learning map modification tools can have differential effects on cryoEM densities. In this perspective, we evaluate these effects to show that machine learning tools generally improve densities for biomacromolecules while generating unpredictable results for ligands. This unpredictable behavior manifests both in quantitative metrics of map quality and in qualitative investigations of modified maps. The results presented here highlight the power and potential of machine learning tools in cryoEM, while also illustrating some of the risks of their unexamined use.
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24
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Blomgren LKM, Huber M, Mackinnon SR, Bürer C, Baslé A, Yue WW, Froese DS, McCorvie TJ. Dynamic inter-domain transformations mediate the allosteric regulation of human 5, 10-methylenetetrahydrofolate reductase. Nat Commun 2024; 15:3248. [PMID: 38622112 PMCID: PMC11018872 DOI: 10.1038/s41467-024-47174-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved catalytic domain (CD) a unique regulatory domain (RD) that confers feedback inhibition by SAM. Here we determine the cryo-electron microscopy structures of human MTHFR bound to SAM and its demethylated product S-adenosyl-L-homocysteine (SAH). In the active state, with the RD bound to a single SAH, the CD is flexible and exposes its active site for catalysis. However, in the inhibited state the RD pocket is remodelled, exposing a second SAM-binding site that was previously occluded. Dual-SAM bound MTHFR demonstrates a substantially rearranged inter-domain linker that reorients the CD, inserts a loop into the active site, positions Tyr404 to bind the cofactor FAD, and blocks substrate access. Our data therefore explain the long-distance regulatory mechanism of MTHFR inhibition, underpinned by the transition between dual-SAM and single-SAH binding in response to cellular methylation status.
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Affiliation(s)
- Linnea K M Blomgren
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, CH-8032, Switzerland
| | - Melanie Huber
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, CH-8032, Switzerland
| | - Sabrina R Mackinnon
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, CH-8032, Switzerland
| | - Arnaud Baslé
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Wyatt W Yue
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
- Centre for Medicines Discovery, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zürich, University of Zürich, Zürich, CH-8032, Switzerland.
| | - Thomas J McCorvie
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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25
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de Moura TR, Purta E, Bernat A, Martín-Cuevas E, Kurkowska M, Baulin E, Mukherjee S, Nowak J, Biela A, Rawski M, Glatt S, Moreno-Herrero F, Bujnicki J. Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic Acids Res 2024; 52:3419-3432. [PMID: 38426934 PMCID: PMC11014237 DOI: 10.1093/nar/gkae144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/25/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics.
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Affiliation(s)
- Tales Rocha de Moura
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Elżbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Agata Bernat
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Eva M Martín-Cuevas
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Małgorzata Kurkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Eugene F Baulin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Jakub Nowak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Artur P Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michał Rawski
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
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26
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Thongchol J, Yu Z, Harb L, Lin Y, Koch M, Theodore M, Narsaria U, Shaevitz J, Gitai Z, Wu Y, Zhang J, Zeng L. Removal of Pseudomonas type IV pili by a small RNA virus. Science 2024; 384:eadl0635. [PMID: 38574145 PMCID: PMC11126211 DOI: 10.1126/science.adl0635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa. The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
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Affiliation(s)
- Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Zihao Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yiruo Lin
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Matthias Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew Theodore
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Utkarsh Narsaria
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Joshua Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
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27
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Liu X, Yu L, Xia Z, Li J, Meng W, Min L, Li F, Wang X. Purification, identification and Cryo-EM structure of prostatic acid phosphatase in human semen. Biochem Biophys Res Commun 2024; 702:149652. [PMID: 38341922 DOI: 10.1016/j.bbrc.2024.149652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Prostatic acid phosphatase (PAP) is a glycoprotein that plays a crucial role in the hydrolysis of phosphate ester present in prostatic exudates. It is a well-established indicator for prostate cancer due to its elevated serum levels in disease progression. Despite its abundance in semen, PAP's influence on male fertility has not been extensively studied. In our study, we report a significantly optimized method for purifying human endogenous PAP, achieving remarkably high efficiency and active protein recovery rate. This achievement allowed us to better analyze and understand the PAP protein. We determined the cryo-electron microscopic (Cryo-EM) structure of prostatic acid phosphatase in its physiological state for the first time. Our structural and gel filtration analysis confirmed the formation of a tight homodimer structure of human PAP. This functional homodimer displayed an elongated conformation in the cryo-EM structure compared to the previously reported crystal structure. Additionally, there was a notable 5-degree rotation in the angle between the α domain and α/β domain of each monomer. Through structural analysis, we revealed three potential glycosylation sites: Asn94, Asn220, and Asn333. These sites contained varying numbers and forms of glycosyl units, suggesting sugar moieties influence PAP function. Furthermore, we found that the active sites of PAP, His44 and Asp290, are located between the two protein domains. Overall, our study not only provide an optimized approach for PAP purification, but also offer crucial insights into its structural characteristics. These findings lay the groundwork for further investigations into the physiological function and potential therapeutic applications of this important protein.
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Affiliation(s)
- Xuanzhong Liu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Lin Yu
- Department of Andrology/Sichuan Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610066, Sichuan Province, China
| | - Zhili Xia
- Department of General Surgery, The First Hospital of Lanzhou University, The First Clinical Medical School of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Jialu Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Wenbo Meng
- Department of General Surgery, The First Hospital of Lanzhou University, The First Clinical Medical School of Lanzhou University, Lanzhou, 730000, Gansu Province, China
| | - Ling Min
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Fuping Li
- Department of Andrology/Sichuan Human Sperm Bank, West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, 610066, Sichuan Province, China.
| | - Xiang Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China.
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28
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Jamali K, Käll L, Zhang R, Brown A, Kimanius D, Scheres SHW. Automated model building and protein identification in cryo-EM maps. Nature 2024; 628:450-457. [PMID: 38408488 PMCID: PMC11006616 DOI: 10.1038/s41586-024-07215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality to those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy to those built by humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will therefore remove bottlenecks and increase objectivity in cryo-EM structure determination.
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Affiliation(s)
| | - Lukas Käll
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Zhang
- Washington University in St Louis, St Louis, MO, USA
| | - Alan Brown
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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29
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Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM. Structural basis of prostaglandin efflux by MRP4. Nat Struct Mol Biol 2024; 31:621-632. [PMID: 38216659 PMCID: PMC11145372 DOI: 10.1038/s41594-023-01176-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 11/07/2023] [Indexed: 01/14/2024]
Abstract
Multidrug resistance protein 4 (MRP4) is a broadly expressed ATP-binding cassette transporter that is unique among the MRP subfamily for transporting prostanoids, a group of signaling molecules derived from unsaturated fatty acids. To better understand the basis of the substrate selectivity of MRP4, we used cryogenic-electron microscopy to determine six structures of nanodisc-reconstituted MRP4 at various stages throughout its transport cycle. Substrate-bound structures of MRP4 in complex with PGE1, PGE2 and the sulfonated-sterol DHEA-S reveal a common binding site that accommodates a diverse set of organic anions and suggest an allosteric mechanism for substrate-induced enhancement of MRP4 ATPase activity. Our structure of a catalytically compromised MRP4 mutant bound to ATP-Mg2+ is outward-occluded, a conformation previously unobserved in the MRP subfamily and consistent with an alternating-access transport mechanism. Our study provides insights into the endogenous function of this versatile efflux transporter and establishes a basis for MRP4-targeted drug design.
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Affiliation(s)
- Sergei Pourmal
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Program in Chemistry and Chemical Biology, University of California, San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Evan Green
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
- Exelixis, Alameda, CA, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Ilan E Chemmama
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Brightseed, South San Francisco, CA, USA
| | - Giselle M Knudsen
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
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30
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Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJ. High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Nat Commun 2024; 15:2265. [PMID: 38480681 PMCID: PMC10937634 DOI: 10.1038/s41467-024-46375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
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Affiliation(s)
- Victoria I Cushing
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Adrian F Koh
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands
| | - Junjie Feng
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Kaste Jurgaityte
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | | | | | - Marion Barbazanges
- Department of Chemistry, Imperial College London, London, UK
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Bodo Scheiper
- Department of Chemistry, Imperial College London, London, UK
| | - Ash K Bahl
- Carrick Therapeutics, Nova UCD, Bellfield Innovation Park, Dublin 4, Ireland
| | | | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands.
| | - Basil J Greber
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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31
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Deng J, Cui Q. Efficient Sampling of Cavity Hydration in Proteins with Nonequilibrium Grand Canonical Monte Carlo and Polarizable Force Fields. J Chem Theory Comput 2024; 20:1897-1911. [PMID: 38417108 DOI: 10.1021/acs.jctc.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Prediction of the hydration levels of protein cavities and active sites is important to both mechanistic analysis and ligand design. Due to the unique microscopic environment of these buried water molecules, a polarizable model is expected to be crucial for an accurate treatment of protein internal hydration in simulations. Here we adapt a nonequilibrium candidate Monte Carlo approach for conducting grand canonical Monte Carlo simulations with the Drude polarizable force field. The GPU implementation enables the efficient sampling of internal cavity hydration levels in biomolecular systems. We also develop an enhanced sampling approach referred to as B-walking, which satisfies detailed balance and readily combines with grand canonical integration to efficiently calculate quantitative binding free energies of water to protein cavities. Applications of these developments are illustrated in a solvent box and the polar ligand binding site in trypsin. Our simulation results show that including electronic polarization leads to a modest but clear improvement in the description of water position and occupancy compared to the crystal structure. The B-walking approach enhances the range of water sampling in different chemical potential windows and thus improves the accuracy of water binding free energy calculations.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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32
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Roisné-Hamelin F, Liu HW, Taschner M, Li Y, Gruber S. Structural basis for plasmid restriction by SMC JET nuclease. Mol Cell 2024; 84:883-896.e7. [PMID: 38309275 DOI: 10.1016/j.molcel.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state.
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Affiliation(s)
- Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Yan Li
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland.
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33
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Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R. Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses. Proc Natl Acad Sci U S A 2024; 121:e2320493121. [PMID: 38427602 DOI: 10.1073/pnas.2320493121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/05/2024] [Indexed: 03/03/2024] Open
Abstract
Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T's "arms." Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.
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Affiliation(s)
| | - Lily Xu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Xueting Zhou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
| | - Rui Huang
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Grace Nye
- Department of Biochemistry, Stanford University, Stanford, CA 94305
| | - Shanshan Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiming Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305
- Department of Biochemistry, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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34
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Chmielewski D, Su GC, Kaelber JT, Pintilie GD, Chen M, Jin J, Auguste AJ, Chiu W. Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses. PNAS NEXUS 2024; 3:pgae102. [PMID: 38525304 PMCID: PMC10959069 DOI: 10.1093/pnasnexus/pgae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024]
Abstract
Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) reconstructions, which impose icosahedral symmetry on the viral particles. Using cryogenic electron tomography (cryo-ET), we revealed a polarized symmetry defect in the icosahedral lattice of Chikungunya virus (CHIKV) in situ, similar to the late budding particles, suggesting the inherent imperfect symmetry originates from the final pinch-off of assembled virions. We further demonstrated this imperfect symmetry is also present in in vitro purified CHIKV and Mayaro virus, another arthritogenic alphavirus. We employed a subparticle-based single-particle analysis protocol to circumvent the icosahedral imperfection and boosted the resolution of the structure of the CHIKV to ∼3 Å resolution, which revealed detailed molecular interactions between glycoprotein E1-E2 heterodimers in the transmembrane region and multiple lipid-like pocket factors located in a highly conserved hydrophobic pocket. This complementary use of in situ cryo-ET and single-particle cryo-EM approaches provides a more precise structural description of near-icosahedral viruses and valuable insights to guide the development of structure-based antiviral therapies against alphaviruses.
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Affiliation(s)
- David Chmielewski
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Guan-Chin Su
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Grigore D Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Jing Jin
- Vitalant Research Institute, San Francisco, CA 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA
| | - Albert J Auguste
- Department of Entomology, College of Agriculture and Life Sciences, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Wah Chiu
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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35
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Feng MF, Chen YX, Shen HB. DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score. J Struct Biol 2024; 216:108059. [PMID: 38160703 DOI: 10.1016/j.jsb.2023.108059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality for 3D cryo-EM density maps, using a deep-learning algorithm based on map-model fit score. DeepQs is a parameter-free method for users and incorporates structural information between map and its related atomic model into well-trained models by deep learning. More specifically, the DeepQs approach leverages the interplay between map and atomic model through predefined map-model fit score, Q-score. DeepQs can get close results to the ground truth map-model fit scores with only cryo-EM map as input. In experiments, DeepQs demonstrates the lowest root mean square error with standard method Fourier shell correlation metric and high correlation with map-model fit score, Q-score, when compared with other local quality estimation methods in high-resolution dataset (<=5 Å). DeepQs can also be applied to evaluate the quality of the post-processed maps. In both cases, DeepQs runs faster by using GPU acceleration. Our program is available at http://www.csbio.sjtu.edu.cn/bioinf/DeepQs for academic use.
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Affiliation(s)
- Ming-Feng Feng
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yu-Xuan Chen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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36
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation. IUCRJ 2024; 11:140-151. [PMID: 38358351 PMCID: PMC10916293 DOI: 10.1107/s2052252524001246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Maya Topf
- Birkbeck, University of London, London, United Kingdom
| | | | | | | | | | | | | | | | - Sai J. Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Ryan Pye
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | | | - Zhe Wang
- EMBL-EBI, Cambridge, United Kingdom
| | | | | | - Martyn D. Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, United Kingdom
| | - Jasmine Y. Young
- RCSB Protein Data Bank, The State University of New Jersey, NJ, USA
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37
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Tsai YX, Chang NE, Reuter K, Chang HT, Yang TJ, von Bülow S, Sehrawat V, Zerrouki N, Tuffery M, Gecht M, Grothaus IL, Colombi Ciacchi L, Wang YS, Hsu MF, Khoo KH, Hummer G, Hsu STD, Hanus C, Sikora M. Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 2024; 187:1296-1311.e26. [PMID: 38428397 DOI: 10.1016/j.cell.2024.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/18/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Abstract
Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.
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Affiliation(s)
- Yu-Xi Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Ning-En Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Klaus Reuter
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Hao-Ting Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Jing Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany
| | - Vidhi Sehrawat
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Kraków, Poland
| | - Noémie Zerrouki
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France
| | - Matthieu Tuffery
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France
| | - Michael Gecht
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany
| | - Isabell Louise Grothaus
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interfaces Group, Faculty of Production Engineering, Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes, University of Bremen, 28359 Bremen, Germany
| | - Yong-Sheng Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Kay-Hooi Khoo
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt, Germany
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Hiroshima 739-8526, Japan.
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266, Université Paris-Cité, 75014 Paris, France; GHU Psychiatrie et Neurosciences de Paris, 75014 Paris, France.
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, 60438 Frankfurt, Germany; Malopolska Centre of Biotechnology, Jagiellonian University, 31-007 Kraków, Poland.
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38
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580363. [PMID: 38405886 PMCID: PMC10888765 DOI: 10.1101/2024.02.14.580363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 Å resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hevatib Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
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39
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. eLife 2024; 12:RP92462. [PMID: 38381130 PMCID: PMC10942615 DOI: 10.7554/elife.92462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Yuqi Shi
- Thermo Fisher ScientificSan JoseUnited States
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Katleen Willibal
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Nathan D Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - H Ronald Kaback
- Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech UniversityLubbockUnited States
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
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40
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Xu M, Neelands T, Powers AS, Liu Y, Miller SD, Pintilie GD, Bois JD, Dror RO, Chiu W, Maduke M. CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism. eLife 2024; 12:RP90648. [PMID: 38345841 PMCID: PMC10942593 DOI: 10.7554/elife.90648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Abstract
CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.
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Affiliation(s)
- Mengyuan Xu
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Torben Neelands
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Alexander S Powers
- Department of Chemistry, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Yan Liu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
| | - Steven D Miller
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Grigore D Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - J Du Bois
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
- Department of Computer Science, Stanford UniversityStanfordUnited States
- Department of Structural Biology, Stanford UniversityStanfordUnited States
- Institute for Computational and Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford UniversityStanfordUnited States
- Department of Bioengineering and Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Merritt Maduke
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
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41
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Kleywegt GJ, Adams PD, Butcher SJ, Lawson CL, Rohou A, Rosenthal PB, Subramaniam S, Topf M, Abbott S, Baldwin PR, Berrisford JM, Bricogne G, Choudhary P, Croll TI, Danev R, Ganesan SJ, Grant T, Gutmanas A, Henderson R, Heymann JB, Huiskonen JT, Istrate A, Kato T, Lander GC, Lok SM, Ludtke SJ, Murshudov GN, Pye R, Pintilie GD, Richardson JS, Sachse C, Salih O, Scheres SHW, Schroeder GF, Sorzano COS, Stagg SM, Wang Z, Warshamanage R, Westbrook JD, Winn MD, Young JY, Burley SK, Hoch JC, Kurisu G, Morris K, Patwardhan A, Velankar S. Community recommendations on cryoEM data archiving and validation: Outcomes of a wwPDB/EMDB workshop on cryoEM data management, deposition and validation. ARXIV 2024:arXiv:2311.17640v3. [PMID: 38076521 PMCID: PMC10705588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and consensus recommendations resulting from the workshop. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.
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Affiliation(s)
| | - Paul D Adams
- Lawrence Berkeley Laboratory, Berkeley, CA, USA and University of California, Berkeley, CA, USA
| | | | - Catherine L Lawson
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | | | | | | | - Maya Topf
- Birkbeck, University of London, London, UK
| | | | | | | | | | | | | | | | - Sai J Ganesan
- University of California at San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John D Westbrook
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Martyn D Winn
- Science and Technology Facilities Council, Research Complex at Harwell, Oxon, UK
| | - Jasmine Y Young
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Rutgers, The State University of New Jersey, USA
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42
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Park J, Kim H, Gestaut D, Lim S, Opoku-Nsiah KA, Leitner A, Frydman J, Roh SH. A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. Nat Commun 2024; 15:1007. [PMID: 38307855 PMCID: PMC10837153 DOI: 10.1038/s41467-024-45242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding.
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Affiliation(s)
- Junsun Park
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Hyunmin Kim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - Daniel Gestaut
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Seyeon Lim
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | | | - Alexander Leitner
- Institute of Molecular Systems Biology, Dept of Biology, ETH Zurich, Zurich, 8093, Switzerland
| | - Judith Frydman
- Dept of Biology and Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Soung-Hun Roh
- School of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea.
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43
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Ghanim GE, Sekne Z, Balch S, van Roon AMM, Nguyen THD. 2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein. Nat Commun 2024; 15:746. [PMID: 38272871 PMCID: PMC10811338 DOI: 10.1038/s41467-024-45002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that extends telomeric repeats at eukaryotic chromosome ends to counterbalance telomere loss caused by incomplete genome replication. Human telomerase is comprised of two distinct functional lobes tethered by telomerase RNA (hTR): a catalytic core, responsible for DNA extension; and a Hinge and ACA (H/ACA) box RNP, responsible for telomerase biogenesis. H/ACA RNPs also have a general role in pseudouridylation of spliceosomal and ribosomal RNAs, which is critical for the biogenesis of the spliceosome and ribosome. Much of our structural understanding of eukaryotic H/ACA RNPs comes from structures of the human telomerase H/ACA RNP. Here we report a 2.7 Å cryo-electron microscopy structure of the telomerase H/ACA RNP. The significant improvement in resolution over previous 3.3 Å to 8.2 Å structures allows us to uncover new molecular interactions within the H/ACA RNP. Many disease mutations are mapped to these interaction sites. The structure also reveals unprecedented insights into a region critical for pseudouridylation in canonical H/ACA RNPs. Together, our work advances understanding of telomerase-related disease mutations and the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
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Affiliation(s)
| | - Zala Sekne
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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44
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. RESEARCH SQUARE 2024:rs.3.rs-3864137. [PMID: 38343795 PMCID: PMC10854310 DOI: 10.21203/rs.3.rs-3864137/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | - Grigore D. Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc, South San Francisco, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc, South San Francisco, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Chenghua Shao
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc, South San Francisco, USA
| | - Venkat Abbaraju
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L. Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F. Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P. Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R. Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luisa U. Schäfer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J. Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F. Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C. Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature’s Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D. Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F. Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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45
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Basanta B, Nugroho K, Yan NL, Kline GM, Powers ET, Tsai FJ, Wu M, Hansel-Harris A, Chen JS, Forli S, Kelly JW, Lander GC. The conformational landscape of human transthyretin revealed by cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576879. [PMID: 38328110 PMCID: PMC10849623 DOI: 10.1101/2024.01.23.576879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Transthyretin (TTR) is a natively tetrameric thyroxine transporter found in blood and cerebrospinal fluid whose misfolding and aggregation causes transthyretin amyloidosis. A rational drug design campaign identified the small molecule tafamidis (Vyndaqel/Vyndamax) as an effective stabilizer of the native TTR fold, and this aggregation inhibitor is regulatory agency-approved for the treatment of TTR amyloidosis. Despite 50 years of structural studies on TTR and this triumph of structure-based drug design, there remains a notable dearth of structural information available to understand ligand binding allostery and amyloidogenic TTR unfolding intermediates. We used single-particle cryo-electron microscopy (cryo-EM) to investigate the conformational landscape of this 55 kiloDalton tetramer in the absence and presence of one or two ligands, revealing inherent asymmetries in the tetrameric architecture and previously unobserved conformational states. These findings provide critical mechanistic insights into negatively cooperative ligand binding and the structural pathways responsible for TTR amyloidogenesis. This study underscores the capacity of cryo-EM to provide new insights into protein structures that have been historically considered too small to visualize and to identify pharmacological targets suppressed by the confines of the crystal lattice, opening uncharted territory in structure-based drug design.
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Affiliation(s)
- Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Karina Nugroho
- Department of Chemistry, Scripps Research; La Jolla, CA, USA
| | - Nicholas L. Yan
- Department of Chemistry, Scripps Research; La Jolla, CA, USA
| | | | - Evan T. Powers
- Department of Chemistry, Scripps Research; La Jolla, CA, USA
| | - Felix J. Tsai
- Department of Chemistry, Scripps Research; La Jolla, CA, USA
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Althea Hansel-Harris
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Jason S. Chen
- Automated Synthesis Facility, Scripps Research, La Jolla, CA 92037, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | | | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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46
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Sweeney A, Mulvaney T, Maiorca M, Topf M. ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures. J Med Chem 2024; 67:199-212. [PMID: 38157562 PMCID: PMC10788898 DOI: 10.1021/acs.jmedchem.3c01134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Cryo-electron microscopy (cryo-EM), through resolution advancements, has become pivotal in structure-based drug discovery. However, most cryo-EM structures are solved at 3-4 Å resolution, posing challenges for small-molecule docking and structure-based virtual screening due to issues in the precise positioning of ligands and the surrounding side chains. We present ChemEM, a software package that employs cryo-EM data for the accurate docking of one or multiple ligands in a protein-binding site. Validated against a highly curated benchmark of high- and medium-resolution cryo-EM structures and the corresponding high-resolution controls, ChemEM displayed impressive performance, accurately placing ligands in all but one case, often surpassing cryo-EM PDB-deposited solutions. Even without including the cryo-EM density, the ChemEM scoring function outperformed the well-established AutoDock Vina score. Using ChemEM, we illustrate that valuable information can be extracted from maps at medium resolution and underline the utility of cryo-EM structures for drug discovery.
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Affiliation(s)
- Aaron Sweeney
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
| | - Thomas Mulvaney
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
| | - Mauro Maiorca
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
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47
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Bick T, Dominiak PM, Wendler P. Exploiting the full potential of cryo-EM maps. BBA ADVANCES 2024; 5:100113. [PMID: 38292063 PMCID: PMC10825613 DOI: 10.1016/j.bbadva.2024.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 02/01/2024] Open
Abstract
The Coulomb potential maps generated by electron microscopy (EM) experiments contain not only information about the position but also about the charge state of the atom. This feature of EM maps allows the identification of specific ions and the protonation state of amino acid side chains in the sample. Here, we summarize qualitative observations of charges in EM maps, discuss the difficulties in interpreting the charge in Coulomb potential maps with respect to distinguishing it from radiation damage, and outline considerations to implement the correct charge in fitting algorithms.
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Affiliation(s)
- Thomas Bick
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
| | - Paulina M. Dominiak
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, 14476 Potsdam Golm, Germany
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48
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Nishimura M, Fujii T, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y, Kurumizaka H. Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties. Commun Biol 2024; 7:61. [PMID: 38191828 PMCID: PMC10774305 DOI: 10.1038/s42003-023-05694-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.
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Affiliation(s)
- Masahiro Nishimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, 111 TW, Alexander Drive, Research Triangle Park, NC, 27707, USA
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yuki Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka, 812-0054, Japan.
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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49
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Turner J, Abbott S, Fonseca N, Pye R, Carrijo L, Duraisamy AK, Salih O, Wang Z, Kleywegt GJ, Morris KL, Patwardhan A, Burley SK, Crichlow G, Feng Z, Flatt JW, Ghosh S, Hudson BP, Lawson CL, Liang Y, Peisach E, Persikova I, Sekharan M, Shao C, Young J, Velankar S, Armstrong D, Bage M, Bueno WM, Evans G, Gaborova R, Ganguly S, Gupta D, Harrus D, Tanweer A, Bansal M, Rangannan V, Kurisu G, Cho H, Ikegawa Y, Kengaku Y, Kim JY, Niwa S, Sato J, Takuwa A, Yu J, Hoch JC, Baskaran K, Xu W, Zhang W, Ma X. EMDB-the Electron Microscopy Data Bank. Nucleic Acids Res 2024; 52:D456-D465. [PMID: 37994703 PMCID: PMC10767987 DOI: 10.1093/nar/gkad1019] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023] Open
Abstract
The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30 000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.
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50
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Chen M, Schmid MF, Chiu W. Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models. Nat Methods 2024; 21:37-40. [PMID: 37973972 PMCID: PMC10860619 DOI: 10.1038/s41592-023-02082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023]
Abstract
Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.
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Affiliation(s)
- Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
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