1
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Singer A, Yang R. Alignment of density maps in Wasserstein distance. BIOLOGICAL IMAGING 2024; 4:e5. [PMID: 38617997 PMCID: PMC11016369 DOI: 10.1017/s2633903x24000059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 04/16/2024]
Abstract
In this article, we propose an algorithm for aligning three-dimensional objects when represented as density maps, motivated by applications in cryogenic electron microscopy. The algorithm is based on minimizing the 1-Wasserstein distance between the density maps after a rigid transformation. The induced loss function enjoys a more benign landscape than its Euclidean counterpart and Bayesian optimization is employed for computation. Numerical experiments show improved accuracy and efficiency over existing algorithms on the alignment of real protein molecules. In the context of aligning heterogeneous pairs, we illustrate a potential need for new distance functions.
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Affiliation(s)
- Amit Singer
- Department of Mathematics, Princeton University, Princeton, NJ, USA
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Ruiyi Yang
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
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2
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He B, Zhang F, Feng C, Yang J, Gao X, Han R. Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features. Nat Commun 2024; 15:1593. [PMID: 38383438 PMCID: PMC10881975 DOI: 10.1038/s41467-024-45861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we present a fast and accurate global and local cryo-EM density map alignment method called CryoAlign, that leverages local density feature descriptors to capture spatial structure similarities. CryoAlign is a feature-based cryo-EM map alignment tool, in which the employment of feature-based architecture enables the rapid establishment of point pair correspondences and robust estimation of alignment parameters. Extensive experimental evaluations demonstrate the superiority of CryoAlign over the existing methods in terms of both alignment accuracy and speed.
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Affiliation(s)
- Bintao He
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, China
| | - Fa Zhang
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Chenjie Feng
- College of Medical Information and Engineering, Ningxia Medical University, Yinchuan, 750004, China
| | - Jianyi Yang
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia.
| | - Renmin Han
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, 266237, China.
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3
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Sweeney A, Mulvaney T, Maiorca M, Topf M. ChemEM: Flexible Docking of Small Molecules in Cryo-EM Structures. J Med Chem 2024; 67:199-212. [PMID: 38157562 PMCID: PMC10788898 DOI: 10.1021/acs.jmedchem.3c01134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Cryo-electron microscopy (cryo-EM), through resolution advancements, has become pivotal in structure-based drug discovery. However, most cryo-EM structures are solved at 3-4 Å resolution, posing challenges for small-molecule docking and structure-based virtual screening due to issues in the precise positioning of ligands and the surrounding side chains. We present ChemEM, a software package that employs cryo-EM data for the accurate docking of one or multiple ligands in a protein-binding site. Validated against a highly curated benchmark of high- and medium-resolution cryo-EM structures and the corresponding high-resolution controls, ChemEM displayed impressive performance, accurately placing ligands in all but one case, often surpassing cryo-EM PDB-deposited solutions. Even without including the cryo-EM density, the ChemEM scoring function outperformed the well-established AutoDock Vina score. Using ChemEM, we illustrate that valuable information can be extracted from maps at medium resolution and underline the utility of cryo-EM structures for drug discovery.
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Affiliation(s)
- Aaron Sweeney
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
| | - Thomas Mulvaney
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
| | - Mauro Maiorca
- Leibniz Institute of Virology (LIV), Hamburg 20251, Germany
- Centre for Structural Systems Biology, Hamburg 22607, Germany
- Universitätsklinikum Hamburg
Eppendorf (UKE), Hamburg 20246, Germany
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4
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Tai L, Yin G, Huang X, Sun F, Zhu Y. In-cell structural insight into the stability of sperm microtubule doublet. Cell Discov 2023; 9:116. [PMID: 37989994 PMCID: PMC10663601 DOI: 10.1038/s41421-023-00606-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/21/2023] [Indexed: 11/23/2023] Open
Abstract
The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
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Affiliation(s)
- Linhua Tai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guoliang Yin
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong, China.
| | - Yun Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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5
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Fäßler F, Javoor MG, Datler J, Döring H, Hofer FW, Dimchev G, Hodirnau VV, Faix J, Rottner K, Schur FK. ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning. SCIENCE ADVANCES 2023; 9:eadd6495. [PMID: 36662867 PMCID: PMC9858492 DOI: 10.1126/sciadv.add6495] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/20/2022] [Indexed: 05/10/2023]
Abstract
Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform-specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
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Affiliation(s)
- Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Hermann Döring
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Florian W. Hofer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Georgi Dimchev
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Klemens Rottner
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Florian K.M. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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6
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Wang J, Liu J, Gisriel CJ, Wu S, Maschietto F, Flesher DA, Lolis E, Lisi GP, Brudvig GW, Xiong Y, Batista VS. How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM. J Struct Biol 2022; 214:107902. [PMID: 36202310 DOI: 10.1016/j.jsb.2022.107902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.
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Affiliation(s)
- Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA.
| | - Jinchan Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | | | - Shenping Wu
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | | | - David A Flesher
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Elias Lolis
- Department of Pharmacology, Yale University, New Haven, CT 06520-8066, USA
| | - George P Lisi
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA; Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06511-8499, USA
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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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Joseph AP, Malhotra S, Burnley T, Winn MD. Overview and applications of map and model validation tools in the CCP-EM software suite. Faraday Discuss 2022; 240:196-209. [PMID: 35916020 PMCID: PMC9642004 DOI: 10.1039/d2fd00103a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has recently been established as a powerful technique for solving macromolecular structures. Although the best resolutions achievable are improving, a significant majority of data are still resolved at resolutions worse than 3 Å, where it is non-trivial to build or fit atomic models. The map reconstructions and atomic models derived from the maps are also prone to errors accumulated through the different stages of data processing. Here, we highlight the need to evaluate both model geometry and fit to data at different resolutions. Assessment of cryo-EM structures from SARS-CoV-2 highlights a bias towards optimising the model geometry to agree with the most common conformations, compared to the agreement with data. We present the CoVal web service which provides multiple validation metrics to reflect the quality of atomic models derived from cryo-EM data of structures from SARS-CoV-2. We demonstrate that further refinement can lead to improvement of the agreement with data without the loss of geometric quality. We also discuss the recent CCP-EM developments aimed at addressing some of the current shortcomings.
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Affiliation(s)
- Agnel Praveen Joseph
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Sony Malhotra
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Tom Burnley
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
| | - Martyn D. Winn
- Scientific Computing Department, Science and Technology Facilities CouncilDidcot OX11 0FAUK
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9
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Abstract
Adeno-associated virus (AAV) has a single-stranded DNA genome encapsidated in a small icosahedrally symmetric protein shell with 60 subunits. AAV is the leading delivery vector in emerging gene therapy treatments for inherited disorders, so its structure and molecular interactions with human hosts are of intense interest. A wide array of electron microscopic approaches have been used to visualize the virus and its complexes, depending on the scientific question, technology available, and amenability of the sample. Approaches range from subvolume tomographic analyses of complexes with large and flexible host proteins to detailed analysis of atomic interactions within the virus and with small ligands at resolutions as high as 1.6 Å. Analyses have led to the reclassification of glycan receptors as attachment factors, to structures with a new-found receptor protein, to identification of the epitopes of antibodies, and a new understanding of possible neutralization mechanisms. AAV is now well-enough characterized that it has also become a model system for EM methods development. Heralding a new era, cryo-EM is now also being deployed as an analytic tool in the process development and production quality control of high value pharmaceutical biologics, namely AAV vectors.
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Affiliation(s)
- Scott
M. Stagg
- Department
of Biological Sciences, Florida State University, Tallahassee, Florida 32306, United States
- Institute
of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States
| | - Craig Yoshioka
- Department
of Biomedical Engineering, Oregon Health
& Science University, Portland Oregon 97239, United States
| | - Omar Davulcu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Michael S. Chapman
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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10
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Lubbe L, Sewell BT, Woodward JD, Sturrock ED. Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization. EMBO J 2022; 41:e110550. [PMID: 35818993 PMCID: PMC9379546 DOI: 10.15252/embj.2021110550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
Hypertension (high blood pressure) is a major risk factor for cardiovascular disease, which is the leading cause of death worldwide. The somatic isoform of angiotensin I‐converting enzyme (sACE) plays a critical role in blood pressure regulation, and ACE inhibitors are thus widely used to treat hypertension and cardiovascular disease. Our current understanding of sACE structure, dynamics, function, and inhibition has been limited because truncated, minimally glycosylated forms of sACE are typically used for X‐ray crystallography and molecular dynamics simulations. Here, we report the first cryo‐EM structures of full‐length, glycosylated, soluble sACE (sACES1211). Both monomeric and dimeric forms of the highly flexible apo enzyme were reconstructed from a single dataset. The N‐ and C‐terminal domains of monomeric sACES1211 were resolved at 3.7 and 4.1 Å, respectively, while the interacting N‐terminal domains responsible for dimer formation were resolved at 3.8 Å. Mechanisms are proposed for intradomain hinging, cooperativity, and homodimerization. Furthermore, the observation that both domains were in the open conformation has implications for the design of sACE modulators.
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Affiliation(s)
- Lizelle Lubbe
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryan Trevor Sewell
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Jeremy D Woodward
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Edward D Sturrock
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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11
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Meyer NL, Chapman MS. Adeno-associated virus (AAV) cell entry: structural insights. Trends Microbiol 2022; 30:432-451. [PMID: 34711462 PMCID: PMC11225776 DOI: 10.1016/j.tim.2021.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Adeno-associated virus (AAV) is the leading vector in emerging treatments of inherited diseases. Higher transduction efficiencies and cellular specificity are required for broader clinical application, motivating investigations of virus-host molecular interactions during cell entry. High-throughput methods are identifying host proteins more comprehensively, with subsequent molecular studies revealing unanticipated complexity and serotype specificity. Cryogenic electron microscopy (cryo-EM) provides a path towards structural details of these sometimes heterogeneous virus-host complexes, and is poised to illuminate more fully the steps in entry. Here presented, is progress in understanding the distinct steps of glycan attachment, and receptor-mediated entry/trafficking. Comparison with structures of antibody complexes provides new insights on immune neutralization with implications for the design of improved gene therapy vectors.
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Affiliation(s)
- Nancy L Meyer
- Pacific Northwest Cryo-EM Center, Oregon Health and Science University (OHSU) Center for Spatial Systems Biomedicine, Portland, OR, USA
| | - Michael S Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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12
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Stsiapanava A, Xu C, Nishio S, Han L, Yamakawa N, Carroni M, Tunyasuvunakool K, Jumper J, de Sanctis D, Wu B, Jovine L. Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH. Nat Struct Mol Biol 2022; 29:190-193. [PMID: 35273390 PMCID: PMC8930769 DOI: 10.1038/s41594-022-00729-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/21/2022] [Indexed: 12/25/2022]
Abstract
Glycoprotein 2 (GP2) and uromodulin (UMOD) filaments protect against gastrointestinal and urinary tract infections by acting as decoys for bacterial fimbrial lectin FimH. By combining AlphaFold2 predictions with X-ray crystallography and cryo-EM, we show that these proteins contain a bipartite decoy module whose new fold presents the high-mannose glycan recognized by FimH. The structure rationalizes UMOD mutations associated with kidney diseases and visualizes a key epitope implicated in cast nephropathy. AlphaFold2 predictions, X-ray crystallography and cryo-EM analyses reveal how related human glycoproteins GP2 and uromodulin catch pathogenic bacteria by presenting a high-mannose glycan that acts as a decoy for fimbrial adhesin FimH.
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Affiliation(s)
- Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chenrui Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Nao Yamakawa
- US 41-UMS 2014-PLBS, Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | | | | | - Bin Wu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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13
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Yamashita K, Palmer CM, Burnley T, Murshudov GN. Cryo-EM single-particle structure refinement and map calculation using Servalcat. Acta Crystallogr D Struct Biol 2021; 77:1282-1291. [PMID: 34605431 PMCID: PMC8489229 DOI: 10.1107/s2059798321009475] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/11/2021] [Indexed: 11/10/2022] Open
Abstract
In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo - Fc difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo - Fc map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at ∼1.8 Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.
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Affiliation(s)
- Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, United Kingdom
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0FA, United Kingdom
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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14
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Cryo-EM structure and kinetics reveal electron transfer by 2D diffusion of cytochrome c in the yeast III-IV respiratory supercomplex. Proc Natl Acad Sci U S A 2021; 118:2021157118. [PMID: 33836592 DOI: 10.1073/pnas.2021157118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Energy conversion in aerobic organisms involves an electron current from low-potential donors, such as NADH and succinate, to dioxygen through the membrane-bound respiratory chain. Electron transfer is coupled to transmembrane proton transport, which maintains the electrochemical proton gradient used to produce ATP and drive other cellular processes. Electrons are transferred from respiratory complexes III to IV (CIII and CIV) by water-soluble cytochrome (cyt.) c In Saccharomyces cerevisiae and some other organisms, these complexes assemble into larger CIII2CIV1/2 supercomplexes, the functional significance of which has remained enigmatic. In this work, we measured the kinetics of the S. cerevisiae supercomplex cyt. c-mediated QH2:O2 oxidoreductase activity under various conditions. The data indicate that the electronic link between CIII and CIV is confined to the surface of the supercomplex. Single-particle electron cryomicroscopy (cryo-EM) structures of the supercomplex with cyt. c show the positively charged cyt. c bound to either CIII or CIV or along a continuum of intermediate positions. Collectively, the structural and kinetic data indicate that cyt. c travels along a negatively charged patch on the supercomplex surface. Thus, rather than enhancing electron transfer rates by decreasing the distance that cyt. c must diffuse in three dimensions, formation of the CIII2CIV1/2 supercomplex facilitates electron transfer by two-dimensional (2D) diffusion of cyt. c This mechanism enables the CIII2CIV1/2 supercomplex to increase QH2:O2 oxidoreductase activity and suggests a possible regulatory role for supercomplex formation in the respiratory chain.
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15
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Cryo-EM density maps adjustment for subtraction, consensus and sharpening. J Struct Biol 2021; 213:107780. [PMID: 34469787 DOI: 10.1016/j.jsb.2021.107780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022]
Abstract
Electron cryomicroscopy (cryo-EM) has emerged as a powerful structural biology instrument to solve near-atomic three-dimensional structures. Despite the fast growth in the number of density maps generated from cryo-EM data, comparison tools among these reconstructions are still lacking. Current proposals to compare cryo-EM data derived volumes perform map subtraction based on adjustment of each volume grey level to the same scale. We present here a more sophisticated way of adjusting the volumes before comparing, which implies adjustment of grey level scale and spectrum energy, but keeping phases intact inside a mask and imposing the results to be strictly positive. The adjustment that we propose leaves the volumes in the same numeric frame, allowing to perform operations among the adjusted volumes in a more reliable way. This adjustment can be a preliminary step for several applications such as comparison through subtraction, map sharpening, or combination of volumes through a consensus that selects the best resolved parts of each input map. Our development might also be used as a sharpening method using an atomic model as a reference. We illustrate the applicability of this algorithm with the reconstructions derived of several experimental examples. This algorithm is implemented in Xmipp software package and its applications are user-friendly accessible through the cryo-EM image processing framework Scipion.
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16
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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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17
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Palermo G, Sugita Y, Wriggers W, Amaro RE. Faces of Contemporary CryoEM Information and Modeling. J Chem Inf Model 2021; 60:2407-2409. [PMID: 32452204 DOI: 10.1021/acs.jcim.0c00481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California 92093-0340, United States
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18
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He J, Huang SY. Full-length de novo protein structure determination from cryo-EM maps using deep learning. Bioinformatics 2021; 37:3480-3490. [PMID: 33978686 DOI: 10.1093/bioinformatics/btab357] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/03/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Advances in microscopy instruments and image processing algorithms have led to an increasing number of cryo-EM maps. However, building accurate models for the EM maps at 3-5 Å resolution remains a challenging and time-consuming process. With the rapid growth of deposited EM maps, there is an increasing gap between the maps and reconstructed/modeled 3-dimensional (3D) structures. Therefore, automatic reconstruction of atomic-accuracy full-atomstructures fromEMmaps is pressingly needed. RESULTS We present a semi-automatic de novo structure determination method using a deep learningbased framework, named as DeepMM, which builds atomic-accuracy all-atom models from cryo-EM maps at near-atomic resolution. In our method, the main-chain and Cα positions as well as their amino acid and secondary structure types are predicted in the EM map using Densely Connected Convolutional Networks. DeepMM was extensively validated on 40 simulated maps at 5 Å resolution and 30 experimental maps at 2.6-4.8 Å resolution as well as an EMDB-wide data set of 2931 experimental maps at 2.6-4.9 Å resolution, and compared with state-of-the-art algorithms including RosettaES, MAINMAST, and Phenix. Overall, our DeepMM algorithm obtained a significant improvement over existing methods in terms of both accuracy and coverage in building full-length protein structures on all test sets, demonstrating the efficacy and general applicability of DeepMM. AVAILABILITY http://huanglab.phys.hust.edu.cn/DeepMM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiahua He
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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19
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Han X, Terashi G, Christoffer C, Chen S, Kihara D. VESPER: global and local cryo-EM map alignment using local density vectors. Nat Commun 2021; 12:2090. [PMID: 33828103 PMCID: PMC8027200 DOI: 10.1038/s41467-021-22401-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of maps is an essential step for structure modeling, comparison of maps, and for database search. Here, we developed VESPER, which captures the similarity of underlying molecular structures embedded in density maps by taking local gradient directions into consideration. Compared to existing methods, VESPER achieved substantially more accurate global and local alignment of maps as well as database retrieval.
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Affiliation(s)
- Xusi Han
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Siyang Chen
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Department of Computer Science, Purdue University, West Lafayette, IN, USA.
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20
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van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure 2021; 29:913-921.e4. [PMID: 33823127 DOI: 10.1016/j.str.2021.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
With the advent of the resolution revolution in cryoelectron microscopy (cryo-EM), low-resolution refinement is common, and likewise increases the need for a reliable force field. Here, we report on the incorporation of the OPLS3e force field with the VSGB2.1 solvation model in the structure determination package Phenix. Our results show significantly improved structure quality and reduced ligand strain at lower resolution for X-ray refinement. For refinement of cryo-EM-based structures, we find comparable quality structures, goodness-of-fit, and reduced ligand strain. We also show how structure quality and ligand strain are related to the map-model cross-correlation as a function of data weight, and how that can detect overfitting. Signs of overfitting are found in over half of our cryo-EM dataset, which can be remedied by a re-refinement at a lower data weight. Finally, a start-to-end script for refining structures with Phenix/OPLS3e is available in the Schrödinger 2020-3 distribution.
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Affiliation(s)
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V Sobolev
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
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21
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Cragnolini T, Sahota H, Joseph AP, Sweeney A, Malhotra S, Vasishtan D, Topf M. TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows. Acta Crystallogr D Struct Biol 2021; 77:41-47. [PMID: 33404524 PMCID: PMC7787107 DOI: 10.1107/s2059798320014928] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and workflows to perform these tasks are described.
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Affiliation(s)
- Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Agnel Praveen Joseph
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Aaron Sweeney
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
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