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Gucwa M, Bijak V, Zheng H, Murzyn K, Minor W. CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data. IUCRJ 2024; 11:871-877. [PMID: 39141478 PMCID: PMC11364027 DOI: 10.1107/s2052252524007073] [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: 04/10/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024]
Abstract
Identifying and characterizing metal-binding sites (MBS) within macromolecular structures is imperative for elucidating their biological functions. CheckMyMetal (CMM) is a web based tool that facilitates the interactive validation of MBS in structures determined through X-ray crystallography and cryo-electron microscopy (cryo-EM). Recent updates to CMM have significantly enhanced its capability to efficiently handle large datasets generated from cryo-EM structural analyses. In this study, we address various challenges inherent in validating MBS within both X-ray and cryo-EM structures. Specifically, we examine the difficulties associated with accurately identifying metals and modeling their coordination environments by considering the ongoing reproducibility challenges in structural biology and the critical importance of well annotated, high-quality experimental data. CMM employs a sophisticated framework of rules rooted in the valence bond theory for MBS validation. We explore how CMM validation parameters correlate with the resolution of experimentally derived structures of macromolecules and their complexes. Additionally, we showcase the practical utility of CMM by analyzing a representative cryo-EM structure. Through a comprehensive examination of experimental data, we demonstrate the capability of CMM to advance MBS characterization and identify potential instances of metal misassignment.
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Affiliation(s)
- Michal Gucwa
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesville22908USA
- Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
- Doctoral School of Exact and Natural SciencesJagiellonian UniversityKrakowPoland
| | - Vanessa Bijak
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesville22908USA
| | - Heping Zheng
- Bioinformatics CenterHunan University College of BiologyChangshaHunan410082People’s Republic of China
| | - Krzysztof Murzyn
- Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesville22908USA
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2
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Bochtler M. X-rays, electrons, and neutrons as probes of atomic matter. Structure 2024; 32:630-643.e6. [PMID: 38412856 DOI: 10.1016/j.str.2024.01.015] [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: 11/29/2022] [Revised: 03/21/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
X-rays, electrons, and neutrons probe different properties of matter. X-rays feel electron density (ED). Electrons sense the electrostatic potential (ESP) of electrons and nuclei. Neutrons are sensitive to nuclear coherent scattering length (NCSL). While NCSL maps are widely understood to be different, ED and ESP maps are tacitly assumed to be similar. Here, I show that the belief in ED and ESP map equivalence is mistaken, but contains a grain of truth. Using density functional theory (DFT), the Bethe-Mott (BM) relation, and the Thomas-Fermi (TF) and Cromer-Mann (CM) atomic models, I show that ED and ESP maps are indeed more similar to each other than to NCSL maps. Nevertheless, peak and integrated map values depend differently on the atomic order number and on the contributions from electrons in the inner and outer CM shells. ED and ESP maps also differ in the sign and relative magnitude of excess charge effects.
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Affiliation(s)
- Matthias Bochtler
- IIMCB, Trojdena 4, 02-109 Warsaw, Poland; Polish Academy of Sciences, IBB, Pawinskiego 5a, 02-106 Warsaw, Poland.
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3
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Jorgensen C, Ulmschneider MB, Searson PC. Modeling Substrate Entry into the P-Glycoprotein Efflux Pump at the Blood-Brain Barrier. J Med Chem 2023; 66:16615-16627. [PMID: 38097510 DOI: 10.1021/acs.jmedchem.3c01069] [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] [Indexed: 12/29/2023]
Abstract
We report molecular dynamics simulations of rhodamine entry into the central binding cavity of P-gp in the inward open conformation. Rhodamine can enter the inner volume via passive transport across the luminal membrane or lateral diffusion in the lipid bilayer. Entry into the inner volume is determined by the aperture angle at the apex of the protein, with a critical angle of 27° for rhodamine. The central binding cavity has an aqueous phase with a few lipids, which significantly reduces substrate diffusion. Within the central binding cavity, we identified regions with relatively weak binding, suggesting that the combination of reduced mobility and weak substrate binding confines rhodamine to enable the completion of the efflux cycle. Tariquidar, a P-gp inhibitor, aggregates at the lower arms of the P-gp, suggesting that inhibition involves steric hindrance of entry into the inner volume and/or steric hindrance of access of ATP to the nucleotide-binding domains.
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Affiliation(s)
- Christian Jorgensen
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Peter C Searson
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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4
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Pražnikar J. Using graphlet degree vectors to predict atomic displacement parameters in protein structures. Acta Crystallogr D Struct Biol 2023; 79:1109-1119. [PMID: 37987168 PMCID: PMC10833351 DOI: 10.1107/s2059798323009142] [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: 06/26/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
In structural biology, atomic displacement parameters, commonly used in the form of B values, describe uncertainties in atomic positions. Their distribution over the structure can provide hints on local structural reliability and mobility. A spatial macromolecular model can be represented by a graph whose nodes are atoms and whose edges correspond to all interatomic contacts within a certain distance. Small connected subgraphs, called graphlets, provide information about the wiring of a particular atom. The multiple linear regression approach based on this information aims to predict a distribution of values of isotropic atomic displacement parameters (B values) within a protein structure, given the atomic coordinates and molecular packing. By modeling the dynamic component of atomic uncertainties, this method allows the B values obtained from experimental crystallographic or cryo-electron microscopy studies to be reproduced relatively well.
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Affiliation(s)
- Jure Pražnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper, Slovenia
- Department of Biochemistry, Molecular and Structural Biology, Institute Jožef Stefan, Jamova 39, Ljubljana, Slovenia
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5
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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023; 18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. AREAS COVERED This review explores the relationship between X-ray crystallography and other modern structural determination methods. It examines the integration of data acquired from diverse biochemical and biophysical techniques with those derived from structural biology. Additionally, the paper offers insights into the influence of AI on X-ray crystallography, emphasizing how integrating AI with experimental approaches can revolutionize our comprehension of biological processes and interactions. EXPERT OPINION Investing in science is crucially emphasized due to its significant role in drug discovery and advancements in healthcare. X-ray crystallography remains an essential source of structural biology data for drug discovery. Recent advances in biochemical, spectroscopic, and bioinformatic methods, along with the integration of AI techniques, hold the potential to revolutionize drug discovery when effectively combined with robust data management practices.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Szczygiel
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
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6
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Lugmayr W, Kotov V, Goessweiner-Mohr N, Wald J, DiMaio F, Marlovits TC. StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement. Nat Protoc 2023; 18:239-264. [PMID: 36323866 DOI: 10.1038/s41596-022-00757-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/08/2022] [Indexed: 01/13/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) data represent density maps of macromolecular systems at atomic or near-atomic resolution. However, building and refining 3D atomic models by using data from cryo-EM maps is not straightforward and requires significant hands-on experience and manual intervention. We recently developed StarMap, an easy-to-use interface between the popular structural display program ChimeraX and Rosetta, a powerful molecular modeling engine. StarMap offers a general approach for refining structural models of biological macromolecules into cryo-EM density maps by combining Monte Carlo sampling with local density-guided optimization, Rosetta-based all-atom refinement and real-space B-factor calculations in a straightforward workflow. StarMap includes options for structural symmetry, local refinements and independent model validation. The overall quality of the refinement and the structure resolution is then assessed via analytical outputs, such as magnification calibration (pixel size calibration) and Fourier shell correlations. Z-scores reported by StarMap provide an easily interpretable indicator of the goodness of fit for each residue and can be plotted to evaluate structural models and improve local residue refinements, as well as to identify flexible regions and potentially functional sites in large macromolecular complexes. The protocol requires general computer skills, without the need for coding expertise, because most parts of the workflow can be operated by clicking tabs within the ChimeraX graphical user interface. Time requirements for the model refinement depend on the size and quality of the input data; however, this step can typically be completed within 1 d. The analytical parts of the workflow are completed within minutes.
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Affiliation(s)
- Wolfgang Lugmayr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria
| | - Vadim Kotov
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Evotec SE, Hamburg, Germany
| | - Nikolaus Goessweiner-Mohr
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.,Johannes Kepler University, Institute of Biophysics, Linz, Austria
| | - Jiri Wald
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany.,CSSB Centre for Structural Systems Biology, Hamburg, Germany.,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany.,Research Institute of Molecular Pathology (IMP), Vienna, Austria.,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria
| | - Frank DiMaio
- University of Washington, Department of Biochemistry, Seattle, WA, USA
| | - Thomas C Marlovits
- University Medical Center Hamburg-Eppendorf (UKE), Institute of Structural and Systems Biology, Hamburg, Germany. .,CSSB Centre for Structural Systems Biology, Hamburg, Germany. .,Deutsches Elektronen Synchrotron (DESY), Hamburg, Germany. .,Research Institute of Molecular Pathology (IMP), Vienna, Austria. .,Institute for Molecular Biotechnology (IMBA), Austrian Academy of Sciences, Vienna, Austria.
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7
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Beton JG, Cragnolini T, Kaleel M, Mulvaney T, Sweeney A, Topf M. Integrating model simulation tools and
cryo‐electron
microscopy. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Joseph George Beton
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck and University College London London UK
| | - Manaz Kaleel
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Thomas Mulvaney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB) Leibniz‐Institut für Virologie (LIV) Hamburg Germany
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8
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Narayanan RP, Procyk J, Nandi P, Prasad A, Xu Y, Poppleton E, Williams D, Zhang F, Yan H, Chiu PL, Stephanopoulos N, Šulc P. Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures. ACS NANO 2022; 16:14086-14096. [PMID: 35980981 PMCID: PMC9590280 DOI: 10.1021/acsnano.2c04013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein-DNA linker identity and length; (2) optimizing the design of protein-DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein-DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. These tools will facilitate the design of complex hybrid protein-DNA nanostructures that seamlessly integrate the two different biomolecules.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jonah Procyk
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Xu
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Dewight Williams
- Eyring Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Petr Šulc
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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9
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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10
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The reproducible normality of the crystallographic B-factor. Anal Biochem 2022; 645:114594. [DOI: 10.1016/j.ab.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/20/2022]
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11
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Machine learning to estimate the local quality of protein crystal structures. Sci Rep 2021; 11:23599. [PMID: 34880321 PMCID: PMC8654820 DOI: 10.1038/s41598-021-02948-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Low-resolution electron density maps can pose a major obstacle in the determination and use of protein structures. Herein, we describe a novel method, called quality assessment based on an electron density map (QAEmap), which evaluates local protein structures determined by X-ray crystallography and could be applied to correct structural errors using low-resolution maps. QAEmap uses a three-dimensional deep convolutional neural network with electron density maps and their corresponding coordinates as input and predicts the correlation between the local structure and putative high-resolution experimental electron density map. This correlation could be used as a metric to modify the structure. Further, we propose that this method may be applied to evaluate ligand binding, which can be difficult to determine at low resolution.
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12
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Pintilie G, Chiu W. Validation, analysis and annotation of cryo-EM structures. Acta Crystallogr D Struct Biol 2021; 77:1142-1152. [PMID: 34473085 PMCID: PMC8411978 DOI: 10.1107/s2059798321006069] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/09/2021] [Indexed: 11/08/2023] Open
Abstract
The process of turning 2D micrographs into 3D atomic models of the imaged macromolecules has been under rapid development and scrutiny in the field of cryo-EM. Here, some important methods for validation at several stages in this process are described. Firstly, how Fourier shell correlation of two independent maps and phase randomization beyond a certain frequency address the assessment of map resolution is reviewed. Techniques for local resolution estimation and map sharpening are also touched upon. The topic of validating models which are either built de novo or based on a known atomic structure fitted into a cryo-EM map is then approached. Map-model comparison using Q-scores and Fourier shell correlation plots is used to assure the agreement of the model with the observed map density. The importance of annotating the model with B factors to account for the resolvability of individual atoms in the map is illustrated. Finally, the timely topic of detecting and validating water molecules and metal ions in maps that have surpassed ∼2 Å resolution is described.
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Affiliation(s)
- Grigore Pintilie
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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13
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Minor W, Jaskolski M, Martin SJ, Dauter Z. Dr. Alexander Wlodawer-celebrating five decades of service to the structural biology community. FEBS J 2021; 288:4160-4164. [PMID: 34286923 DOI: 10.1111/febs.16064] [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: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 11/28/2022]
Abstract
This 75th birthday tribute to our Editorial Board member Alexander Wlodawer recounts his decades-long service to the community of structural biology researchers. His former and current colleagues tell the story of his upbringing and education, followed by an account of his dedication to quality and rigor in crystallography and structural science. The FEBS Journal Editor-in-Chief Seamus Martin further highlights Alex's outstanding contributions to the journal's success over many years.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University and Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Seamus J Martin
- Department of Genetics, The Smurfit Institute, Trinity College, Dublin, Ireland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
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14
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Ginn HM. Vagabond: bond-based parametrization reduces overfitting for refinement of proteins. Acta Crystallogr D Struct Biol 2021; 77:424-437. [PMID: 33825703 PMCID: PMC8025884 DOI: 10.1107/s2059798321000826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/24/2021] [Indexed: 11/10/2022] Open
Abstract
Structural biology methods have delivered over 150 000 high-resolution structures of macromolecules, which have fundamentally altered our understanding of biology and our approach to developing new medicines. However, the description of molecular flexibility is instrinsically flawed and in almost all cases, regardless of the experimental method used for structure determination, there remains a strong overfitting bias during molecular model building and refinement. In the worst case this can lead to wholly incorrect structures and thus incorrect biological interpretations. Here, by reparametrizing the description of these complex structures in terms of bonds rather than atomic positions, and by modelling flexibility using a deterministic ensemble of structures, it is demonstrated that structures can be described using fewer parameters than in conventional refinement. The current implementation, applied to X-ray diffraction data, significantly reduces the extent of overfitting, allowing the experimental data to reveal more biological information in electron-density maps.
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Affiliation(s)
- Helen M. Ginn
- Division of Life Sciences, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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15
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Chojnowski G, Sobolev E, Heuser P, Lamzin VS. The accuracy of protein models automatically built into cryo-EM maps with ARP/wARP. Acta Crystallogr D Struct Biol 2021; 77:142-150. [PMID: 33559604 PMCID: PMC7869898 DOI: 10.1107/s2059798320016332] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/16/2020] [Indexed: 11/26/2022] Open
Abstract
A new module of the ARP/wARP suite for automated model building into cryo-EM maps is presented. Recent developments in cryogenic electron microscopy (cryo-EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high-resolution cryo-EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo-EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main-chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo-EM maps is comparable to that of X-ray crystallographic models at similar local cryo-EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
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Affiliation(s)
- Grzegorz Chojnowski
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Egor Sobolev
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Philipp Heuser
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Victor S Lamzin
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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16
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Refinement of a cryo-EM structure of hERG: Bridging structure and function. Biophys J 2021; 120:738-748. [PMID: 33476597 DOI: 10.1016/j.bpj.2021.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 01/16/2023] Open
Abstract
The human-ether-a-go-go-related gene (hERG) encodes the voltage-gated potassium channel (KCNH2 or Kv11.1, commonly known as hERG). This channel plays a pivotal role in the stability of phase 3 repolarization of the cardiac action potential. Although a high-resolution cryo-EM structure is available for its depolarized (open) state, the structure surprisingly did not feature many functionally important interactions established by previous biochemical and electrophysiology experiments. Using molecular dynamics flexible fitting (MDFF), we refined the structure and recovered the missing functionally relevant salt bridges in hERG in its depolarized state. We also performed electrophysiology experiments to confirm the functional relevance of a novel salt bridge predicted by our refinement protocol. Our work shows how refinement of a high-resolution cryo-EM structure helps to bridge the existing gap between the structure and function in the voltage-sensing domain (VSD) of hERG.
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17
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Alshammari M, He J. Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction - A Case Study. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2020; 2020:110. [PMID: 35838376 PMCID: PMC9279007 DOI: 10.1145/3388440.3414708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cryo-electron microscopy is a major structure determination technique for large molecular machines and membrane-associated complexes. Although atomic structures have been determined directly from cryo-EM density maps with high resolutions, current structure determination methods for medium resolution (5 to 10 Å) cryo-EM maps are limited by the availability of structure templates. Secondary structure traces are lines detected from a cryo-EM density map for α-helices and β-strands of a protein. When combined with secondary structure sequence segments predicted from a protein sequence, it is possible to generate a set of likely topologies of α-traces and β-sheet traces. A topology describes the overall folding relationship among secondary structures; it is a critical piece of information for deriving the corresponding atomic structure. We propose a method for protein structure prediction that combines three sources of information: the secondary structure traces detected from the cryo-EM density map, predicted secondary structure sequence segments, and amino acid contact pairs predicted using MULTICOM. A case study shows that using amino acid contact prediction from MULTICOM improves the ranking of the true topology. Our observations convey that using a small set of highly voted secondary structure contact pairs enhances the ranking in all experiments conducted for this case.
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18
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Wang J, Perez-Cruet JM, Huang HL, Reiss K, Gisriel CJ, Banerjee G, Kaur D, Ghosh I, Dziarski A, Gunner MR, Batista VS, Brudvig GW. Identification of a Na +-Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II. Biochemistry 2020; 59:2823-2831. [PMID: 32650633 DOI: 10.1021/acs.biochem.0c00303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions and one redox-inactive Ca2+ ion, with two nearby bound Cl- ions. Sodium is a common counterion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Here, we find that the oxygen-evolution activity of spinach PSII increases with Na+ concentration, particularly at high pH. A Na+-specific binding site next to the OEC, becomes available after deprotonation of the D1-H337 amino acid residue, is suggested by the analysis of two recently published PSII cryo-electron microscopy maps in combination with quantum mechanical calculations and multiconformation continuum electrostatics simulations.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
| | - Joshua M Perez-Cruet
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Hao-Li Huang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Christopher J Gisriel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gourab Banerjee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Divya Kaur
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Ipsita Ghosh
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alisha Dziarski
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - M R Gunner
- Department of Physics, City College of New York (CCNY), New York, New York 10031, United States.,Department of Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States.,Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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19
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Monzon AM, Necci M, Quaglia F, Walsh I, Zanotti G, Piovesan D, Tosatto SCE. Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. Int J Mol Sci 2020; 21:ijms21124496. [PMID: 32599863 PMCID: PMC7349999 DOI: 10.3390/ijms21124496] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/12/2023] Open
Abstract
Intrinsically disordered protein regions are commonly defined from missing electron density in X-ray structures. Experimental evidence for long disorder regions (LDRs) of at least 30 residues was so far limited to manually curated proteins. Here, we describe a comprehensive and large-scale analysis of experimental LDRs for 3133 unique proteins, demonstrating an increasing coverage of intrinsic disorder in the Protein Data Bank (PDB) in the last decade. The results suggest that long missing residue regions are a good quality source to annotate intrinsically disordered regions and perform functional analysis in large data sets. The consensus approach used to define LDRs allows to evaluate context dependent disorder and provide a common definition at the protein level.
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Affiliation(s)
- Alexander Miguel Monzon
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
| | - Marco Necci
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
| | - Federica Quaglia
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
| | - Ian Walsh
- Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore;
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
- Correspondence: (D.P.); (S.C.E.T.)
| | - Silvio C. E. Tosatto
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy; (A.M.M.); (M.N.); (F.Q.); (G.Z.)
- Correspondence: (D.P.); (S.C.E.T.)
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20
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Srivastava A, Tiwari SP, Miyashita O, Tama F. Integrative/Hybrid Modeling Approaches for Studying Biomolecules. J Mol Biol 2020; 432:2846-2860. [DOI: 10.1016/j.jmb.2020.01.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
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21
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Gruza B, Chodkiewicz ML, Krzeszczakowska J, Dominiak PM. Refinement of organic crystal structures with multipolar electron scattering factors. Acta Crystallogr A Found Adv 2020; 76:92-109. [PMID: 31908353 PMCID: PMC8127334 DOI: 10.1107/s2053273319015304] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022] Open
Abstract
A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near-atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high-quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X-ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen-Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure-factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci. 4, 1587-1592] or modelled with theoretical quantum-mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer-resolution diffraction data.
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Affiliation(s)
- Barbara Gruza
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Michał Leszek Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Joanna Krzeszczakowska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, Warsaw, 02-089, Poland
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22
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Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K. FACT caught in the act of manipulating the nucleosome. Nature 2020; 577:426-431. [PMID: 31775157 PMCID: PMC7441595 DOI: 10.1038/s41586-019-1820-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/07/2019] [Indexed: 01/21/2023]
Abstract
The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone known as 'facilitates chromatin transcription' (FACT1) (consisting of subunits SPT16 and SSRP1) promotes both disassembly and reassembly of nucleosomes during gene transcription, DNA replication and DNA repair2. However, the mechanism by which FACT causes these opposing outcomes is unknown. Here we report two cryo-electron-microscopic structures of human FACT in complex with partially assembled subnucleosomes, with supporting biochemical and hydrogen-deuterium exchange data. We find that FACT is engaged in extensive interactions with nucleosomal DNA and all histone variants. The large DNA-binding surface on FACT appears to be protected by the carboxy-terminal domains of both of its subunits, and this inhibition is released by interaction with H2A-H2B, allowing FACT-H2A-H2B to dock onto a complex containing DNA and histones H3 and H4 (ref. 3). SPT16 binds nucleosomal DNA and tethers H2A-H2B through its carboxy-terminal domain by acting as a placeholder for DNA. SSRP1 also contributes to DNA binding, and can assume two conformations, depending on whether a second H2A-H2B dimer is present. Our data suggest a compelling mechanism for how FACT maintains chromatin integrity during polymerase passage, by facilitating removal of the H2A-H2B dimer, stabilizing intermediate subnucleosomal states and promoting nucleosome reassembly. Our findings reconcile discrepancies regarding the many roles of FACT and underscore the dynamic interactions between histone chaperones and nucleosomes.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305
| | - Keda Zhou
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305
| | - Naifu Zhang
- The University of Texas at Dallas, Department of Chemistry and Biochemistry, Dallas, TX 75080
| | - Hui Wei
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Yong Zi Tan
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
| | - Zhening Zhang
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027,Biochemistry and Molecular Biophysics Dept., Columbia University Medical Center, New York, NY 10032
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Sheena D'Arcy
- The University of Texas at Dallas, Department of Chemistry and Biochemistry, Dallas, TX 75080
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305,Howard Hughes Medical Institute
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23
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Abstract
Single particle cryogenic electron microscopy (cryo-EM) is transforming structural biology by enabling the analysis of difficult macromolecular specimens, such as membrane proteins or large complexes with flexible elements, at near atomic resolution with an accuracy close to that of X-ray crystallography. As the technique continues to improve, it is important to assess and exploit its full potential to produce the most possible reliable atomic models. Here we propose to use the experimental images as the data for refinement and validation, instead of the reconstructed maps as currently used. This procedure, which is in spirit quite similar to that used in X-ray crystallography where the data include experimental phases, should contribute to improve the quality of the cryo-EM atomic models.
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Affiliation(s)
- Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, Cachan, 94235, France
| | - Jorge Navaza
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, Cachan, 94235, France
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24
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Khatib F, Desfosses A, Koepnick B, Flatten J, Popović Z, Baker D, Cooper S, Gutsche I, Horowitz S. Building de novo cryo-electron microscopy structures collaboratively with citizen scientists. PLoS Biol 2019; 17:e3000472. [PMID: 31714936 PMCID: PMC6850521 DOI: 10.1371/journal.pbio.3000472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
With the rapid improvement of cryo-electron microscopy (cryo-EM) resolution, new computational tools are needed to assist and improve upon atomic model building and refinement options. This communication demonstrates that microscopists can now collaborate with the players of the computer game Foldit to generate high-quality de novo structural models. This development could greatly speed the generation of excellent cryo-EM structures when used in addition to current methods.
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Affiliation(s)
- Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, United States of America
- * E-mail: (FB); (SH)
| | - Ambroise Desfosses
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Jeff Flatten
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - Zoran Popović
- Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Seth Cooper
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts, United States of America
| | - Irina Gutsche
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Scott Horowitz
- Department of Chemistry and Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado, United States of America
- * E-mail: (FB); (SH)
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25
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Klaholz BP. Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis. Acta Crystallogr D Struct Biol 2019; 75:878-881. [PMID: 31588919 PMCID: PMC6778849 DOI: 10.1107/s2059798319013391] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 01/05/2023] Open
Abstract
In structural biology, deriving and refining atomic models into maps obtained from X-ray crystallography or cryo electron microscopy (cryo-EM) is essential for the detailed interpretation of a structure and its functional implications through interactions so that for example hydrogen bonds, drug specificity and associated molecular mechanisms can be analysed. This commentary summarizes the latest features of the Phenix software and also highlights the fact that cryo-EM increasingly contributes to data depositions in the PDB and EMDB.
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Affiliation(s)
- Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, Illkirch 67404, France
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
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26
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Carter R, Luchini A, Liotta L, Haymond A. Next Generation Techniques for Determination of Protein-Protein Interactions: Beyond the Crystal Structure. CURRENT PATHOBIOLOGY REPORTS 2019; 7:61-71. [PMID: 33094031 PMCID: PMC7577580 DOI: 10.1007/s40139-019-00198-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW We discuss recent advancements in structural biology methods for investigating sites of protein-protein interactions. We will inform readers outside the field of structural biology about techniques beyond crystallography, and how these different technologies can be utilized for drug development. RECENT FINDINGS Advancements in cryo-electron microscopy (cryoEM) and micro-electron diffraction (microED) may change how we view atomic resolution structural biology, such that well-ordered macrocrystals of protein complexes are not required for interface identification. However, some drug discovery applications, such as lead peptide compound generation, may not require atomic resolution; mass spectrometry techniques can provide an expedited path to generation of lead compounds. New crosslinking compounds, more user-friendly data analysis, and novel protocols such as protein painting can advance drug discovery programs, even in the absence of atomic resolution structural data. Finally, artificial intelligence and machine learning methods, while never truly replacing experimental methods, may provide rational ways to stratify potential druggable regions identified with mass spectrometry into higher and lower priority candidates. SUMMARY Electron diffraction of nanocrystals combines the benefits of both x-ray diffraction and cryoEM, and may prove to be the next generation of atomic resolution protein-protein interface identification. However, in situations such as peptide drug discovery, mass spectrometry techniques supported by advancements in computational methods will likely prove sufficient to support drug discovery efforts. In addition, these methods can be significantly faster than any crystallographic or cryoEM methods for identification of interacting regions.
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Affiliation(s)
- Rachel Carter
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
| | - Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA
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27
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Chen L, Baker B, Santos E, Sheep M, Daftarian D. A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform. MEDICINES (BASEL, SWITZERLAND) 2019; 6:E86. [PMID: 31390767 PMCID: PMC6789601 DOI: 10.3390/medicines6030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/22/2022]
Abstract
Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high-resolution X-ray dataset (<1.5 Å) as the reference dataset. The distal block distance, side-chain length, phi, psi, and first chi angle of the residues in the reference dataset are collected and saved as a database of the histogram-based outlier score (HBOS). The HBOS value of the residues in target cryo-EM proteins can be read from this HBOS database. Results: Protein residues with a HBOS value greater than ten are labeled as outliers by default. Four datasets containing proteins derived from cryo-EM density maps were tested with this probabilistic anomaly detection model. Conclusions: According to the proposed model, a visualization assistant tool was designed for Chimera, a protein visualization platform.
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Affiliation(s)
- Lin Chen
- Department of Computer Science, Valdosta State University, Valdosta, GA 31693, USA.
| | - Brandon Baker
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Eduardo Santos
- Department of Natural Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Michell Sheep
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
| | - Darius Daftarian
- Department of Mathematics & Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA
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28
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Kidmose RT, Juhl J, Nissen P, Boesen T, Karlsen JL, Pedersen BP. Namdinator - automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCRJ 2019; 6:526-531. [PMID: 31316797 PMCID: PMC6608625 DOI: 10.1107/s2052252519007619] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/25/2019] [Indexed: 05/20/2023]
Abstract
Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool.
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Affiliation(s)
- Rune Thomas Kidmose
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Jonathan Juhl
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Poul Nissen
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Thomas Boesen
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Jesper Lykkegaard Karlsen
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
- Correspondence e-mail: ,
| | - Bjørn Panyella Pedersen
- Centre for Structural Biology, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
- Correspondence e-mail: ,
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29
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Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem Sci 2019; 44:837-848. [PMID: 31078399 DOI: 10.1016/j.tibs.2019.04.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Haruaki Yanagisawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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30
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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Sun Z, Liu Q, Qu G, Feng Y, Reetz MT. Utility of B-Factors in Protein Science: Interpreting Rigidity, Flexibility, and Internal Motion and Engineering Thermostability. Chem Rev 2019; 119:1626-1665. [PMID: 30698416 DOI: 10.1021/acs.chemrev.8b00290] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manfred T. Reetz
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
- Chemistry Department, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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Wang Y, Shekhar M, Thifault D, Williams CJ, McGreevy R, Richardson J, Singharoy A, Tajkhorshid E. Constructing atomic structural models into cryo-EM densities using molecular dynamics - Pros and cons. J Struct Biol 2018; 204:319-328. [PMID: 30092279 PMCID: PMC6394829 DOI: 10.1016/j.jsb.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/31/2018] [Accepted: 08/05/2018] [Indexed: 01/11/2023]
Abstract
Accurate structure determination from electron density maps at 3-5 Å resolution necessitates a balance between extensive global and local sampling of atomistic models, yet with the stereochemical correctness of backbone and sidechain geometries. Molecular Dynamics Flexible Fitting (MDFF), particularly through a resolution-exchange scheme, ReMDFF, provides a robust way of achieving this balance for hybrid structure determination. Employing two high-resolution density maps, namely that of β-galactosidase at 3.2 Å and TRPV1 at 3.4 Å, we showcase the quality of ReMDFF-generated models, comparing them against ones submitted by independent research groups for the 2015-2016 Cryo-EM Model Challenge. This comparison offers a clear evaluation of ReMDFF's strengths and shortcomings, and those of data-guided real-space refinements in general. ReMDFF results scored highly on the various metric for judging the quality-of-fit and quality-of-model. However, some systematic discrepancies are also noted employing a Molprobity analysis, that are reproducible across multiple competition entries. A space of key refinement parameters is explored within ReMDFF to observe their impact within the final model. Choice of force field parameters and initial model seem to have the most significant impact on ReMDFF model-quality. To this end, very recently developed CHARMM36m force field parameters provide now more refined ReMDFF models than the ones originally submitted to the Cryo-EM challenge. Finally, a set of good-practices is prescribed for the community to benefit from the MDFF developments.
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Affiliation(s)
- Yuhang Wang
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Darren Thifault
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, United States
| | | | - Ryan McGreevy
- Center for Biophysics and Quantitative Biology, College of Medicine, Department of Biochemistry, Beckman Institute for Advanced Science and Technology, and University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jane Richardson
- Department of Biochemistry, Duke University, Durham, NC 27710, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, United States.
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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Ereño-Orbea J, Sicard T, Cui H, Akula I, Julien JP. Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques. J Vis Exp 2018. [PMID: 30035760 PMCID: PMC6124603 DOI: 10.3791/57750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Glycoproteins on the surface of cells play critical roles in cellular function, including signalling, adhesion and transport. On leukocytes, several of these glycoproteins possess immunoglobulin (Ig) folds and are central to immune recognition and regulation. Here, we present a platform for the design, expression and biophysical characterization of the extracellular domain of human B cell receptor CD22. We propose that these approaches are broadly applicable to the characterization of mammalian glycoprotein ectodomains containing Ig domains. Two suspension human embryonic kidney (HEK) cell lines, HEK293F and HEK293S, are used to express glycoproteins harbouring complex and high-mannose glycans, respectively. These recombinant glycoproteins with different glycoforms allow investigating the effect of glycan size and composition on ligand binding. We discuss protocols for studying the kinetics and thermodynamics of glycoprotein binding to biologically relevant ligands and therapeutic antibody candidates. Recombinant glycoproteins produced in HEK293S cells are amenable to crystallization due to glycan homogeneity, reduced flexibility and susceptibility to endoglycosidase H treatment. We present methods for soaking glycoprotein crystals with heavy atoms and small molecules for phase determination and analysis of ligand binding, respectively. The experimental protocols discussed here hold promise for the characterization of mammalian glycoproteins to give insight into their function and investigate the mechanism of action of therapeutics.
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Affiliation(s)
- June Ereño-Orbea
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Taylor Sicard
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto
| | - Hong Cui
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Indira Akula
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute; Department of Biochemistry, University of Toronto; Department of Immunology, University of Toronto;
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Wang J, Liu Z, Frank J, Moore PB. Identification of ions in experimental electrostatic potential maps. IUCRJ 2018; 5:375-381. [PMID: 30002838 PMCID: PMC6038950 DOI: 10.1107/s2052252518006292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/24/2018] [Indexed: 05/06/2023]
Abstract
Cryo-electron microscopy (cryo-EM) directly images the distribution of electrostatic potential (ESP) within macromolecules, and thus can provide much more information about atomic charge than X-ray crystallography. The electron-scattering length of an isolated ion is quite different from that of the corresponding neutral atom. The difference is very large at small scattering angles where the effects of electron distributions are largest, but becomes smaller at high scattering angles where nuclear charge determines outcomes. For this reason, in cryo-EM maps that have been solved at resolutions lower than ∼2.5 Å, peaks corresponding to anions will always be less prominent than those of cations, and may even be negative. Furthermore, if a map of this kind is smeared computationally after the fact, which reduces its effective resolution, anion peaks will diminish in size, cation peaks will grow and peaks that represent uncharged atoms will remain about the same. These effects can be used to determine the sign of the charges carried by the ions associated with a macromolecule and even estimate their magnitudes. The ESP value for a cation in a cation-anion pair is smaller than the value of the cation in isolation, but the ESP value for the anion in the ionic pair is greater than the value of the anion in isolation. The experimental range of ESP values for Mg2+ relative to that of the closest C1' atom is found to be between 0.57 and 1.27.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Correspondence e-mail:
| | - Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Peter B. Moore
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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Nicholls RA, Tykac M, Kovalevskiy O, Murshudov GN. Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM. Acta Crystallogr D Struct Biol 2018; 74:492-505. [PMID: 29872001 PMCID: PMC6096485 DOI: 10.1107/s2059798318007313] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/15/2018] [Indexed: 11/10/2022] Open
Abstract
Recent advances in instrumentation and software have resulted in cryo-EM rapidly becoming the method of choice for structural biologists, especially for those studying the three-dimensional structures of very large macromolecular complexes. In this contribution, the tools available for macromolecular structure refinement into cryo-EM reconstructions that are available via CCP-EM are reviewed, specifically focusing on REFMAC5 and related tools. Whilst originally designed with a view to refinement against X-ray diffraction data, some of these tools have been able to be repurposed for cryo-EM owing to the same principles being applicable to refinement against cryo-EM maps. Since both techniques are used to elucidate macromolecular structures, tools encapsulating prior knowledge about macromolecules can easily be transferred. However, there are some significant qualitative differences that must be acknowledged and accounted for; relevant differences between these techniques are highlighted. The importance of phases is considered and the potential utility of replacing inaccurate amplitudes with their expectations is justified. More pragmatically, an upper bound on the correlation between observed and calculated Fourier coefficients, expressed in terms of the Fourier shell correlation between half-maps, is demonstrated. The importance of selecting appropriate levels of map blurring/sharpening is emphasized, which may be facilitated by considering the behaviour of the average map amplitude at different resolutions, as well as the utility of simultaneously viewing multiple blurred/sharpened maps. Features that are important for the purposes of computational efficiency are discussed, notably the Divide and Conquer pipeline for the parallel refinement of large macromolecular complexes. Techniques that have recently been developed or improved in Coot to facilitate and expedite the building, fitting and refinement of atomic models into cryo-EM maps are summarized. Finally, a tool for symmetry identification from a given map or coordinate set, ProSHADE, which can identify the point group of a map and thus may be used during deposition as well as during molecular visualization, is introduced.
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Affiliation(s)
- Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Michal Tykac
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Oleg Kovalevskiy
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, England
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Bartesaghi A, Aguerrebere C, Falconieri V, Banerjee S, Earl LA, Zhu X, Grigorieff N, Milne JLS, Sapiro G, Wu X, Subramaniam S. Atomic Resolution Cryo-EM Structure of β-Galactosidase. Structure 2018; 26:848-856.e3. [PMID: 29754826 DOI: 10.1016/j.str.2018.04.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/02/2018] [Accepted: 04/05/2018] [Indexed: 01/30/2023]
Abstract
The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design.
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Affiliation(s)
- Alberto Bartesaghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Cecilia Aguerrebere
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Soojay Banerjee
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Xing Zhu
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Guillermo Sapiro
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Xiongwu Wu
- Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Neumann P, Dickmanns A, Ficner R. Validating Resolution Revolution. Structure 2018; 26:785-795.e4. [PMID: 29606592 DOI: 10.1016/j.str.2018.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 11/19/2022]
Abstract
Recent advances in instrumentation and image-processing software have resulted in a resolution revolution in cryo-electron microscopy (cryo-EM) and a surge in the popularity of this technique. However, despite technical progress and hundreds of structures determined so far, development of standards assessing the agreement between the cryo-EM map and the respective model has fallen behind. Here we establish a validation procedure evaluating this agreement and applied it to a set of 565 cryo-EM structures. Analysis of the results revealed that three-quarters of the validated structures exhibit moderate or low agreement between the map and the corresponding model, mostly due to limited structural features possessed by these maps. Model re-refinement significantly improved the agreement for only one-fifth of the structures, reaffirming the necessity to re-evaluate map resolution. The presented procedure provides an approach to re-estimate the resolution of cryo-EM map areas interpreted by the model.
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Affiliation(s)
- Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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Chen L, He J, Sazzed S, Walker R. An Investigation of Atomic Structures Derived from X-ray Crystallography and Cryo-Electron Microscopy Using Distal Blocks of Side-Chains. Molecules 2018. [PMID: 29518032 PMCID: PMC5967250 DOI: 10.3390/molecules23030610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.
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Affiliation(s)
- Lin Chen
- Department of Mathematics and Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA.
| | - Jing He
- Department of Computer Science, Old Dominion University; Norfolk, VA 23529, USA.
| | - Salim Sazzed
- Department of Computer Science, Old Dominion University; Norfolk, VA 23529, USA.
| | - Rayshawn Walker
- Department of Mathematics and Computer Science, Elizabeth City State University, Elizabeth City, NC 27909, USA.
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Grimes JM, Hall DR, Ashton AW, Evans G, Owen RL, Wagner A, McAuley KE, von Delft F, Orville AM, Sorensen T, Walsh MA, Ginn HM, Stuart DI. Where is crystallography going? Acta Crystallogr D Struct Biol 2018; 74:152-166. [PMID: 29533241 PMCID: PMC5947779 DOI: 10.1107/s2059798317016709] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022] Open
Abstract
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
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Affiliation(s)
- Jonathan M. Grimes
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David R. Hall
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Alun W. Ashton
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Gwyndaf Evans
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Robin L. Owen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Katherine E. McAuley
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Frank von Delft
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Allen M. Orville
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Thomas Sorensen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Martin A. Walsh
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Helen M. Ginn
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
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Abstract
Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa) while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kilodaltons in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions at the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology.
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Affiliation(s)
- Susannah C. Shoemaker
- Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544, USA
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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