1
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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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2
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Zhang Z, Cai Y, Zhang B, Zheng W, Freddolino L, Zhang G, Zhou X. DEMO-EM2: assembling protein complex structures from cryo-EM maps through intertwined chain and domain fitting. Brief Bioinform 2024; 25:bbae113. [PMID: 38517699 PMCID: PMC10959074 DOI: 10.1093/bib/bbae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024] Open
Abstract
The breakthrough in cryo-electron microscopy (cryo-EM) technology has led to an increasing number of density maps of biological macromolecules. However, constructing accurate protein complex atomic structures from cryo-EM maps remains a challenge. In this study, we extend our previously developed DEMO-EM to present DEMO-EM2, an automated method for constructing protein complex models from cryo-EM maps through an iterative assembly procedure intertwining chain- and domain-level matching and fitting for predicted chain models. The method was carefully evaluated on 27 cryo-electron tomography (cryo-ET) maps and 16 single-particle EM maps, where DEMO-EM2 models achieved an average TM-score of 0.92, outperforming those of state-of-the-art methods. The results demonstrate an efficient method that enables the rapid and reliable solution of challenging cryo-EM structure modeling problems.
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Affiliation(s)
- Ziying Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Yaxian Cai
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Biao Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Xiaogen Zhou
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
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3
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Park J, Joung I, Joo K, Lee J. Application of conformational space annealing to the protein structure modeling using cryo-EM maps. J Comput Chem 2023; 44:2332-2346. [PMID: 37585026 DOI: 10.1002/jcc.27200] [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: 12/08/2022] [Revised: 04/26/2023] [Accepted: 07/16/2023] [Indexed: 08/17/2023]
Abstract
Conformational space annealing (CSA), a global optimization method, has been applied to various protein structure modeling tasks. In this paper, we applied CSA to the cryo-EM structure modeling task by combining the python subroutine of CSA (PyCSA) and the fast relax (FastRelax) protocol of PyRosetta. Refinement of initial structures generated from two methods, rigid fitting of predicted structures to the Cryo-EM map and de novo protein modeling by tracing the Cryo-EM map, was performed by CSA. In the refinement of the rigid-fitted structures, the final models showed that CSA can generate reliable atomic structures of proteins, even when large movements of protein domains were required. In the de novo modeling case, although the overall structural qualities of the final models were rather dependent on the initial models, the final models generated by CSA showed improved MolProbity scores and cross-correlation coefficients to the maps. These results suggest that CSA can accomplish flexible fitting and refinement together by sampling diverse conformations effectively and thus can be utilized for cryo-EM structure modeling.
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Affiliation(s)
| | | | - Keehyoung Joo
- Center for Advanced Computations, Korea Institute for Advanced Study, Seoul, South Korea
| | - Jooyoung Lee
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea
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4
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Toward Real Real-Space Refinement of Atomic Models. Int J Mol Sci 2022; 23:ijms232012101. [PMID: 36292954 PMCID: PMC9603565 DOI: 10.3390/ijms232012101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples. These atomic images and, consequently, the maps for the respective models, can be expressed analytically as functions of coordinates, atomic displacement parameters, and the local resolution. This work discusses the practical feasibility of such calculation for the real-space refinement of macromolecular atomic models.
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5
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Alnabati E, Esquivel-Rodriguez J, Terashi G, Kihara D. MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field. Front Mol Biosci 2022; 9:935411. [PMID: 35959463 PMCID: PMC9358042 DOI: 10.3389/fmolb.2022.935411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
An increasing number of protein complex structures are determined by cryo-electron microscopy (cryo-EM). When individual protein structures have been determined and are available, an important task in structure modeling is to fit the individual structures into the density map. Here, we designed a method that fits the atomic structures of proteins in cryo-EM maps of medium to low resolutions using Markov random fields, which allows probabilistic evaluation of fitted models. The accuracy of our method, MarkovFit, performed better than existing methods on datasets of 31 simulated cryo-EM maps of resolution 10 Å , nine experimentally determined cryo-EM maps of resolution less than 4 Å , and 28 experimentally determined cryo-EM maps of resolution 6 to 20 Å .
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Affiliation(s)
- Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | | | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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6
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He J, Lin P, Chen J, Cao H, Huang SY. Model building of protein complexes from intermediate-resolution cryo-EM maps with deep learning-guided automatic assembly. Nat Commun 2022; 13:4066. [PMID: 35831370 PMCID: PMC9279371 DOI: 10.1038/s41467-022-31748-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 06/30/2022] [Indexed: 12/29/2022] Open
Abstract
Advances in microscopy instruments and image processing algorithms have led to an increasing number of cryo-electron microscopy (cryo-EM) maps. However, building accurate models into intermediate-resolution EM maps remains challenging and labor-intensive. Here, we propose an automatic model building method of multi-chain protein complexes from intermediate-resolution cryo-EM maps, named EMBuild, by integrating AlphaFold structure prediction, FFT-based global fitting, domain-based semi-flexible refinement, and graph-based iterative assembling on the main-chain probability map predicted by a deep convolutional network. EMBuild is extensively evaluated on diverse test sets of 47 single-particle EM maps at 4.0-8.0 Å resolution and 16 subtomogram averaging maps of cryo-ET data at 3.7-9.3 Å resolution, and compared with state-of-the-art approaches. We demonstrate that EMBuild is able to build high-quality complex structures that are comparably accurate to the manually built PDB structures from the cryo-EM maps. These results demonstrate the accuracy and reliability of EMBuild in automatic model building.
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Affiliation(s)
- Jiahua He
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Peicong Lin
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Ji Chen
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hong Cao
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Sheng-You Huang
- School of Physics and Key Laboratory of Molecular Biophysics of MOE, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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7
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Zhu Z, Deng Z, Wang Q, Wang Y, Zhang D, Xu R, Guo L, Wen H. Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design. Front Pharmacol 2022; 13:939555. [PMID: 35837274 PMCID: PMC9275593 DOI: 10.3389/fphar.2022.939555] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue. An explosion in high-resolution ion channel structures paved way for structure-based rational drug design and the state-of-the-art simulation and machine learning techniques dramatically improved the efficiency and effectiveness of computer-aided drug design. Here we present an overview of how simulation and machine learning-based methods fundamentally changed the ion channel-related drug design at different levels, as well as the emerging trends in the field.
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Affiliation(s)
- Zhengdan Zhu
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Beijing Institute of Big Data Research, Beijing, China
| | - Zhenfeng Deng
- DP Technology, Beijing, China
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | | | | | - Duo Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- DP Technology, Beijing, China
| | - Ruihan Xu
- DP Technology, Beijing, China
- National Engineering Research Center of Visual Technology, Peking University, Beijing, China
| | | | - Han Wen
- DP Technology, Beijing, China
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8
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Wang C, Zeng J, Wang J. Structural basis of bacteriophage lambda capsid maturation. Structure 2022; 30:637-645.e3. [PMID: 35026161 DOI: 10.1016/j.str.2021.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/12/2021] [Accepted: 12/15/2021] [Indexed: 01/10/2023]
Abstract
Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins initially assemble into a precursor capsid (procapsid) and subsequent genome packaging triggers morphological expansion of the shell. An auxiliary protein is required to stabilize the expanded capsid structure. To investigate the capsid maturation mechanism, we determined the cryo-electron microscopy structures of the bacteriophage lambda procapsid and mature capsid at 3.88 Å and 3.76 Å resolution, respectively. Besides primarily rigid body movements of common features of the major capsid protein gpE, large-scale structural rearrangements of other domains occur simultaneously. Assembly of intercapsomers within the procapsid is facilitated by layer-stacking effects at 3-fold vertices. Upon conformational expansion of the capsid shell, the missing top layer is fulfilled by cementing the gpD protein against the internal pressure of DNA packaging. Our structures illuminate the assembly mechanisms of dsDNA viruses.
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Affiliation(s)
- Chang Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Jianwei Zeng
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China.
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, P. R. China.
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9
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Warshamanage R, Yamashita K, Murshudov GN. EMDA: A Python package for Electron Microscopy Data Analysis. J Struct Biol 2021; 214:107826. [PMID: 34915128 PMCID: PMC8935390 DOI: 10.1016/j.jsb.2021.107826] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 12/01/2022]
Abstract
An open-source Python library EMDA for cryo-EM map and model manipulation is presented with a specific focus on validation. The use of several functionalities in the library is presented through several examples. The utility of local correlation as a metric for identifying map-model differences and unmodeled regions in maps, and how it is used as a metric of map-model validation is demonstrated. The mapping of local correlation to individual atoms, and its use to draw insights on local signal variations are discussed. EMDA’s likelihood-based map overlay is demonstrated by carrying out a superposition of two domains in two related structures. The overlay is carried out first to bring both maps into the same coordinate frame and then to estimate the relative movement of domains. Finally, the map magnification refinement in EMDA is presented with an example to highlight the importance of adjusting the map magnification in structural comparison studies.
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Affiliation(s)
- Rangana Warshamanage
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Keitaro Yamashita
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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10
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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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11
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Zhang B, Zhang W, Pearce R, Zhang Y, Shen HB. Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. J Phys Chem B 2021; 125:528-538. [PMID: 33397114 DOI: 10.1021/acs.jpcb.0c09903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rigid-body fitting of predicted structural models into cryo-electron microscopy (cryo-EM) density maps is a necessary procedure for density map-guided protein structure determination and prediction. We proposed a novel multiobjective optimization protocol, MOFIT, which performs a rigid-body density-map fitting based on particle swarm optimization (PSO). MOFIT was tested on a large set of 292 nonhomologous single-domain proteins. Starting from structural models predicted by I-TASSER, MOFIT achieved an average coordinate root-mean-square deviation of 2.46 Å, which was 1.57, 2.79, and 3.95 Å lower than three leading single-objective function-based methods, where the differences were statistically significant with p-values of 1.65 × 10-6, 6.36 × 10-8, and 6.44 × 10-11 calculated using two-tail Student's t tests. Detailed analyses showed that the major advantages of MOFIT lie in the multiobjective protocol and the extensive PSO search simulations guided by the composite objective functions, which integrates complementary correlation coefficients from the global structure, local fragments, and individual residues with the cryo-EM density maps.
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Affiliation(s)
- Biao Zhang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenyi Zhang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China
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12
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Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020; 153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023] Open
Abstract
Knowledge of protein structure is paramount to the understanding of biological function, developing new therapeutics, and making detailed mechanistic hypotheses. Therefore, methods to accurately elucidate three-dimensional structures of proteins are in high demand. While there are a few experimental techniques that can routinely provide high-resolution structures, such as x-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, which have been developed to determine the structures of proteins, these techniques each have shortcomings and thus cannot be used in all cases. However, additionally, a large number of experimental techniques that provide some structural information, but not enough to assign atomic positions with high certainty have been developed. These methods offer sparse experimental data, which can also be noisy and inaccurate in some instances. In cases where it is not possible to determine the structure of a protein experimentally, computational structure prediction methods can be used as an alternative. Although computational methods can be performed without any experimental data in a large number of studies, inclusion of sparse experimental data into these prediction methods has yielded significant improvement. In this Perspective, we cover many of the successes of integrative modeling, computational modeling with experimental data, specifically for protein folding, protein-protein docking, and molecular dynamics simulations. We describe methods that incorporate sparse data from cryo-EM, NMR, mass spectrometry, electron paramagnetic resonance, small-angle x-ray scattering, Förster resonance energy transfer, and genetic sequence covariation. Finally, we highlight some of the major challenges in the field as well as possible future directions.
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Affiliation(s)
- Justin T. Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
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13
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Gao J, Gui M, Xiang Y. Structural intermediates in the low pH-induced transition of influenza hemagglutinin. PLoS Pathog 2020; 16:e1009062. [PMID: 33253316 PMCID: PMC7728236 DOI: 10.1371/journal.ppat.1009062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
The hemagglutinin (HA) glycoproteins of influenza viruses play a key role in binding host cell receptors and in mediating virus-host cell membrane fusion during virus infection. Upon virus entry, HA is triggered by low pH and undergoes large structural rearrangements from a prefusion state to a postfusion state. While structures of prefusion state and postfusion state of HA have been reported, the intermediate structures remain elusive. Here, we report two distinct low pH intermediate conformations of the influenza virus HA using cryo-electron microscopy (cryo-EM). Our results show that a decrease in pH from 7.8 to 5.2 triggers the release of fusion peptides from the binding pockets and then causes a dramatic conformational change in the central helices, in which the membrane-proximal ends of the central helices unwind to an extended form. Accompanying the conformational changes of the central helices, the stem region of the HA undergoes an anticlockwise rotation of 9.5 degrees and a shift of 15 Å. The HA head, after being stabilized by an antibody, remains unchanged compared to the neutral pH state. Thus, the conformational change of the HA stem region observed in our research is likely to be independent of the HA head. These results provide new insights into the structural transition of HA during virus entry.
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Affiliation(s)
- Jingjing Gao
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Miao Gui
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- * E-mail: (MG); (YX)
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- * E-mail: (MG); (YX)
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14
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Powell LA, Miller A, Fox JM, Kose N, Klose T, Kim AS, Bombardi R, Tennekoon RN, Dharshan de Silva A, Carnahan RH, Diamond MS, Rossmann MG, Kuhn RJ, Crowe JE. Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site. Cell Host Microbe 2020; 28:699-711.e7. [PMID: 32783883 PMCID: PMC7666055 DOI: 10.1016/j.chom.2020.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/25/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease burden, no approved therapies or licensed vaccines exist. Here, we describe human monoclonal antibodies (mAbs) that bind to and neutralize multiple distantly related alphaviruses. These mAbs compete for an antigenic site and prevent attachment to the recently discovered Mxra8 alphavirus receptor. Three cryoelectron microscopy structures of Fab in complex with Ross River (RRV), Mayaro, or chikungunya viruses reveal a conserved footprint of the broadly neutralizing mAb RRV-12 in a region of the E2 glycoprotein B domain. This mAb neutralizes virus in vitro by preventing virus entry and spread and is protective in vivo in mouse models. Thus, the RRV-12 mAb and its defined epitope have potential as a therapeutic agent or target of vaccine design against multiple emerging arthritogenic alphavirus infections.
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Affiliation(s)
- Laura A Powell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Julie M Fox
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Arthur S Kim
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Robin Bombardi
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA
| | - Rashika N Tennekoon
- Genetech Research Institute, Colombo, Sri Lanka; Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defence University, Colombo, Sri Lanka
| | - A Dharshan de Silva
- Genetech Research Institute, Colombo, Sri Lanka; Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defence University, Colombo, Sri Lanka
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Markey Center for Structural Biology and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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15
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Zhang B, Zhang X, Pearce R, Shen HB, Zhang Y. A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps. J Mol Biol 2020; 432:5365-5377. [PMID: 32771523 DOI: 10.1016/j.jmb.2020.07.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022]
Abstract
The rapid progress of cryo-electron microscopy (cryo-EM) in structural biology has raised an urgent need for robust methods to create and refine atomic-level structural models using low-resolution EM density maps. We propose a new protocol to create initial models using I-TASSER protein structure prediction, followed by EM density map-based rigid-body structure fitting, flexible fragment adjustment and atomic-level structure refinement simulations. The protocol was tested on a large set of 285 non-homologous proteins and generated structural models with correct folds for 260 proteins, where 28% had RMSDs below 2 Å. Compared to other state-of-the-art methods, the major advantage of the proposed pipeline lies in the uniform structure prediction and refinement protocol, as well as the extensive structural re-assembly simulations, which allow for low-to-medium resolution EM density map-guided structure modeling starting from amino acid sequences. Interestingly, the quality of both the image fitting and subsequent structure refinement was found to be strongly correlated with the correctness of the initial I-TASSER models; this is mainly due to the different correlation patterns observed between force field and structural quality for the models with template modeling score (or TM-score, a metric quantifying the similarity of models to the native) above and below a threshold of 0.5. Overall, the results demonstrate a new avenue that is ready to use for large-scale cryo-EM-based structure modeling and atomic-level density map-guided structure refinement.
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Affiliation(s)
- Biao Zhang
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xi Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Wang L, Wang R, Wang L, Ben H, Yu L, Gao F, Shi X, Yin C, Zhang F, Xiang Y, Zhang L. Structural Basis for Neutralization and Protection by a Zika Virus-Specific Human Antibody. Cell Rep 2020; 26:3360-3368.e5. [PMID: 30893607 DOI: 10.1016/j.celrep.2019.02.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/26/2022] Open
Abstract
We previously reported a human monoclonal antibody, ZK2B10, capable of protection against Zika virus (ZIKV) infection and microcephaly in developing mouse embryos. Here, we report the structural features and mechanism of action of ZK2B10. The crystal structure at a resolution of 2.32 Å revealed that the epitope is located on the lateral ridge of DIII of the envelope glycoprotein. Cryo-EM structure with mature ZIKV showed that the antibody binds to DIIIs around the icosahedral 2-fold, 3-fold, and 5-fold axes, a distinct feature compared to those reported for DIII-specific antibodies. The binding of ZK2B10 to ZIKV has no detectable effect on viral attachment to target cells or on conformational changes of the E glycoprotein in the acidic environment, suggesting that ZK2B10 functions at steps between the formation of the fusion intermediate and membrane fusion. These results provide structural and mechanistic insights into how ZK2B10 mediates protection against ZIKV infection.
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Affiliation(s)
- Lin Wang
- Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ruoke Wang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lei Wang
- Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haijing Ben
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lei Yu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
| | - Fei Gao
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chibiao Yin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
| | - Fuchun Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Beijing Advanced Innovation Center for Structural Biology, Center for Global Health and Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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17
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Cryo-EM structure of eastern equine encephalitis virus in complex with heparan sulfate analogues. Proc Natl Acad Sci U S A 2020; 117:8890-8899. [PMID: 32245806 DOI: 10.1073/pnas.1910670117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Eastern equine encephalitis virus (EEEV), a mosquito-borne icosahedral alphavirus found mainly in North America, causes human and equine neurotropic infections. EEEV neurovirulence is influenced by the interaction of the viral envelope protein E2 with heparan sulfate (HS) proteoglycans from the host's plasma membrane during virus entry. Here, we present a 5.8-Å cryoelectron microscopy (cryo-EM) structure of EEEV complexed with the HS analog heparin. "Peripheral" HS binding sites were found to be associated with the base of each of the E2 glycoproteins that form the 60 quasi-threefold spikes (q3) and the 20 sites associated with the icosahedral threefold axes (i3). In addition, there is one HS site at the vertex of each q3 and i3 spike (the "axial" sites). Both the axial and peripheral sites are surrounded by basic residues, suggesting an electrostatic mechanism for HS binding. These residues are highly conserved among EEEV strains, and therefore a change in these residues might be linked to EEEV neurovirulence.
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18
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Akbar S, Mozumder S, Sengupta J. Retrospect and Prospect of Single Particle Cryo-Electron Microscopy: The Class of Integral Membrane Proteins as an Example. J Chem Inf Model 2020; 60:2448-2457. [DOI: 10.1021/acs.jcim.9b01015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shirin Akbar
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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19
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Alnabati E, Kihara D. Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps. Molecules 2019; 25:molecules25010082. [PMID: 31878333 PMCID: PMC6982917 DOI: 10.3390/molecules25010082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 01/16/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.
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Affiliation(s)
- Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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20
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Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Cell Rep 2019; 25:3136-3147.e5. [PMID: 30540945 PMCID: PMC6302666 DOI: 10.1016/j.celrep.2018.11.067] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/01/2018] [Accepted: 11/15/2018] [Indexed: 01/08/2023] Open
Abstract
Alphaviruses are enveloped pathogens that cause arthritis and encephalitis. Here, we report a 4.4-Å cryoelectron microscopy (cryo-EM) structure of eastern equine encephalitis virus (EEEV), an alphavirus that causes fatal encephalitis in humans. Our analysis provides insights into viral entry into host cells. The envelope protein E2 showed a binding site for the cellular attachment factor heparan sulfate. The presence of a cryptic E2 glycan suggests how EEEV escapes surveillance by lectin-expressing myeloid lineage cells, which are sentinels of the immune system. A mechanism for nucleocapsid core release and disassembly upon viral entry was inferred based on pH changes and capsid dissociation from envelope proteins. The EEEV capsid structure showed a viral RNA genome binding site adjacent to a ribosome binding site for viral genome translation following genome release. Using five Fab-EEEV complexes derived from neutralizing antibodies, our investigation provides insights into EEEV host cell interactions and protective epitopes relevant to vaccine design. EEEV cryo-EM structure shows the basis of receptor binding and pH-triggered disassembly Cryptic envelope protein glycosylation interferes with immune detection EEEV RNA genome binding site on capsid protein has an extended conformation Antibody inhibition of EEEV entry involves cross-linking of viral envelope proteins
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21
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A new inactivation method to facilitate cryo-EM of enveloped, RNA viruses requiring high containment: A case study using Venezuelan Equine Encephalitis Virus (VEEV). J Virol Methods 2019; 277:113792. [PMID: 31786314 DOI: 10.1016/j.jviromet.2019.113792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 01/07/2023]
Abstract
The challenges associated with operating electron microscopes (EM) in biosafety level 3 and 4 containment facilities have slowed progress of cryo-EM studies of high consequence viruses. We address this gap in a case study of Venezuelan Equine Encephalitis Virus (VEEV) strain TC-83. Chemical inactivation of viruses may physically distort structure, and hence to verify retention of native structure, we selected VEEV strain TC-83 to develop this methodology as this virus has a 4.8 Å resolution cryo-EM structure. In our method, amplified VEEV TC-83 was concentrated directly from supernatant through a 30 % sucrose cushion, resuspended, and chemically inactivated with 1 % glutaraldehyde. A second 30 % sucrose cushion removed any excess glutaraldehyde that might interfere with single particle analyses. A cryo-EM map of fixed, inactivated VEEV was determined to a resolution of 7.9 Å. The map retained structural features of the native virus such as the icosahedral symmetry, and the organization of the capsid core and the trimeric spikes. Our results suggest that our strategy can easily be adapted for inactivation of other enveloped, RNA viruses requiring BSL-3 or BSL-4 for cryo-EM. However, the validation of inactivation requires the oversight of Biosafety Committee for each Institution.
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22
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Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1631817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
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23
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Bonomi M, Vendruscolo M. Determination of protein structural ensembles using cryo-electron microscopy. Curr Opin Struct Biol 2019; 56:37-45. [DOI: 10.1016/j.sbi.2018.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
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24
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Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy. Biophys J 2019; 114:1604-1613. [PMID: 29642030 PMCID: PMC5954442 DOI: 10.1016/j.bpj.2018.02.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/05/2018] [Accepted: 02/20/2018] [Indexed: 11/21/2022] Open
Abstract
Cryo-electron microscopy is rapidly emerging as a powerful technique to determine the structures of complex macromolecular systems elusive to other techniques. Because many of these systems are highly dynamical, characterizing their movements is also a crucial step to unravel their biological functions. To achieve this goal, we report an integrative modeling approach to simultaneously determine structure and dynamics of macromolecular systems from cryo-electron microscopy density maps. By quantifying the level of noise in the data and dealing with their ensemble-averaged nature, this approach enables the integration of multiple sources of information to model ensembles of structures and infer their populations. We illustrate the method by characterizing structure and dynamics of the integral membrane receptor STRA6, thus providing insights into the mechanisms by which it interacts with retinol binding protein and translocates retinol across the membrane.
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25
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Structural basis of a potent human monoclonal antibody against Zika virus targeting a quaternary epitope. Proc Natl Acad Sci U S A 2019; 116:1591-1596. [PMID: 30642974 DOI: 10.1073/pnas.1815432116] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Zika virus (ZIKV) is a major human pathogen and member of the Flavivirus genus in the Flaviviridae family. In contrast to most other insect-transmitted flaviviruses, ZIKV also can be transmitted sexually and from mother to fetus in humans. During recent outbreaks, ZIKV infections have been linked to microcephaly, congenital disease, and Guillain-Barré syndrome. Neutralizing antibodies have potential as therapeutic agents. We report here a 4-Å-resolution cryo-electron microscopy structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195. The footprint of the ZIKV-195 Fab fragment expands across two adjacent envelope (E) protein protomers. ZIKV neutralization by this antibody is presumably accomplished by cross-linking the E proteins, which likely prevents formation of E protein trimers required for fusion of the viral and cellular membranes. A single dose of ZIKV-195 administered 5 days after virus inoculation showed marked protection against lethality in a stringent mouse model of infection.
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26
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Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R. Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling. Structure 2018; 27:175-188.e6. [PMID: 30393052 DOI: 10.1016/j.str.2018.09.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 08/07/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map as well as other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-source Integrative Modeling Platform (http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.
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Affiliation(s)
| | - Samuel Hanot
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Michael Nilges
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | | | - Riccardo Pellarin
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France.
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27
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Sharma KK, Marzinek JK, Tantirimudalige SN, Bond PJ, Wohland T. Single-molecule studies of flavivirus envelope dynamics: Experiment and computation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 143:38-51. [PMID: 30223001 DOI: 10.1016/j.pbiomolbio.2018.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/06/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022]
Abstract
Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes. Here, we review different single-molecule sensitive fluorescence methods that are employed to investigate flaviviruses. In particular, we review how (i) time-resolved Förster resonance energy transfer (trFRET) was applied to probe dengue envelope conformations; (ii) FRET-fluorescence correlation spectroscopy to investigate dengue envelope intrinsic dynamics and (iii) single particle tracking to follow the path of dengue viruses in cells. We also discuss how such methods may be supported by molecular dynamics (MD) simulations over a range of spatio-temporal scales, to provide complementary data on the structure and dynamics of flaviviral systems. We describe recent improvements in multiscale MD approaches that allowed the simulation of dengue particle envelopes in near-atomic resolution. We hope this review is an incentive for setting up and applying similar single-molecule studies and combine them with MD simulations to investigate structural dynamics of entire flavivirus particles over the nanosecond-to-millisecond time-scale and follow viruses during infection in cells over milliseconds to minutes.
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Affiliation(s)
- Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Jan K Marzinek
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Peter J Bond
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Department of Chemistry, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore.
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28
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Cryo-EM structure of the SARS coronavirus spike glycoprotein in complex with its host cell receptor ACE2. PLoS Pathog 2018; 14:e1007236. [PMID: 30102747 PMCID: PMC6107290 DOI: 10.1371/journal.ppat.1007236] [Citation(s) in RCA: 567] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 08/23/2018] [Accepted: 07/23/2018] [Indexed: 02/05/2023] Open
Abstract
The trimeric SARS coronavirus (SARS-CoV) surface spike (S) glycoprotein consisting of three S1-S2 heterodimers binds the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediates fusion of the viral and cellular membranes through a pre- to postfusion conformation transition. Here, we report the structure of the SARS-CoV S glycoprotein in complex with its host cell receptor ACE2 revealed by cryo-electron microscopy (cryo-EM). The complex structure shows that only one receptor-binding domain of the trimeric S glycoprotein binds ACE2 and adopts a protruding “up” conformation. In addition, we studied the structures of the SARS-CoV S glycoprotein and its complexes with ACE2 in different in vitro conditions, which may mimic different conformational states of the S glycoprotein during virus entry. Disassociation of the S1-ACE2 complex from some of the prefusion spikes was observed and characterized. We also characterized the rosette-like structures of the clustered SARS-CoV S2 trimers in the postfusion state observed on electron micrographs. Structural comparisons suggested that the SARS-CoV S glycoprotein retains a prefusion architecture after trypsin cleavage into the S1 and S2 subunits and acidic pH treatment. However, binding to the receptor opens up the receptor-binding domain of S1, which could promote the release of the S1-ACE2 complex and S1 monomers from the prefusion spike and trigger the pre- to postfusion conformational transition. The global outbreak of SARS in 2002–2003 was caused by infection by a human coronavirus, SARS-CoV. Although the virus has been extensively studied with regard to epidemiology, virology, clinical features and other aspects, there are still no approved antiviral drugs and vaccines to treat and prevent infections of SARS-CoV. The spike (S) glycoprotein of the coronavirus, responsible for host cell attachment and mediating host cell membrane and viral membrane fusion during infection, is key to the viral life cycle and a major target for antiviral drugs and vaccines. In this study, we report the structures of different conformational states of the SARS-CoV S glycoprotein during virus entry. Specifically, we found that the S glycoprotein retains the prefusion trimer structure after trypsin cleavage and low-pH treatment. Additionally, binding with host cell receptor ACE2 promotes the release of S1 subunits from the S trimer and triggers the pre- to postfusion conformational transition. Our results provide new insights for understanding the mechanisms involved in coronavirus S glycoprotein-mediated virus entry.
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29
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Chen L, He J. Using Combined Features to Analyze Atomic Structures Derived from Cryo-EM Density Maps. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2018; 2018:651-655. [PMID: 37434945 PMCID: PMC10335752 DOI: 10.1145/3233547.3233709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. Many atomic structures have been derived from cryo-EM density maps of about 3Å resolution. Side-chain conformations are well determined in density maps with super-resolutions such as 1-2Å. It is desirable to have a statistical method to detect anomalous side-chains without a super-resolution density map. In this study, we analyzed structures derived from X-ray density maps with higher than 1.5Å resolution and those from cryo-EM density maps with 2-4 Å and 4-6 Å resolutions respectively. We introduce a histogram-based outlier score (HBOS) for anomaly detection in protein models built from cryo-EM density maps. This method uses the statistics derived from X-ray dataset (<1.5Å) as the reference and combines five features involving the distal block distance, side-chain length, phi, psi, and first chi angle of the residue. Higher percentages of anomalies were observed in the cryo-EM models than in the super-resolution X-ray models. Lower percentages of anomalies were observed in cryo-EM models derived after January 2017 than those derived before 2017.
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Affiliation(s)
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529
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30
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Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr D Struct Biol 2018; 74:531-544. [PMID: 29872004 PMCID: PMC6096492 DOI: 10.1107/s2059798318006551] [Citation(s) in RCA: 1616] [Impact Index Per Article: 269.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/27/2018] [Indexed: 02/23/2023] Open
Abstract
This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People’s Republic of China
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Randy J. Read
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, England
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87545, USA
| | - Alexandre Urzhumtsev
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy, France
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
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31
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Chen X, Liu M, Tian Y, Li J, Qi Y, Zhao D, Wu Z, Huang M, Wong CCL, Wang HW, Wang J, Yang H, Xu Y. Cryo-EM structure of human mTOR complex 2. Cell Res 2018; 28:518-528. [PMID: 29567957 DOI: 10.1038/s41422-018-0029-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/02/2018] [Accepted: 02/24/2018] [Indexed: 02/07/2023] Open
Abstract
Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) plays an essential role in regulating cell proliferation through phosphorylating AGC protein kinase family members, including AKT, PKC and SGK1. The functional core complex consists of mTOR, mLST8, and two mTORC2-specific components, Rictor and mSin1. Here we investigated the intermolecular interactions within mTORC2 complex and determined its cryo-electron microscopy structure at 4.9 Å resolution. The structure reveals a hollow rhombohedral fold with a 2-fold symmetry. The dimerized mTOR serves as a scaffold for the complex assembly. The N-terminal half of Rictor is composed of helical repeat clusters and binds to mTOR through multiple contacts. mSin1 is located close to the FRB domain and catalytic cavity of mTOR. Rictor and mSin1 together generate steric hindrance to inhibit binding of FKBP12-rapamycin to mTOR, revealing the mechanism for rapamycin insensitivity of mTORC2. The mTOR dimer in mTORC2 shows more compact conformation than that of mTORC1 (rapamycin sensitive), which might result from the interaction between mTOR and Rictor-mSin1. Structural comparison shows that binding of Rictor and Raptor (mTORC1-specific component) to mTOR is mutually exclusive. Our study provides a basis for understanding the assembly of mTORC2 and a framework to further characterize the regulatory mechanism of mTORC2 pathway.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Mengjie Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yuan Tian
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yilun Qi
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Dan Zhao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Min Huang
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Catherine C L Wong
- National Center for Protein Science Shanghai, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201210, China.,Center for Precision Medicine Multi-Omics Research (CPMMOR), Peking University Health Science Center, Beijing, 100871, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing, 100871, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jiawei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huirong Yang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. .,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. .,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. .,Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. .,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China. .,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China.
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32
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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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33
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Hasan SS, Sevvana M, Kuhn RJ, Rossmann MG. Structural biology of Zika virus and other flaviviruses. Nat Struct Mol Biol 2018; 25:13-20. [PMID: 29323278 DOI: 10.1038/s41594-017-0010-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/11/2017] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is an enveloped, icosahedral flavivirus that has structural and functional similarities to other human flavivirus pathogens such as dengue (DENV), West Nile (WNV) and Japanese encephalitis (JEV) viruses. ZIKV infections have been linked to fetal microcephaly and the paralytic Guillain-Barré syndrome. This review provides a comparative structural analysis of the assembly, maturation and host-cell entry of ZIKV with other flaviviruses, especially DENV. We also discuss the mechanisms of neutralization by antibodies.
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Affiliation(s)
- S Saif Hasan
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Madhumati Sevvana
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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34
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Rigid-Body Fitting of Atomic Models on 3D Density Maps of Electron Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:219-235. [PMID: 30617832 DOI: 10.1007/978-981-13-2200-6_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cryo electron microscopy has revolutionarily evolved for the determination of the 3D structure of macromolecular complexes. The modeling procedures on the 3D density maps of electron microscopy are roughly classified into three categories: fitting, de novo modeling and refinement. The registered atomic models from the maps have mostly been hand-built and auto-refined. Several programs aiming at automatic modeling have also been developed using various kinds of molecular representations. Among these three classes of the modeling procedures, the rigid body fitting is reviewed here, because it is the most basic modeling process applied before the other steps. The fitting problems are classified as the fittings of single subunit or multiple subunits, and the fittings on global or local parts of maps. A higher resolution map enables more local fitting. Various molecular representations have been employed in the fitting programs. A point and digital image models are generally used to represent molecules, but new representations, such as the Gaussian mixture model, have been applied recently.
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35
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Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 2017; 114:13708-13713. [PMID: 29229840 DOI: 10.1073/pnas.1716614114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS.
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36
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Abstract
Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
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37
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Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses. Sci Rep 2017; 7:5484. [PMID: 28710447 PMCID: PMC5511168 DOI: 10.1038/s41598-017-05824-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/02/2017] [Indexed: 11/09/2022] Open
Abstract
Whereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a reconstruction of the capsid of Cafeteria roenbergensis virus (CroV), one of the largest viruses analyzed by cryo-electron microscopy (cryo-EM) to date. The CroV capsid has a diameter of 3,000 Å and a Triangulation number of 499. Unlike related mimiviruses, the CroV capsid is not decorated with glycosylated surface fibers, but features 30 Å-long surface protrusions that are formed by loops of the major capsid protein. Based on the orientation of capsomers in the cryo-EM reconstruction, we propose that the capsids of CroV and related giant viruses are assembled by a newly conceived assembly pathway that initiates at a five-fold vertex and continuously proceeds outwards in a spiraling fashion.
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38
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Zhou N, Wang H, Wang J. EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. Sci Rep 2017; 7:2664. [PMID: 28572576 PMCID: PMC5453991 DOI: 10.1038/s41598-017-02725-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/18/2017] [Indexed: 01/17/2023] Open
Abstract
The resolution of electron-potential maps in single-particle cryo-electron microscopy (cryoEM) is approaching atomic or near- atomic resolution. However, no program currently exists for de novo cryoEM model building at resolutions exceeding beyond 3.5 Å. Here, we present a program, EMBuilder, based on template matching, to generate cryoEM models at high resolution. The program identifies features in both secondary-structure and Cα stages. In the secondary structure stage, helices and strands are identified with pre-computed templates, and the voxel size of the entire map is then refined to account for microscopic magnification errors. The identified secondary structures are then extended from both ends in the Cα stage via a log-likelihood (LLK) target function, and if possible, the side chains are also assigned. This program can build models of large proteins (~1 MDa) in a reasonable amount of time (~1 day) and thus has the potential to greatly decrease the manual workload required for model building of high-resolution cryoEM maps.
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Affiliation(s)
- Niyun Zhou
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hongwei Wang
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. .,School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
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39
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A human antibody against Zika virus crosslinks the E protein to prevent infection. Nat Commun 2017; 8:14722. [PMID: 28300075 PMCID: PMC5356071 DOI: 10.1038/ncomms14722] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
The recent Zika virus (ZIKV) epidemic has been linked to unusual and severe clinical manifestations including microcephaly in fetuses of infected pregnant women and Guillian-Barré syndrome in adults. Neutralizing antibodies present a possible therapeutic approach to prevent and control ZIKV infection. Here we present a 6.2 Å resolution three-dimensional cryo-electron microscopy (cryoEM) structure of an infectious ZIKV (strain H/PF/2013, French Polynesia) in complex with the Fab fragment of a highly therapeutic and neutralizing human monoclonal antibody, ZIKV-117. The antibody had been shown to prevent fetal infection and demise in mice. The structure shows that ZIKV-117 Fabs cross-link the monomers within the surface E glycoprotein dimers as well as between neighbouring dimers, thus preventing the reorganization of E protein monomers into fusogenic trimers in the acidic environment of endosomes.
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40
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Wang H, Wang J. How cryo-electron microscopy and X-ray crystallography complement each other. Protein Sci 2017; 26:32-39. [PMID: 27543495 PMCID: PMC5192981 DOI: 10.1002/pro.3022] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 11/09/2022]
Abstract
With the ability to resolve structures of macromolecules at atomic resolution, X-ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo-EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X-ray crystallography and cryo-EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms.
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Affiliation(s)
- Hong‐Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences School of Life SciencesTsinghua UniversityBeijing100084
- Tsinghua‐Peking Joint Center for Life SciencesTsinghua UniversityBeijing100084
| | - Jia‐Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, Ministry of Education Key Laboratory of Protein Sciences School of Life SciencesTsinghua UniversityBeijing100084
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41
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4.4 Å Resolution Cryo-EM structure of human mTOR Complex 1. Protein Cell 2016; 7:878-887. [PMID: 27909983 PMCID: PMC5205667 DOI: 10.1007/s13238-016-0346-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/11/2016] [Indexed: 11/30/2022] Open
Abstract
Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from growth factors, cellular energy levels, stress and amino acids to control cell growth and proliferation through regulating translation, autophagy and metabolism. Here we determined the cryo-electron microscopy structure of human mTORC1 at 4.4 Å resolution. The mTORC1 comprises a dimer of heterotrimer (mTOR-Raptor-mLST8) mediated by the mTOR protein. The complex adopts a hollow rhomboid shape with 2-fold symmetry. Notably, mTORC1 shows intrinsic conformational dynamics. Within the complex, the conserved N-terminal caspase-like domain of Raptor faces toward the catalytic cavity of the kinase domain of mTOR. Raptor shows no caspase activity and therefore may bind to TOS motif for substrate recognition. Structural analysis indicates that FKBP12-Rapamycin may generate steric hindrance for substrate entry to the catalytic cavity of mTORC1. The structure provides a basis to understand the assembly of mTORC1 and a framework to characterize the regulatory mechanism of mTORC1 pathway.
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42
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Kuzu G, Keskin O, Nussinov R, Gursoy A. PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Acta Crystallogr D Struct Biol 2016; 72:1137-1148. [PMID: 27710935 PMCID: PMC5053140 DOI: 10.1107/s2059798316013541] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.
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Affiliation(s)
- Guray Kuzu
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey
- Chemical and Biological Engineering, College of Engineering, Koc University, 34450 Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- Computer Engineering, Koc University, 34450 Istanbul, Turkey
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43
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Abstract
Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse.
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Affiliation(s)
- Akshata R Naik
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Kenneth T Lewis
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Bhanu P Jena
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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44
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Zhang J, Pan X, Yan K, Sun S, Gao N, Sui SF. Mechanisms of ribosome stalling by SecM at multiple elongation steps. eLife 2015; 4. [PMID: 26670735 PMCID: PMC4737659 DOI: 10.7554/elife.09684] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022] Open
Abstract
Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling. However, the underlying molecular mechanism is still not clear at the atomic level. Here, we present two cryo-EM structures of the SecM-stalled ribosomes at 3.3–3.7 Å resolution, which reveal two different stalling mechanisms at distinct elongation steps of the translation cycle: one is due to the inactivation of ribosomal peptidyl-transferase center which inhibits peptide bond formation with the incoming prolyl-tRNA; the other is the prolonged residence of the peptidyl-RNA at the hybrid A/P site which inhibits the full-scale tRNA translocation. These results demonstrate an elegant control of translation cycle by regulatory peptides through a continuous, dynamic reshaping of the functional center of the ribosome. DOI:http://dx.doi.org/10.7554/eLife.09684.001 Many genes code for proteins that carry out essential tasks. The instructions in a gene are first copied into a messenger RNA (mRNA), and a molecular machine known as a ribosome reads the copied instructions in groups of three letters at a time (called codons). The ribosome translates the order of the codons into a sequence of amino acids; each amino acid is carried into the ribosome by a transfer RNA (tRNA) molecule. As it translates, the ribosome joins each new amino acid to the one before it, like the links in a chain. Finally, the newly built protein chain passes through a tunnel to exit the ribosome. Ribosomes do not build all proteins at a constant rate; there are many examples of proteins that stall when they are in the ribosome exit tunnel. It is thought that this stalling is an important way for cells to control the expression of proteins. SecM is a bacterial protein that stalls while it is being made. Previous research has shown that a sequence of amino acids in SecM (called the arrest sequence) interacts with components of the ribosome tunnel. This interaction leads to stalling, and regulates the translation of another important bacterial protein (called SecA) that is encoded downstream on the same mRNA as SecM. If SecM-induced stalling takes place, the translation of SecA actually increases. Nevertheless, it remains poorly understood how SecM stalls in the ribosome. Zhang et al. have now solved the structures of SecM proteins stalled inside ribosomes using a method called cryo-electron microscopy. This approach identified two different states of SecM present in the ribosome, which corresponded to two different stalling mechanisms. The addition of an amino acid to a growing protein occurs in stages. First, the tRNA that carries the amino acid to the ribosome and bind to it in a region known as the A-site. After this, the tRNA moves to the P-site where the attached amino acid is incorporated into the elongating protein chain. Zhang et al. observed that the arrest sequence of SecM and the ribosome tunnel interact extensively. These interactions are strong and alter the configuration of both the A-site and P-site of the ribosome. This has two major consequences for translation. First, the tRNA cannot be stably accommodated in the A-site and secondly, its passage to the P-site is slowed down. Both these mechanisms contribute to stalling. This study provides a detailed analysis of how the ribosome can adjust to control translation. It also highlights that codon-specific control of translation constitutes an important component of how gene expression is regulated. DOI:http://dx.doi.org/10.7554/eLife.09684.002
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Affiliation(s)
- Jun Zhang
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xijiang Pan
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kaige Yan
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ning Gao
- Ministry of Education Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
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45
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Long F, Fong RH, Austin SK, Chen Z, Klose T, Fokine A, Liu Y, Porta J, Sapparapu G, Akahata W, Doranz BJ, Crowe JE, Diamond MS, Rossmann MG. Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity. Proc Natl Acad Sci U S A 2015; 112:13898-903. [PMID: 26504196 PMCID: PMC4653152 DOI: 10.1073/pnas.1515558112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes severe acute and chronic disease in humans. Although highly inhibitory murine and human monoclonal antibodies (mAbs) have been generated, the structural basis of their neutralizing activity remains poorly characterized. Here, we determined the cryo-EM structures of chikungunya virus-like particles complexed with antibody fragments (Fab) of two highly protective human mAbs, 4J21 and 5M16, that block virus fusion with host membranes. Both mAbs bind primarily to sites within the A and B domains, as well as to the B domain's β-ribbon connector of the viral glycoprotein E2. The footprints of these antibodies on the viral surface were consistent with results from loss-of-binding studies using an alanine scanning mutagenesis-based epitope mapping approach. The Fab fragments stabilized the position of the B domain relative to the virus, particularly for the complex with 5M16. This finding is consistent with a mechanism of neutralization in which anti-CHIKV mAbs that bridge the A and B domains impede movement of the B domain away from the underlying fusion loop on the E1 glycoprotein and therefore block the requisite pH-dependent fusion of viral and host membranes.
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Affiliation(s)
- Feng Long
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | | | - Stephen K Austin
- Departments of Medicine, Molecular Microbiology, Pathology, and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Zhenguo Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Yue Liu
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Jason Porta
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
| | - Gopal Sapparapu
- Department of Pediatrics, Vanderbilt University, Nashville, TN 37232
| | | | | | - James E Crowe
- Department of Pediatrics, Vanderbilt University, Nashville, TN 37232; Departments of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN 37232
| | - Michael S Diamond
- Departments of Medicine, Molecular Microbiology, Pathology, and Immunology, Washington University School of Medicine, St. Louis, MO 63110
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;
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46
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Fox JM, Long F, Edeling MA, Lin H, van Duijl-Richter MKS, Fong RH, Kahle KM, Smit JM, Jin J, Simmons G, Doranz BJ, Crowe JE, Fremont DH, Rossmann MG, Diamond MS. Broadly Neutralizing Alphavirus Antibodies Bind an Epitope on E2 and Inhibit Entry and Egress. Cell 2015; 163:1095-1107. [PMID: 26553503 DOI: 10.1016/j.cell.2015.10.050] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/18/2015] [Accepted: 10/19/2015] [Indexed: 01/12/2023]
Abstract
We screened a panel of mouse and human monoclonal antibodies (MAbs) against chikungunya virus and identified several with inhibitory activity against multiple alphaviruses. Passive transfer of broadly neutralizing MAbs protected mice against infection by chikungunya, Mayaro, and O'nyong'nyong alphaviruses. Using alanine-scanning mutagenesis, loss-of-function recombinant proteins and viruses, and multiple functional assays, we determined that broadly neutralizing MAbs block multiple steps in the viral lifecycle, including entry and egress, and bind to a conserved epitope on the B domain of the E2 glycoprotein. A 16 Å resolution cryo-electron microscopy structure of a Fab fragment bound to CHIKV E2 B domain provided an explanation for its neutralizing activity. Binding to the B domain was associated with repositioning of the A domain of E2 that enabled cross-linking of neighboring spikes. Our results suggest that B domain antigenic determinants could be targeted for vaccine or antibody therapeutic development against multiple alphaviruses of global concern.
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Affiliation(s)
- Julie M Fox
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Feng Long
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Melissa A Edeling
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hueylie Lin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Rachel H Fong
- Integral Molecular, Inc., Philadelphia, PA 19104, USA
| | | | - Jolanda M Smit
- University of Groningen and University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Jing Jin
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Graham Simmons
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | | | - James E Crowe
- Departments of Pediatrics, Pathology, Microbiology, and Immunology and the Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN 37235, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA.
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47
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Structural Studies of Chikungunya Virus-Like Particles Complexed with Human Antibodies: Neutralization and Cell-to-Cell Transmission. J Virol 2015; 90:1169-77. [PMID: 26537684 DOI: 10.1128/jvi.02364-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/30/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Chikungunya virus is a positive-stranded RNA alphavirus. Structures of chikungunya virus-like particles in complex with strongly neutralizing antibody Fab fragments (8B10 and 5F10) were determined using cryo-electron microscopy and X-ray crystallography. By fitting the crystallographically determined structures of these Fab fragments into the cryo-electron density maps, we show that Fab fragments of antibody 8B10 extend radially from the viral surface and block receptor binding on the E2 glycoprotein. In contrast, Fab fragments of antibody 5F10 bind the tip of the E2 B domain and lie tangentially on the viral surface. Fab 5F10 fixes the B domain rigidly to the surface of the virus, blocking exposure of the fusion loop on glycoprotein E1 and therefore preventing the virus from becoming fusogenic. Although Fab 5F10 can neutralize the wild-type virus, it can also bind to a mutant virus without inhibiting fusion or attachment. Although the mutant virus is no longer able to propagate by extracellular budding, it can, however, enter the next cell by traveling through junctional complexes without being intercepted by a neutralizing antibody to the wild-type virus, thus clarifying how cell-to-cell transmission can occur. IMPORTANCE Alphaviral infections are transmitted mainly by mosquitoes. Chikungunya virus (CHIKV), which belongs to the Alphavirus genus, has a wide distribution in the Old World that has expanded in recent years into the Americas. There are currently no vaccines or drugs against alphaviral infections. Therefore, a better understanding of CHIKV and its associated neutralizing antibodies will aid in the development of effective treatments.
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48
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Wriggers W, He J. Numerical geometry of map and model assessment. J Struct Biol 2015; 192:255-61. [PMID: 26416532 DOI: 10.1016/j.jsb.2015.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/18/2015] [Accepted: 09/24/2015] [Indexed: 10/23/2022]
Abstract
We are describing best practices and assessment strategies for the atomic interpretation of cryo-electron microscopy (cryo-EM) maps. Multiscale numerical geometry strategies in the Situs package and in secondary structure detection software are currently evolving due to the recent increases in cryo-EM resolution. Criteria that aim to predict the accuracy of fitted atomic models at low (worse than 8Å) and medium (4-8 Å) resolutions remain challenging. However, a high level of confidence in atomic models can be achieved by combining such criteria. The observed errors are due to map-model discrepancies and due to the effect of imperfect global docking strategies. Extending the earlier motion capture approach developed for flexible fitting, we use simulated fiducials (pseudoatoms) at varying levels of coarse-graining to track the local drift of structural features. We compare three tracking approaches: naïve vector quantization, a smoothly deformable model, and a tessellation of the structure into rigid Voronoi cells, which are fitted using a multi-fragment refinement approach. The lowest error is an upper bound for the (small) discrepancy between the crystal structure and the EM map due to different conditions in their structure determination. When internal features such as secondary structures are visible in medium-resolution EM maps, it is possible to extend the idea of point-based fiducials to more complex geometric representations such as helical axes, strands, and skeletons. We propose quantitative strategies to assess map-model pairs when such secondary structure patterns are prominent.
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Affiliation(s)
- Willy Wriggers
- Department of Mechanical & Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, United States.
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, United States.
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49
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Veesler D, Kearney BM, Johnson JE. Integration of X-ray crystallography and electron cryo-microscopy in the analysis of virus structure and function. CRYSTALLOGR REV 2015. [DOI: 10.1080/0889311x.2015.1038530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Kanekiyo M, Bu W, Joyce MG, Meng G, Whittle JRR, Baxa U, Yamamoto T, Narpala S, Todd JP, Rao SS, McDermott AB, Koup RA, Rossmann MG, Mascola JR, Graham BS, Cohen JI, Nabel GJ. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site. Cell 2015; 162:1090-100. [PMID: 26279189 PMCID: PMC4757492 DOI: 10.1016/j.cell.2015.07.043] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 05/21/2015] [Accepted: 06/18/2015] [Indexed: 11/19/2022]
Abstract
Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses.
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Affiliation(s)
- Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Bu
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geng Meng
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - James R R Whittle
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Takuya Yamamoto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Srinivas S Rao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Gary J Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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