1
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DiIorio MC, Kulczyk AW. Novel Artificial Intelligence-Based Approaches for Ab Initio Structure Determination and Atomic Model Building for Cryo-Electron Microscopy. MICROMACHINES 2023; 14:1674. [PMID: 37763837 PMCID: PMC10534518 DOI: 10.3390/mi14091674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has emerged as the prevailing method for near-atomic structure determination, shedding light on the important molecular mechanisms of biological macromolecules. However, the inherent dynamics and structural variability of biological complexes coupled with the large number of experimental images generated by a cryo-EM experiment make data processing nontrivial. In particular, ab initio reconstruction and atomic model building remain major bottlenecks that demand substantial computational resources and manual intervention. Approaches utilizing recent innovations in artificial intelligence (AI) technology, particularly deep learning, have the potential to overcome the limitations that cannot be adequately addressed by traditional image processing approaches. Here, we review newly proposed AI-based methods for ab initio volume generation, heterogeneous 3D reconstruction, and atomic model building. We highlight the advancements made by the implementation of AI methods, as well as discuss remaining limitations and areas for future development.
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Affiliation(s)
- Megan C. DiIorio
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Biochemistry & Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
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2
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Bouvier G, Bardiaux B, Pellarin R, Rapisarda C, Nilges M. Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution. Biomolecules 2022; 12:biom12091290. [PMID: 36139128 PMCID: PMC9496541 DOI: 10.3390/biom12091290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/01/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Electron cryo-microscopy (cryo-EM) has emerged as a powerful method by which to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3–5 Å) cryo-EM density maps is a challenging task, in particular because poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when the structure of the subunits is not known, or when significant conformational rearrangement occurs between the isolated and associated form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C-α trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C-α atoms, by using side-chain density when available, as a collection of C-α trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that this approach can correctly segment EM maps into individual subunits and assign amino acid sequences to backbone traces to generate atomic models.
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Affiliation(s)
- Guillaume Bouvier
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, 75015 Paris, France
- Correspondence: (G.B.); (B.B.)
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, 75015 Paris, France
- Correspondence: (G.B.); (B.B.)
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, 75015 Paris, France
| | - Chiara Rapisarda
- Microbiologie Fondamentale et Pathogènicité, University of Bordeaux, CNRS UMR 5234, 33076 Bordeaux, France
- Institut Européen de Chimie et Biologie, University of Bordeaux, 33600 Pessac, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, 75015 Paris, France
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3
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Abstract
Cytidine triphosphate synthase (CTPS), which comprises an ammonia ligase domain and a glutamine amidotransferase domain, catalyzes the final step of de novo CTP biosynthesis. The activity of CTPS is regulated by the binding of four nucleotides and glutamine. While glutamine serves as an ammonia donor for the ATP-dependent conversion of UTP to CTP, the fourth nucleotide GTP acts as an allosteric activator. Models have been proposed to explain the mechanisms of action at the active site of the ammonia ligase domain and the conformational changes derived by GTP binding. However, actual GTP/ATP/UTP binding modes and relevant conformational changes have not been revealed fully. Here, we report the discovery of binding modes of four nucleotides and a glutamine analog 6-diazo-5-oxo-L-norleucine in Drosophila CTPS by cryo-electron microscopy with near-atomic resolution. Interactions between GTP and surrounding residues indicate that GTP acts to coordinate reactions at both domains by directly blocking ammonia leakage and stabilizing the ammonia tunnel. Additionally, we observe the ATP-dependent UTP phosphorylation intermediate and determine interacting residues at the ammonia ligase. A noncanonical CTP binding at the ATP binding site suggests another layer of feedback inhibition. Our findings not only delineate the structure of CTPS in the presence of all substrates but also complete our understanding of the underlying mechanisms of the allosteric regulation and CTP synthesis.
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4
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Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 160:104-120. [PMID: 32866476 PMCID: PMC7914283 DOI: 10.1016/j.pbiomolbio.2020.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/25/2020] [Accepted: 08/16/2020] [Indexed: 12/17/2022]
Abstract
The eukaryotic chaperonin TRiC/CCT plays a major role in assisting the folding of many proteins through an ATP-driven allosteric cycle. Recent structures elucidated by cryo-electron microscopy provide a broad view of the conformations visited at various stages of the chaperonin cycle, including a sequential activation of its subunits in response to nucleotide binding. But we lack a thorough mechanistic understanding of the structure-based dynamics and communication properties that underlie the TRiC/CCT machinery. In this study, we present a computational methodology based on elastic network models adapted to cryo-EM density maps to gain a deeper understanding of the structure-encoded allosteric dynamics of this hexadecameric machine. We have analysed several structures of the chaperonin resolved in different states toward mapping its conformational landscape. Our study indicates that the overall architecture intrinsically favours cooperative movements that comply with the structural variabilities observed in experiments. Furthermore, the individual subunits CCT1-CCT8 exhibit state-dependent sequential events at different states of the allosteric cycle. For example, in the ATP-bound state, subunits CCT5 and CCT4 selectively initiate the lid closure motions favoured by the overall architecture; whereas in the apo form of the heteromer, the subunit CCT7 exhibits the highest predisposition to structural change. The changes then propagate through parallel fluxes of allosteric signals to neighbours on both rings. The predicted state-dependent mechanisms of sequential activation provide new insights into TRiC/CCT intra- and inter-ring signal transduction events.
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Affiliation(s)
- Yan Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - James Krieger
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Karolina Mikulska-Ruminska
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Burak Kaynak
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | | | - José-María Carazo
- Centro Nacional de Biotecnología (CSIC), Darwin, 3, 28049, Madrid, Spain
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh, 800 Murdoch Building, 3420 Forbes Avenue, Pittsburgh, PA, 15261, USA.
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5
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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6
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Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat Methods 2020; 17:699-707. [PMID: 32616928 PMCID: PMC7386730 DOI: 10.1038/s41592-020-0878-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/20/2020] [Indexed: 02/05/2023]
Abstract
The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Kaiming Zhang
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Zhaoming Su
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan, China
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Grigore Pintilie
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Ved V Topkar
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Joseph D Yesselman
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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7
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Engen JR, Komives EA. Complementarity of Hydrogen/Deuterium Exchange Mass Spectrometry and Cryo-Electron Microscopy. Trends Biochem Sci 2020; 45:906-918. [PMID: 32487353 DOI: 10.1016/j.tibs.2020.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022]
Abstract
Methodological improvements in both single particle cryo-electron microscopy (cryo-EM) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) mean that the two methods are being more frequently used together to tackle complex problems in structural biology. There are many benefits to this combination, including for the analysis of low-resolution density, for structural validation, in the analysis of individual proteins versus the same proteins in large complexes, studies of allostery, protein quality control during cryo-EM construct optimization, and in the study of protein movements/dynamics during function. As will be highlighted in this review, through careful considerations of potential sample and conformational heterogeneity, many joint studies have recently been demonstrated, and many future studies using this combination are anticipated.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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8
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Leelananda SP, Lindert S. Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement. J Chem Inf Model 2020; 60:2522-2532. [PMID: 31872764 PMCID: PMC7262651 DOI: 10.1021/acs.jcim.9b00932] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cryo-EM has become one of the prime methods for protein structure elucidation, frequently yielding density maps with near-atomic or medium resolution. If protein structures cannot be deduced unambiguously from the density maps, computational structure refinement tools are needed to generate protein structural models. We have previously developed an iterative Rosetta-MDFF protocol that used cryo-EM densities to refine protein structures. Here we show that, in addition to cryo-EM densities, incorporation of other experimental restraints into the Rosetta-MDFF protocol further improved refined structures. We used NMR chemical shift (CS) data integrated with cryo-EM densities in our hybrid protocol in both the Rosetta step and the molecular dynamics (MD) simulations step. In 15 out of 18 cases for all MD rounds, the refinement results obtained when density maps and NMR chemical shift data were used in combination outperformed those of density map-only refinement. Notably, the improvement in refinement was highest when medium and low-resolution density maps were used. With our hybrid method, the RMSDs of final models obtained were always better than the RMSDs obtained by our previous protocol with just density refinement for both medium (6.9 Å) and low (9 Å) resolution maps. For all the six test proteins with medium resolution density maps (6.9 Å), the final refined structure RMSDs were lower for the hybrid method than for the cryo-EM only refinement. The final refined RMSDs were less than 1.5 Å when our hybrid protocol was used with 4 Å density maps. For four out of the six proteins the final RMSDs were even less than 1 Å. This study demonstrates that by using a combination of cryo-EM and NMR restraints, it is possible to refine structures to atomic resolution, outperforming single restraint refinement. This hybrid protocol will be a valuable tool when only low-resolution cryo-EM density data and NMR chemical shift data are available to refine structures.
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Affiliation(s)
- Sumudu P. Leelananda
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210
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9
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Dodd T, Yan C, Ivanov I. Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy. J Chem Inf Model 2020; 60:2470-2483. [PMID: 32202798 DOI: 10.1021/acs.jcim.0c00087] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in cryoelectron microscopy (cryo-EM) have revolutionized the structural investigation of large macromolecular assemblies. In this review, we first provide a broad overview of modeling methods used for flexible fitting of molecular models into cryo-EM density maps. We give special attention to approaches rooted in molecular simulations-atomistic molecular dynamics and Monte Carlo. Concise descriptions of the methods are given along with discussion of their advantages, limitations, and most popular alternatives. We also describe recent extensions of the widely used molecular dynamics flexible fitting (MDFF) method and discuss how different model-building techniques could be incorporated into new hybrid modeling schemes and simulation workflows. Finally, we provide two illustrative examples of model-building and refinement strategies employing MDFF, cascade MDFF, and RosettaCM. These examples come from recent cryo-EM studies that elucidated transcription preinitiation complexes and shed light on the functional roles of these assemblies in gene expression and gene regulation.
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Affiliation(s)
- Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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10
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Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Cryo-EM map interpretation and protein model-building using iterative map segmentation. Protein Sci 2020; 29:87-99. [PMID: 31599033 PMCID: PMC6933853 DOI: 10.1002/pro.3740] [Citation(s) in RCA: 20] [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: 06/27/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022]
Abstract
A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps.
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Affiliation(s)
- Thomas C. Terwilliger
- Los Alamos National LaboratoryLos AlamosNew Mexico
- New Mexico ConsortiumLos AlamosNew Mexico
| | - Paul D. Adams
- Molecular Biophysics & Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Department of BioengineeringUniversity of California BerkeleyBerkeleyCalifornia
| | - Pavel V. Afonine
- Molecular Biophysics & Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Oleg V. Sobolev
- Molecular Biophysics & Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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11
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Zhou X, Guo CJ, Hu HH, Zhong J, Sun Q, Liu D, Zhou S, Chang CC, Liu JL. Drosophila CTP synthase can form distinct substrate- and product-bound filaments. J Genet Genomics 2019; 46:537-545. [PMID: 31902586 DOI: 10.1016/j.jgg.2019.11.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 01/26/2023]
Abstract
Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells. However, recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells. In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPS, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation.
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Affiliation(s)
- Xian Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Huan-Huan Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianqian Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Dandan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Shuang Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chia Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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12
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Perry TN, Souabni H, Rapisarda C, Fronzes R, Giusti F, Popot JL, Zoonens M, Gubellini F. BAmSA: Visualising transmembrane regions in protein complexes using biotinylated amphipols and electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:466-477. [DOI: 10.1016/j.bbamem.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/30/2022]
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13
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Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps. Nat Methods 2018; 15:905-908. [PMID: 30377346 PMCID: PMC6214191 DOI: 10.1038/s41592-018-0173-1] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/06/2018] [Indexed: 01/31/2023]
Abstract
We report a fully automated procedure for the optimization and interpretation of reconstructions from cryo-electron microscopy (cryo-EM) data, available in Phenix as phenix.map_to_model. We applied our approach to 476 datasets with resolution of 4.5 Å or better, including reconstructions of 47 ribosomes and 32 other protein-RNA complexes. The median fraction of residues in the deposited structures reproduced automatically was 71% for reconstructions determined at resolutions of 3 Å or better and 47% for those at resolutions worse than 3 Å.
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Affiliation(s)
- Thomas C Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM, USA.
- New Mexico Consortium, Los Alamos, NM, USA.
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Pavel V Afonine
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, China
| | - Oleg V Sobolev
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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14
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Terwilliger TC, Adams PD, Afonine PV, Sobolev OV. Map segmentation, automated model-building and their application to the Cryo-EM Model Challenge. J Struct Biol 2018; 204:338-343. [PMID: 30063987 PMCID: PMC6163059 DOI: 10.1016/j.jsb.2018.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/11/2018] [Accepted: 07/27/2018] [Indexed: 11/27/2022]
Abstract
A recently-developed method for identifying a compact, contiguous region representing the unique part of a density map was applied to 218 Cryo-EM maps with resolutions of 4.5 Å or better. The key elements of the segmentation procedure are (1) identification of all regions of density above a threshold and (2) choice of a unique set of these regions, taking symmetry into consideration, that maximize connectivity and compactness. This segmentation approach was then combined with tools for automated map sharpening and model-building to generate models for the 12 maps in the 2016 Cryo-EM Model Challenge in a fully automated manner. The resulting models have completeness from 24% to 82% and RMS distances from reference interpretations of 0.6 Å-2.1 Å.
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Affiliation(s)
- Thomas C Terwilliger
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87544, USA.
| | - Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Pavel V Afonine
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA; Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai 200444, People's Republic of China
| | - Oleg V Sobolev
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
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15
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Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Nat Methods 2018; 15:947-954. [PMID: 30377372 PMCID: PMC6636682 DOI: 10.1038/s41592-018-0172-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022]
Abstract
Increasingly, cryo-electron microscopy (cryo-EM) is used to determine the structures of RNA-protein assemblies, but nearly all maps determined with this method have biologically important regions where the local resolution does not permit RNA coordinate tracing. To address these omissions, we present de novo ribonucleoprotein modeling in real space through assembly of fragments together with experimental density in Rosetta (DRRAFTER). We show that DRRAFTER recovers near-native models for a diverse benchmark set of RNA-protein complexes including the spliceosome, mitochondrial ribosome, and CRISPR-Cas9-sgRNA complexes; rigorous blind tests include yeast U1 snRNP and spliceosomal P complex maps. Additionally, to aid in model interpretation, we present a method for reliable in situ estimation of DRRAFTER model accuracy. Finally, we apply DRRAFTER to recently determined maps of telomerase, the HIV-1 reverse transcriptase initiation complex, and the packaged MS2 genome, demonstrating the acceleration of accurate model building in challenging cases.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Shiheng Liu
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Kevin P Larsen
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines, California NanoSystems Institute, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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16
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Pintilie G, Chiu W. Assessment of structural features in Cryo-EM density maps using SSE and side chain Z-scores. J Struct Biol 2018; 204:564-571. [PMID: 30144506 DOI: 10.1016/j.jsb.2018.08.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/18/2018] [Accepted: 08/21/2018] [Indexed: 10/28/2022]
Abstract
We introduce a new method for assessing resolvability of structural features in density maps from Cryo-Electron Microscopy (Cryo-EM) using fitted or derived models. It calculates Z-scores for secondary structure elements (SSEs) and side chains. Z-scores capture how much larger the cross-correlation score (CCS) is for atoms in such features at their placed locations compared to the CCS at displaced positions. Z-scores are larger when the structural features are well-resolved, as confirmed by visual analysis. This method was applied to all 66 maps submitted to the 2015/2016 EMDB map challenge. For each map, the fitted model provided by the map committee was used in this assessment. The average Z-scores for each map and fitted model correlate moderately well with reported map resolutions (r2 = 0.45 for SSE Z-scores and r2 = 0.56 for side chain Z-scores). Rankings of the submitted maps based on average Z-scores seem to more closely agree with visual analysis. Z-scores can also be used to pinpoint which parts of a model are well-resolved in a map, and which parts of the model may need further fitting or refinement to make the model better match the density.
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Affiliation(s)
- Grigore Pintilie
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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17
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Cassidy CK, Himes BA, Luthey-Schulten Z, Zhang P. CryoEM-based hybrid modeling approaches for structure determination. Curr Opin Microbiol 2018; 43:14-23. [PMID: 29107896 PMCID: PMC5934336 DOI: 10.1016/j.mib.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 12/21/2022]
Abstract
Recent advances in cryo-electron microscopy (cryoEM) have dramatically improved the resolutions at which vitrified biological specimens can be studied, revealing new structural and mechanistic insights over a broad range of spatial scales. Bolstered by these advances, much effort has been directed toward the development of hybrid modeling methodologies for the construction and refinement of high-fidelity atomistic models from cryoEM data. In this brief review, we will survey the key elements of cryoEM-based hybrid modeling, providing an overview of available computational tools and strategies as well as several recent applications.
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Affiliation(s)
- C Keith Cassidy
- Department of Physics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Benjamin A Himes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
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18
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Abstract
Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.
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Affiliation(s)
- Ingemar André
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Lund, Sweden.
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19
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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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20
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Boland A, Chang L, Barford D. The potential of cryo-electron microscopy for structure-based drug design. Essays Biochem 2017; 61:543-560. [PMID: 29118099 DOI: 10.1042/ebc20170032] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022]
Abstract
Structure-based drug design plays a central role in therapeutic development. Until recently, protein crystallography and NMR have dominated experimental approaches to obtain structural information of biological molecules. However, in recent years rapid technical developments in single particle cryo-electron microscopy (cryo-EM) have enabled the determination to near-atomic resolution of macromolecules ranging from large multi-subunit molecular machines to proteins as small as 64 kDa. These advances have revolutionized structural biology by hugely expanding both the range of macromolecules whose structures can be determined, and by providing a description of macromolecular dynamics. Cryo-EM is now poised to similarly transform the discipline of structure-based drug discovery. This article reviews the potential of cryo-EM for drug discovery with reference to protein ligand complex structures determined using this technique.
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Affiliation(s)
- Andreas Boland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Leifu Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
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21
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Leelananda SP, Lindert S. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. J Chem Theory Comput 2017; 13:5131-5145. [PMID: 28949136 DOI: 10.1021/acs.jctc.7b00464] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when medium-resolution maps (6.9 Å) were used. Beginning from an average starting structure root mean square deviation (RMSD) to native of 4.66 Å, our protocol was able to refine the structures to bring the average refined structure RMSD to 1.66 Å when 4 Å density maps were used. The protocol also successfully refined the HIV-1 CTD guided by an experimental 5 Å density map.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
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22
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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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