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Cuervo A, Losana P, Carrascosa JL. Observation of Bacteriophage Ultrastructure by Cryo-Electron Microscopy. Methods Mol Biol 2024; 2734:13-25. [PMID: 38066360 DOI: 10.1007/978-1-0716-3523-0_2] [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] [Indexed: 12/18/2023]
Abstract
Transmission electron microscopy (TEM) is an ideal method to observe and determine the structure of bacteriophages. From early studies by negative staining to the present atomic structure models derived from cryo-TEM, bacteriophage detection, classification, and structure determination have been mostly done by electron microscopy. Although embedding in metal salts has been a routine method for virus observation for many years, the preservation of bacteriophages in a thin layer of fast frozen buffer has proven to be the most convenient preparation method for obtaining images using cryo-electron microscopy (cryo-EM). In this technique, frozen samples are observed at liquid nitrogen temperature, and the images are acquired using different recording media. The incorporation of direct electron detectors has been a fundamental step in achieving atomic resolution images of a number of viruses. These projection images can be numerically combined using different approaches to render a three-dimensional model of the virus. For those viral components exhibiting any symmetry, averaging can nowadays achieve atomic structures in most cases. Image processing methods have also evolved to improve the resolution in asymmetric viral components or regions showing different types of symmetries (symmetry mismatch).
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Affiliation(s)
- Ana Cuervo
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| | - Patricia Losana
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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2
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Herzog AM, Göbel K, Marongiu L, Ruetalo N, Alonso MC, Leischner C, Busch C, Burkard M, Lauer UM, Geurink PP, Knobeloch KP, Schindler M, Fritz G, Venturelli S. Compounds derived from Humulus lupulus inhibit SARS-CoV-2 papain-like protease and virus replication. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 123:155176. [PMID: 37976697 DOI: 10.1016/j.phymed.2023.155176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Selected natural compounds exhibit very good antiviral properties. Especially, the medicinal plant Humulus lupulus (hop) contains several secondary plant metabolites some of which have previously shown antiviral activities. Among them, the prenylated chalcone xanthohumol (XN) demonstrated to be a potent inhibitor of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro). HYPOTHESIS/PURPOSE Following the finding that xanthohumol (XN) is a potent inhibitor of SARS-CoV-2 Mpro, the effect of XN and its major derivatives isoxanthohumol (IXN), 6-prenylnaringenin (6-PN), and 8-prenylnaringenin (8-PN) from hops on SARS-CoV-2 papain-like protease (PLpro) were investigated. STUDY DESIGN The modulatory effect of the hop compounds on PLpro were studied first in silico and then in vitro. In addition, the actual effect of hop compounds on the replication of SARS-CoV-2 in host cells was investigated. METHODS In silico docking analysis was used to predict the binding affinity of hop compounds to the active site of PLpro. A recombinant PLpro was cloned, purified, characterized, and analyzed by small-angle X-ray scattering (SAXS), deISGylation assays, and kinetic analyses. Antiviral activity of hop compounds was assessed using the fluorescently labeled wildtype SARS-CoV-2 (icSARS-CoV-2-mNG) in Caco-2 host cells. RESULTS Our in silico docking suggests that the purified hop compounds bind to the active site of SARS-CoV-2 PLpro blocking the access of its natural substrates. The hop-derived compounds inhibit SARS-CoV-2 PLpro with half maximal inhibitory concentration (IC50) values in the range of 59-162 µM. Furthermore, we demonstrate that XN and 6-PN, in particular, impede viral replication with IC50 values of 3.3 µM and 7.3 µM, respectively. CONCLUSION In addition to the already known inhibition of Mpro by XN, our results show, for the first time, that hop-derived compounds target also SARS-CoV-2 PLpro which is a promising therapeutic target as it contributes to both viral replication and modulation of the immune system. These findings support the possibility to develop new hop-derived antiviral drugs targeting human coronaviruses.
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Affiliation(s)
- Anna-Maria Herzog
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Katharina Göbel
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Luigi Marongiu
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany; Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Christian Leischner
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | | | - Markus Burkard
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine VIII, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, 72076 Tuebingen, Germany.
| | - Günter Fritz
- Department of Cellular Microbiology, University of Hohenheim, 70599 Stuttgart, Germany.
| | - Sascha Venturelli
- Department of Nutritional Biochemistry, University of Hohenheim, 70599 Stuttgart, Germany; Institute of Physiology, Department of Vegetative and Clinical Physiology, University Hospital Tuebingen, 72076 Tuebingen, Germany.
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3
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Ribeiro-Filho HV, Jara GE, Batista FAH, Schleder GR, Costa Tonoli CC, Soprano AS, Guimarães SL, Borges AC, Cassago A, Bajgelman MC, Marques RE, Trivella DBB, Franchini KG, Figueira ACM, Benedetti CE, Lopes-de-Oliveira PS. Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding. PLoS Comput Biol 2022; 18:e1010121. [PMID: 35551296 PMCID: PMC9129039 DOI: 10.1371/journal.pcbi.1010121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/24/2022] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
The nucleocapsid (N) protein of the SARS-CoV-2 virus, the causal agent of COVID-19, is a multifunction phosphoprotein that plays critical roles in the virus life cycle, including transcription and packaging of the viral RNA. To play such diverse roles, the N protein has two globular RNA-binding modules, the N- (NTD) and C-terminal (CTD) domains, which are connected by an intrinsically disordered region. Despite the wealth of structural data available for the isolated NTD and CTD, how these domains are arranged in the full-length protein and how the oligomerization of N influences its RNA-binding activity remains largely unclear. Herein, using experimental data from electron microscopy and biochemical/biophysical techniques combined with molecular modeling and molecular dynamics simulations, we show that, in the absence of RNA, the N protein formed structurally dynamic dimers, with the NTD and CTD arranged in extended conformations. However, in the presence of RNA, the N protein assumed a more compact conformation where the NTD and CTD are packed together. We also provided an octameric model for the full-length N bound to RNA that is consistent with electron microscopy images of the N protein in the presence of RNA. Together, our results shed new light on the dynamics and higher-order oligomeric structure of this versatile protein. The nucleocapsid (N) protein of the SARS-CoV-2 virus plays an essential role in virus particle assembly as it specifically binds to and wraps the virus genomic RNA into a well-organized structure known as the ribonucleoprotein. Understanding how the N protein wraps around the virus RNA is critical for the development of strategies to inhibit virus assembly within host cells. One of the limitations regarding the molecular structure of the ribonucleoprotein, however, is that the N protein has several unstructured and mobile regions that preclude the resolution of its full atomic structure. Moreover, the N protein can form higher-order oligomers, both in the presence and absence of RNA. Here we employed computational methods, supported by experimental data, to simulate the N protein structural dynamics in the absence and presence of RNA. Our data suggest that the N protein forms structurally dynamic dimers in the absence of RNA, with its structured N- and C-terminal domains oriented in extended conformations. In the presence of RNA, however, the N protein assumes a more compact conformation. Our model for the oligomeric structure of the N protein bound to RNA helps to understand how N protein dimers interact to each other to form the ribonucleoprotein.
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Affiliation(s)
- Helder Veras Ribeiro-Filho
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Gabriel Ernesto Jara
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Gabriel Ravanhani Schleder
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Adriana Santos Soprano
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Samuel Leite Guimarães
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Antonio Carlos Borges
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Marcio Chaim Bajgelman
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
| | - Paulo Sergio Lopes-de-Oliveira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- * E-mail: (CEB); (PSLO)
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4
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Behkamal B, Naghibzadeh M, Saberi MR, Tehranizadeh ZA, Pagnani A, Al Nasr K. Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps. Biomolecules 2021; 11:1773. [PMID: 34944417 PMCID: PMC8698881 DOI: 10.3390/biom11121773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 01/15/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4-10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images.
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Affiliation(s)
- Bahareh Behkamal
- Department of Computer Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Mahmoud Naghibzadeh
- Department of Computer Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran;
| | - Mohammad Reza Saberi
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 9177899191, Iran; (M.R.S.); (Z.A.T.)
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad 9177899191, Iran
| | - Zeinab Amiri Tehranizadeh
- Medicinal Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad 9177899191, Iran; (M.R.S.); (Z.A.T.)
| | - Andrea Pagnani
- Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy;
- Italian Institute for Genomic Medicine, IRCCS Candiolo, SP-142, I-10060 Candiolo, Italy
- INFN, Sezione di Torino, I-10125 Torino, Italy
| | - Kamal Al Nasr
- Department of Computer Science, Tennessee State University, Nashville, TN 37209, USA
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5
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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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6
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Costa MGS, Fagnen C, Vénien-Bryan C, Perahia D. A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit). J Chem Inf Model 2020; 60:2419-2423. [DOI: 10.1021/acs.jcim.9b01148] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mauricio G. S. Costa
- Fundacao Oswaldo Cruz, Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900 Rio de Janeiro, Brazil
- Sorbonne Université, UMR 7590, CNRS, Museum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 4 place Jussieu, 75005 Paris, France
- École Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Laboratoire de Biologie et de Pharmacologie Appliquée 61 Av du Président Wilson, 94235 Cachan, France
| | - Charline Fagnen
- Sorbonne Université, UMR 7590, CNRS, Museum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 4 place Jussieu, 75005 Paris, France
- École Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Laboratoire de Biologie et de Pharmacologie Appliquée 61 Av du Président Wilson, 94235 Cachan, France
| | - Catherine Vénien-Bryan
- Sorbonne Université, UMR 7590, CNRS, Museum National d’Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, 4 place Jussieu, 75005 Paris, France
| | - David Perahia
- École Normale Supérieure Paris-Saclay, UMR 8113, CNRS, Laboratoire de Biologie et de Pharmacologie Appliquée 61 Av du Président Wilson, 94235 Cachan, France
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7
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Guerrero-Ferreira RC, Hupfeld M, Nazarov S, Taylor NM, Shneider MM, Obbineni JM, Loessner MJ, Ishikawa T, Klumpp J, Leiman PG. Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells. EMBO J 2019; 38:embj.201899455. [PMID: 30606715 DOI: 10.15252/embj.201899455] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 11/09/2022] Open
Abstract
Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.
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Affiliation(s)
- Ricardo C Guerrero-Ferreira
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mario Hupfeld
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Sergey Nazarov
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nicholas Mi Taylor
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mikhail M Shneider
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Bioengineering, Moscow, Russia
| | - Jagan M Obbineni
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.,Centre for Agricultural Innovations and Advanced Learning (VAIAL), Vellore Institute of Technology, Vellore, India
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Takashi Ishikawa
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Petr G Leiman
- Laboratory of Structural Biology and Biophysics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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Mori T, Kulik M, Miyashita O, Jung J, Tama F, Sugita Y. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning. Structure 2018; 27:161-174.e3. [PMID: 30344106 DOI: 10.1016/j.str.2018.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/22/2018] [Accepted: 09/18/2018] [Indexed: 01/21/2023]
Abstract
Flexible fitting is a powerful technique to build the 3D structures of biomolecules from cryoelectron microscopy (cryo-EM) density maps. One popular method is a cross-correlation coefficient-based approach, where the molecular dynamics (MD) simulation is carried out with the biasing potential that includes the cross-correlation coefficient between the experimental and simulated density maps. Here, we propose efficient parallelization schemes for the calculation of the cross-correlation coefficient to accelerate flexible fitting. Our schemes are tested for small, medium, and large biomolecules using CPU and hybrid CPU + GPU architectures. The scheme for the atomic decomposition MD is suitable for small proteins such as Ca2+-ATPase with the all-atom Go model, while that for the domain decomposition MD is better for larger systems such as ribosome with the all-atom Go or the all-atom explicit solvent models. Our methods allow flexible fitting for various biomolecules with reasonable computational cost. This approach also connects high-resolution structure refinements with investigation of protein structure-function relationship.
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Affiliation(s)
- Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Marta Kulik
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Osamu Miyashita
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Jaewoon Jung
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Florence Tama
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Physics, Graduate School of Science, and Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; RIKEN Center for Biosystems Dynamics Research, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
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9
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Thonghin N, Kargas V, Clews J, Ford RC. Cryo-electron microscopy of membrane proteins. Methods 2018; 147:176-186. [DOI: 10.1016/j.ymeth.2018.04.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022] Open
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10
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Ménade M, Kozlov G, Trempe JF, Pande H, Shenker S, Wickremasinghe S, Li X, Hojjat H, Dicaire MJ, Brais B, McPherson PS, Wong MJH, Young JC, Gehring K. Structures of ubiquitin-like (Ubl) and Hsp90-like domains of sacsin provide insight into pathological mutations. J Biol Chem 2018; 293:12832-12842. [PMID: 29945973 PMCID: PMC6102131 DOI: 10.1074/jbc.ra118.003939] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 01/07/2023] Open
Abstract
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a neurodegenerative disease that is caused by mutations in the SACS gene. The product of this gene is a very large 520-kDa cytoplasmic protein, sacsin, with a ubiquitin-like (Ubl) domain at the N terminus followed by three large sacsin internal repeat (SIRPT) supradomains and C-terminal J and HEPN domains. The SIRPTs are predicted to contain Hsp90-like domains, suggesting a potential chaperone activity. In this work, we report the structures of the Hsp90-like Sr1 domain of SIRPT1 and the N-terminal Ubl domain determined at 1.55- and 2.1-Å resolutions, respectively. The Ubl domain crystallized as a swapped dimer that could be relevant in the context of full-length protein. The Sr1 domain displays the Bergerat protein fold with a characteristic nucleotide-binding pocket, although it binds nucleotides with very low affinity. The Sr1 structure reveals that ARSACS-causing missense mutations (R272H, R272C, and T201K) disrupt protein folding, most likely leading to sacsin degradation. This work lends structural support to the view of sacsin as a molecular chaperone and provides a framework for future studies of this protein.
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Affiliation(s)
- Marie Ménade
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Guennadi Kozlov
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Jean-François Trempe
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Harshit Pande
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Solomon Shenker
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Sihara Wickremasinghe
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Xinlu Li
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Hamed Hojjat
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Marie-Josée Dicaire
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Peter S. McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Michael J. H. Wong
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Jason C. Young
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and
| | - Kalle Gehring
- From the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada and , To whom correspondence should be addressed:
Dept. of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Rm. 473, Montreal, Quebec H3G 0B1, Canada. Tel.:
514-398-7287; E-mail:
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11
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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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12
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Al Nasr K, Yousef F, Jebril R, Jones C. Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem. Molecules 2018; 23:E28. [PMID: 29360779 PMCID: PMC6017786 DOI: 10.3390/molecules23020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 11/17/2022] Open
Abstract
To take advantage of recent advances in genomics and proteomics it is critical that the three-dimensional physical structure of biological macromolecules be determined. Cryo-Electron Microscopy (cryo-EM) is a promising and improving method for obtaining this data, however resolution is often not sufficient to directly determine the atomic scale structure. Despite this, information for secondary structure locations is detectable. De novo modeling is a computational approach to modeling these macromolecular structures based on cryo-EM derived data. During de novo modeling a mapping between detected secondary structures and the underlying amino acid sequence must be identified. DP-TOSS (Dynamic Programming for determining the Topology Of Secondary Structures) is one tool that attempts to automate the creation of this mapping. By treating the correspondence between the detected structures and the structures predicted from sequence data as a constraint graph problem DP-TOSS achieved good accuracy in its original iteration. In this paper, we propose modifications to the scoring methodology of DP-TOSS to improve its accuracy. Three scoring schemes were applied to DP-TOSS and tested: (i) a skeleton-based scoring function; (ii) a geometry-based analytical function; and (iii) a multi-well potential energy-based function. A test of 25 proteins shows that a combination of these schemes can improve the performance of DP-TOSS to solve the topology determination problem for macromolecule proteins.
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Affiliation(s)
- Kamal Al Nasr
- Department of Computer Science, Tennessee State University, Nashville, TN 37209, USA.
| | - Feras Yousef
- Department of Mathematics, The University of Jordan, Amman 11942, Jordan.
| | - Ruba Jebril
- Department of Computer Science, Tennessee State University, Nashville, TN 37209, USA.
| | - Christopher Jones
- Department of Computer Science, Tennessee State University, Nashville, TN 37209, USA.
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13
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Abstract
Transmission Electron Microscopy (TEM) is an ideal method to observe and determine the structure of bacteriophages. From early studies by negative staining to the present atomic structure models derived from cryo-TEM, bacteriophage detection, classification, and structure determination has been mostly done by electron microscopy. Although embedding in metal salts has been a routine method for virus observation for many years, preservation of bacteriophages in a thin layer of fast frozen buffer has proven to be a most convenient preparation method for obtaining images using cryo-electron microscopy (cryo-EM). In this technique, frozen samples are observed at liquid nitrogen temperature and the images are acquired using different recording media. The incorporation of direct electron detectors has been a fundamental step to achieve atomic resolution images of a number of viruses. These projection images can be numerically combined using different approaches to render a three-dimensional model of the virus. For those viral components exhibiting any symmetry, averaging procedures help to render near-atomic resolution structures.
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Affiliation(s)
- Ana Cuervo
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049, Madrid, Spain
| | - José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049, Madrid, Spain.
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14
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Al Nasr K, Jones C, Yousef F, Jebril R. PEM-fitter: A Coarse-Grained Method to Validate Protein Candidate Models. J Comput Biol 2017; 25:21-32. [PMID: 29140718 DOI: 10.1089/cmb.2017.0191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The volumetric images produced by Cryo-Electron Microscopy (cryo-EM) technique are used to model macromolecular assemblies and machines. De novo protein modeling uses these images to computationally model the structure of the molecules. Many candidate conformations are usually generated during the intermediate step. Conventionally, each of these candidates is evaluated by time-consuming approaches such as potential energy. We introduce an initial version of a geometrical screening method that uses the skeleton of the cryo-EM images to evaluate candidate structures. The aim of this method is to reduce the number of native-like candidate conformations and, therefore, reduce the time required for structural evaluation by energy calculations. A test of two datasets was performed. The first dataset contains 10 proteins and shows that our method can successfully detect the correct native structure for the given skeleton among a set of different protein structures. The second dataset contains 12 proteins and shows that our method can filter slightly modified decoy conformations of the same protein. The efficiency of the method is also reported.
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Affiliation(s)
- Kamal Al Nasr
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
| | - Christopher Jones
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
| | - Feras Yousef
- 2 Department of Mathematics, The University of Jordan , Amman, Jordan
| | - Ruba Jebril
- 1 Department of Computer Science, Tennessee State University , Nashville, Tennessee
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15
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Dou H, Burrows DW, Baker ML, Ju T. Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences. Biophys J 2017. [PMID: 28636906 DOI: 10.1016/j.bpj.2017.04.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step. Compared with current methods on both simulated and experimental density maps, our method not only achieves greater accuracy for proteins with large deformations but also runs as fast or faster than many of the other flexible fitting routines.
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Affiliation(s)
- Hang Dou
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri.
| | - Derek W Burrows
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Tao Ju
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, Missouri
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16
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Hoffmann A, Perrier V, Grudinin S. A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717008172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This paper presents a novel fast Fourier transform (FFT)-based exhaustive search method extended to off-grid translational and rotational degrees of freedom. The method combines the advantages of the FFT-based exhaustive search, which samples all the conformations of a system under study on a grid, with a local optimization technique that guarantees to find the nearest optimal off-grid conformation. The method is demonstrated on a fitting problem and can be readily applied to a docking problem. The algorithm first samples a scoring function on a six-dimensional grid of sizeN6using the FFT. This operation has an asymptotic complexity ofO(N6logN). Then, the method performs the off-grid search using a local quadratic approximation of the cost function and the trust-region optimization algorithm. The computation of the quadratic approximation is also accelerated by FFT at the same additional asymptotic cost ofO(N6logN). The method is demonstrated by fitting atomic protein models into several simulated and experimental maps from cryo-electron microscopy. The method is available at https://team.inria.fr/nano-d/software/offgridfit.
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17
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Variability of Protein Structure Models from Electron Microscopy. Structure 2017; 25:592-602.e2. [PMID: 28262392 DOI: 10.1016/j.str.2017.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 01/10/2017] [Accepted: 02/11/2017] [Indexed: 11/23/2022]
Abstract
An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications.
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18
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SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions. J Mol Biol 2017; 429:667-687. [PMID: 28088481 DOI: 10.1016/j.jmb.2017.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 02/06/2023]
Abstract
The radiation-resistant bacterium Deinococcus radiodurans contains two DNA-binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction and manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterised N-terminal extensions. In the case of DrDps1, these extensions have been proposed to be involved in DNA interactions, while in DrDps2, their function has yet to be established. The reported data reveal the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps. The low-resolution small angle X-ray scattering (SAXS) results show that the N-terminal extensions protrude from the spherical shell of both proteins. The SAXS envelope of a truncated form of DrDps1 without the N-terminal extensions appears as a dodecameric sphere, contrasting strongly with the protrusions observed in the full-length models. The effect of iron incorporation into DrDps2 was investigated by static and stopped-flow SAXS measurements, revealing dynamic structural changes upon iron binding and core formation, as reflected by a quick alteration of its radius of gyration. The truncated and full-length versions of DrDps were also compared on the basis of their interaction with DNA to analyse functional roles of the N-terminal extensions. DrDps1 N-terminal protrusions appear to be directly involved with DNA, whilst those from DrDps2 are indirectly associated with DNA binding. Furthermore, detection of DrDps2 in the D. radiodurans membrane fraction suggests that the N-terminus of the protein interacts with the membrane.
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19
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Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release. J Virol 2017; 91:JVI.01795-16. [PMID: 27852845 DOI: 10.1128/jvi.01795-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/02/2016] [Indexed: 11/20/2022] Open
Abstract
The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-like conformation for the procapsid and genome-filled capsids, whereas the putative A-particle and empty capsids that had released the genome had a closed tube-like spike conformation. Between the two conformations, the spikes undergo a significant hinge-like movement that we predicted using a Robetta model of the structure comprising the spike. We conclude that the spike structures likely serve a function during host entry, changing conformation to release the genome, and that the genome may escape from a 5-fold vertex to initiate infection. Finally, the structures illustrate that, similarly to picornaviruses, DWV forms alternate particle conformations implicated in assembly, host attachment, and RNA release. IMPORTANCE Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ectoparasitic mite Varroa destructor have been linked to colony collapse disorder. DWV was purified from infected adult worker bees to pursue biochemical and structural studies that allowed the first glimpse into the conformational changes that may be required during transmission and genome release for DWV.
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20
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Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus. J Virol 2016; 90:9733-9742. [PMID: 27535057 DOI: 10.1128/jvi.01112-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/08/2016] [Indexed: 01/30/2023] Open
Abstract
Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. IMPORTANCE Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time.
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21
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DiMaio F, Chiu W. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps. Methods Enzymol 2016; 579:255-76. [PMID: 27572730 PMCID: PMC5103630 DOI: 10.1016/bs.mie.2016.06.003] [Citation(s) in RCA: 26] [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] [Indexed: 12/03/2022]
Abstract
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.
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Affiliation(s)
- F DiMaio
- University of Washington, Seattle, WA, United States; Institute for Protein Design, University of Washington, Seattle, WA, United States.
| | - W Chiu
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, United States.
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22
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Goh BC, Hadden JA, Bernardi RC, Singharoy A, McGreevy R, Rudack T, Cassidy CK, Schulten K. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes. Annu Rev Biophys 2016; 45:253-78. [PMID: 27145875 DOI: 10.1146/annurev-biophys-062215-011113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed.
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Affiliation(s)
- Boon Chong Goh
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Jodi A Hadden
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Rafael C Bernardi
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Abhishek Singharoy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Ryan McGreevy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Till Rudack
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - C Keith Cassidy
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801;
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23
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McGreevy R, Teo I, Singharoy A, Schulten K. Advances in the molecular dynamics flexible fitting method for cryo-EM modeling. Methods 2016; 100:50-60. [PMID: 26804562 PMCID: PMC4848153 DOI: 10.1016/j.ymeth.2016.01.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
Molecular Dynamics Flexible Fitting (MDFF) is an established technique for fitting all-atom structures of molecules into corresponding cryo-electron microscopy (cryo-EM) densities. The practical application of MDFF is simple but requires a user to be aware of and take measures against a variety of possible challenges presented by each individual case. Some of these challenges arise from the complexity of a molecular structure or the limited quality of available structural models and densities to be interpreted, while others stem from the intricacies of MDFF itself. The current article serves as an overview of the strategies that have been developed since MDFF's inception to overcome common challenges and successfully perform MDFF simulations.
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Affiliation(s)
- Ryan McGreevy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA
| | - Ivan Teo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abhishek Singharoy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA
| | - Klaus Schulten
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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24
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Furukawa Y, Anzai I, Akiyama S, Imai M, Cruz FJC, Saio T, Nagasawa K, Nomura T, Ishimori K. Conformational Disorder of the Most Immature Cu, Zn-Superoxide Dismutase Leading to Amyotrophic Lateral Sclerosis. J Biol Chem 2016; 291:4144-55. [PMID: 26694608 PMCID: PMC4759189 DOI: 10.1074/jbc.m115.683763] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 12/09/2015] [Indexed: 01/15/2023] Open
Abstract
Misfolding of Cu,Zn-superoxide dismutase (SOD1) is a pathological change in the familial form of amyotrophic lateral sclerosis caused by mutations in the SOD1 gene. SOD1 is an enzyme that matures through the binding of copper and zinc ions and the formation of an intramolecular disulfide bond. Pathogenic mutations are proposed to retard the post-translational maturation, decrease the structural stability, and hence trigger the misfolding of SOD1 proteins. Despite this, a misfolded and potentially pathogenic conformation of immature SOD1 remains obscure. Here, we show significant and distinct conformational changes of apoSOD1 that occur only upon reduction of the intramolecular disulfide bond in solution. In particular, loop regions in SOD1 lose their restraint and become significantly disordered upon dissociation of metal ions and reduction of the disulfide bond. Such drastic changes in the solution structure of SOD1 may trigger misfolding and fibrillar aggregation observed as pathological changes in the familial form of amyotrophic lateral sclerosis.
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Affiliation(s)
- Yoshiaki Furukawa
- From the Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522,
| | - Itsuki Anzai
- From the Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, Okazaki 444-8585, Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8585
| | - Mizue Imai
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, and
| | - Fatima Joy C Cruz
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, and
| | - Tomohide Saio
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, and Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kenichi Nagasawa
- From the Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522
| | - Takao Nomura
- From the Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University, Yokohama 223-8522
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, and Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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25
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Alamo L, Qi D, Wriggers W, Pinto A, Zhu J, Bilbao A, Gillilan RE, Hu S, Padrón R. Conserved Intramolecular Interactions Maintain Myosin Interacting-Heads Motifs Explaining Tarantula Muscle Super-Relaxed State Structural Basis. J Mol Biol 2016; 428:1142-1164. [PMID: 26851071 DOI: 10.1016/j.jmb.2016.01.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 01/15/2016] [Accepted: 01/25/2016] [Indexed: 01/08/2023]
Abstract
Tarantula striated muscle is an outstanding system for understanding the molecular organization of myosin filaments. Three-dimensional reconstruction based on cryo-electron microscopy images and single-particle image processing revealed that, in a relaxed state, myosin molecules undergo intramolecular head-head interactions, explaining why head activity switches off. The filament model obtained by rigidly docking a chicken smooth muscle myosin structure to the reconstruction was improved by flexibly fitting an atomic model built by mixing structures from different species to a tilt-corrected 2-nm three-dimensional map of frozen-hydrated tarantula thick filament. We used heavy and light chain sequences from tarantula myosin to build a single-species homology model of two heavy meromyosin interacting-heads motifs (IHMs). The flexibly fitted model includes previously missing loops and shows five intramolecular and five intermolecular interactions that keep the IHM in a compact off structure, forming four helical tracks of IHMs around the backbone. The residues involved in these interactions are oppositely charged, and their sequence conservation suggests that IHM is present across animal species. The new model, PDB 3JBH, explains the structural origin of the ATP turnover rates detected in relaxed tarantula muscle by ascribing the very slow rate to docked unphosphorylated heads, the slow rate to phosphorylated docked heads, and the fast rate to phosphorylated undocked heads. The conservation of intramolecular interactions across animal species and the presence of IHM in bilaterians suggest that a super-relaxed state should be maintained, as it plays a role in saving ATP in skeletal, cardiac, and smooth muscles.
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Affiliation(s)
- Lorenzo Alamo
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
| | - Dan Qi
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, 5115 Hampton Boulevard, Norfolk, VA 23529, USA.
| | - Antonio Pinto
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
| | - Jingui Zhu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
| | - Aivett Bilbao
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
| | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source, 161 Wilson Laboratory, Synchrotron Drive, Ithaca, NY 14853, USA.
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.
| | - Raúl Padrón
- Centro de Biología Estructural, Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas 1020A, Venezuela.
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26
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Rakesh R, Srinivasan N. Improving the Accuracy of Fitted Atomic Models in Cryo-EM Density Maps of Protein Assemblies Using Evolutionary Information from Aligned Homologous Proteins. Methods Mol Biol 2016; 1415:193-209. [PMID: 27115634 DOI: 10.1007/978-1-4939-3572-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cryo-Electron Microscopy (cryo-EM) has become an important technique to obtain structural insights into large macromolecular assemblies. However the resolution of the density maps do not allow for its interpretation at atomic level. Hence they are combined with high resolution structures along with information from other experimental or bioinformatics techniques to obtain pseudo-atomic models. Here, we describe the use of evolutionary conservation of residues as obtained from protein structures and alignments of homologous proteins to detect errors in the fitting of atomic structures as well as improve accuracy of the protein-protein interfacial regions in the cryo-EM density maps.
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Affiliation(s)
- Ramachandran Rakesh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
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27
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Manhas A, Kumar SP, Jha PC. Molecular modeling of Plasmodium falciparum peptide deformylase and structure-based pharmacophore screening for inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra01071g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The role of metal coordination geometry and actinonin (inhibitor) binding was examined to develop pharmacophore-based inhibitor design strategy forPlasmodium falciparumpeptide deformylase.
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Affiliation(s)
- Anu Manhas
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | | | - Prakash Chandra Jha
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
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28
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Bettadapura R, Rasheed M, Vollrath A, Bajaj C. PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps. PLoS Comput Biol 2015; 11:e1004289. [PMID: 26469938 PMCID: PMC4607507 DOI: 10.1371/journal.pcbi.1004289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/14/2015] [Indexed: 11/30/2022] Open
Abstract
There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible structural model of the molecule at the best achievable resolution, and without any missing gaps, one typically aligns (match and fits) the atomistic structure model with the 3D EM map. We discuss a new algorithm and generalized framework, named PF(2) fit (Polar Fast Fourier Fitting) for the best possible structural alignment of atomistic structures with 3D EM. While PF(2) fit enables only a rigid, six dimensional (6D) alignment method, it augments prior work on 6D X-ray structure and 3D EM alignment in multiple ways: Scoring. PF(2) fit includes a new scoring scheme that, in addition to rewarding overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps between the volumes complementary to them. We quantitatively demonstrate how this new complementary scoring scheme improves upon existing approaches. PF(2) fit also includes two scoring functions, the non-uniform exterior penalty and the skeleton-secondary structure score, and implements the scattering potential score as an alternative to traditional Gaussian blurring. Search. PF(2) fit utilizes a fast polar Fourier search scheme, whose main advantage is the ability to search over uniformly and adaptively sampled subsets of the space of rigid-body motions. PF(2) fit also implements a new reranking search and scoring methodology that considerably improves alignment metrics in results obtained from the initial search.
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Affiliation(s)
- Radhakrishna Bettadapura
- Radhakrishna Bettadapura Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Muhibur Rasheed
- Muhibur Rasheed Computational Visualization Center/Department of Mechanical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Antje Vollrath
- Antje Vollrath Institut Computational Mathematics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Chandrajit Bajaj
- Chandrajit Bajaj Computational Visualization Center/Institute of Computational Engineering & Sciences/Department of Computer Science, University of Texas at Austin, Austin, Texas, United States of America
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29
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Farabella I, Vasishtan D, Joseph AP, Pandurangan AP, Sahota H, Topf M. TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits. J Appl Crystallogr 2015; 48:1314-1323. [PMID: 26306092 PMCID: PMC4520291 DOI: 10.1107/s1600576715010092] [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: 11/05/2014] [Accepted: 05/24/2015] [Indexed: 12/21/2022] Open
Abstract
TEMPy is an object-oriented Python library that provides the means to validate density fits in electron microscopy reconstructions. This article highlights several features of particular interest for this purpose and includes some customized examples. Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed. TEMPy (template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature of TEMPy helps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.
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Affiliation(s)
- Irene Farabella
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford OX3 7BN, UK
| | - Agnel Praveen Joseph
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell , Didcot, Oxon OX11 0QX, UK
| | - Arun Prasad Pandurangan
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London , Malet street, London WC1E 7HX, UK
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30
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López-Blanco JR, Chacón P. Structural modeling from electron microscopy data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- José Ramón López-Blanco
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
| | - Pablo Chacón
- Department of Biological Physical Chemistry; Rocasolano Physical Chemistry Institute, CSIC; Madrid Spain
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31
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Vashisth H, Skiniotis G, Brooks CL. Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chem Rev 2014; 114:3353-65. [PMID: 24446720 PMCID: PMC3983124 DOI: 10.1021/cr4005988] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Harish Vashisth
- Department
of Chemical Engineering, University of New
Hampshire, Durham, New Hampshire 03824, United States
| | - Georgios Skiniotis
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles Lee Brooks
- Life Sciences Institute, Department
of Biological Chemistry, and
Biophysics Program, and Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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32
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Kulkarni K, Zhang Z, Chang L, Yang J, da Fonseca PCA, Barford D. Building a pseudo-atomic model of the anaphase-promoting complex. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2236-43. [PMID: 24189235 PMCID: PMC3817697 DOI: 10.1107/s0907444913018593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/04/2013] [Indexed: 11/10/2022]
Abstract
The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14-15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.
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Affiliation(s)
- Kiran Kulkarni
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
| | - Ziguo Zhang
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
| | - Leifu Chang
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
| | - Jing Yang
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
| | - Paula C. A. da Fonseca
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
| | - David Barford
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, England
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33
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iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. J Struct Biol 2013; 184:261-70. [PMID: 23999189 DOI: 10.1016/j.jsb.2013.08.010] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 12/31/2022]
Abstract
Here, we employed the collective motions extracted from Normal Mode Analysis (NMA) in internal coordinates (torsional space) for the flexible fitting of atomic-resolution structures into electron microscopy (EM) density maps. The proposed methodology was validated using a benchmark of simulated cases, highlighting its robustness over the full range of EM resolutions and even over coarse-grained representations. A systematic comparison with other methods further showcased the advantages of this proposed methodology, especially at medium to lower resolutions. Using this method, computational costs and potential overfitting problems are naturally reduced by constraining the search in low-frequency NMA space, where covalent geometry is implicitly maintained. This method also effectively captures the macromolecular changes of a representative set of experimental test cases. We believe that this novel approach will extend the currently available EM hybrid methods to the atomic-level interpretation of large conformational changes and their functional implications.
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34
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Vashisth H, Skiniotis G, Brooks CL. Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. J Phys Chem B 2013; 117:3738-46. [PMID: 23506287 DOI: 10.1021/jp3126297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Flexible fitting computational algorithms are often useful to interpret low-resolution maps of many macromolecular complexes generated by electron microscopy (EM) imaging. One such atomistic simulation technique is molecular dynamics flexible fitting (MDFF), which has been widely applied to generate structural models of large ribonucleoprotein assemblies such as the ribosome. We have previously shown that MDFF simulations of globular proteins are sensitive to the resolution of the target EM map and the strength of restraints used to preserve the secondary structure elements during fitting (Vashisth, H.; et al. Structure 2012, 20, 1453-1462). In this work, we aim to systematically examine the quality of structural models of various nucleic acids obtained via MDFF by varying the map resolution and the strength of structural restraints. We also demonstrate how an enhanced conformational sampling technique for proteins, temperature-accelerated molecular dynamics (TAMD), can be combined with MDFF for the structural refinement of nucleic acids in EM maps. Finally, we also demonstrate application of TAMD-assisted MDFF (TAMDFF) on a RNA/protein complex and suggest that TAMDFF is a viable strategy for enhanced conformational fitting in target maps of ribonucleoprotein complexes.
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Affiliation(s)
- Harish Vashisth
- Department of Chemistry and Biophysics Program, Department of Biological Chemistry, and Biophysics Program, University of Michigan , Ann Arbor, Michigan, USA
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35
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Vashisth H, Skiniotis G, Brooks CL. Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps. Structure 2013; 20:1453-62. [PMID: 22958641 DOI: 10.1016/j.str.2012.08.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/30/2012] [Accepted: 08/06/2012] [Indexed: 01/14/2023]
Abstract
For a variety of problems in structural biology, low-resolution maps generated by electron microscopy imaging are often interpreted with the help of various flexible-fitting computational algorithms. In this work, we systematically analyze the quality of final models of various proteins obtained via molecular dynamics flexible fitting (MDFF) by varying the map-resolution, strength of structural restraints, and the steering forces. We find that MDFF can be extended to understand conformational changes in lower-resolution maps if larger structural restraints and lower steering forces are used to prevent overfitting. We further show that the capabilities of MDFF can be extended by combining it with an enhanced conformational sampling method, temperature-accelerated molecular dynamics (TAMD). Specifically, either TAMD can be used to generate better starting configurations for MDFF fitting or TAMD-assisted MDFF (TAMDFF) can be performed to accelerate conformational search in atomistic simulations.
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Affiliation(s)
- Harish Vashisth
- Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Chem 2006, Ann Arbor, MI 48109, USA.
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36
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Svensson L, Sintorn IM. A Probabilistic Template Model for Finding Macromolecules in MET Volume Images. PATTERN RECOGNITION AND IMAGE ANALYSIS 2013. [DOI: 10.1007/978-3-642-38628-2_101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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37
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Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure 2012; 20:205-14. [PMID: 22325770 PMCID: PMC3328769 DOI: 10.1016/j.str.2011.12.014] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/29/2011] [Accepted: 12/29/2011] [Indexed: 11/10/2022]
Abstract
This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.
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Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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38
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Wriggers W. Conventions and workflows for using Situs. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:344-51. [PMID: 22505255 PMCID: PMC3322594 DOI: 10.1107/s0907444911049791] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/21/2011] [Indexed: 01/11/2023]
Abstract
Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs to be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.
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Affiliation(s)
- Willy Wriggers
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA.
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39
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Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps. J Struct Biol 2012; 177:520-31. [DOI: 10.1016/j.jsb.2011.10.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Revised: 10/22/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
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40
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Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol 2012; 857:331-350. [PMID: 22323229 DOI: 10.1007/978-1-61779-588-6_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera.
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Affiliation(s)
- Keren Lasker
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
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41
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Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, Schulten K. Symmetry-restrained flexible fitting for symmetric EM maps. Structure 2011; 19:1211-8. [PMID: 21893283 DOI: 10.1016/j.str.2011.07.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/21/2011] [Accepted: 07/28/2011] [Indexed: 01/25/2023]
Abstract
Many large biological macromolecules have inherent structural symmetry, being composed of a few distinct subunits, repeated in a symmetric array. These complexes are often not amenable to traditional high-resolution structural determination methods, but can be imaged in functionally relevant states using cryo-electron microscopy (cryo-EM). A number of methods for fitting atomic-scale structures into cryo-EM maps have been developed, including the molecular dynamics flexible fitting (MDFF) method. However, quality and resolution of the cryo-EM map are the major determinants of a method's success. In order to incorporate knowledge of structural symmetry into the fitting procedure, we developed the symmetry-restrained MDFF method. The new method adds to the cryo-EM map-derived potential further restraints on the allowed conformations of a complex during fitting, thereby improving the quality of the resultant structure. The benefit of using symmetry-based restraints during fitting, particularly for medium to low-resolution data, is demonstrated for three different systems.
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Affiliation(s)
- Kwok-Yan Chan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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42
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Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol 2011; 179:269-78. [PMID: 21963794 DOI: 10.1016/j.jsb.2011.09.006] [Citation(s) in RCA: 428] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/16/2011] [Accepted: 09/18/2011] [Indexed: 02/02/2023]
Abstract
Structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. Here we present the integration of several modeling tools into UCSF Chimera. These include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.
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Affiliation(s)
- Zheng Yang
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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43
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The structural biology of ryanodine receptors. SCIENCE CHINA-LIFE SCIENCES 2011; 54:712-24. [DOI: 10.1007/s11427-011-4198-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Accepted: 05/30/2011] [Indexed: 10/18/2022]
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44
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Woetzel N, Lindert S, Stewart PL, Meiler J. BCL::EM-Fit: rigid body fitting of atomic structures into density maps using geometric hashing and real space refinement. J Struct Biol 2011; 175:264-76. [PMID: 21565271 DOI: 10.1016/j.jsb.2011.04.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 04/28/2011] [Accepted: 04/28/2011] [Indexed: 11/30/2022]
Abstract
Cryo-electron microscopy (cryoEM) can visualize large macromolecular assemblies at resolutions often below 10Å and recently as good as 3.8-4.5 Å. These density maps provide important insights into the biological functioning of molecular machineries such as viruses or the ribosome, in particular if atomic-resolution crystal structures or models of individual components of the assembly can be placed into the density map. The present work introduces a novel algorithm termed BCL::EM-Fit that accurately fits atomic-detail structural models into medium resolution density maps. In an initial step, a "geometric hashing" algorithm provides a short list of likely placements. In a follow up Monte Carlo/Metropolis refinement step, the initial placements are optimized by their cross correlation coefficient. The resolution of density maps for a reliable fit was determined to be 10 Å or better using tests with simulated density maps. The algorithm was applied to fitting of capsid proteins into an experimental cryoEM density map of human adenovirus at a resolution of 6.8 and 9.0 Å, and fitting of the GroEL protein at 5.4 Å. In the process, the handedness of the cryoEM density map was unambiguously identified. The BCL::EM-Fit algorithm offers an alternative to the established Fourier/Real space fitting programs. BCL::EM-Fit is free for academic use and available from a web server or as downloadable binary file at http://www.meilerlab.org.
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Affiliation(s)
- Nils Woetzel
- Department of Chemistry, Vanderbilt University, TN 37212, USA
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45
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Beck M, Topf M, Frazier Z, Tjong H, Xu M, Zhang S, Alber F. Exploring the spatial and temporal organization of a cell's proteome. J Struct Biol 2011; 173:483-96. [PMID: 21094684 PMCID: PMC3784337 DOI: 10.1016/j.jsb.2010.11.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome's spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome's organization into a spatially explicit, predictive model of cellular processes.
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Affiliation(s)
- Martin Beck
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Maya Topf
- Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Zachary Frazier
- Program in Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 413E, Los Angeles, CA 90068, USA
| | - Harianto Tjong
- Program in Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 413E, Los Angeles, CA 90068, USA
| | - Min Xu
- Program in Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 413E, Los Angeles, CA 90068, USA
| | - Shihua Zhang
- Program in Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 413E, Los Angeles, CA 90068, USA
| | - Frank Alber
- Program in Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 413E, Los Angeles, CA 90068, USA
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Vasishtan D, Topf M. Scoring functions for cryoEM density fitting. J Struct Biol 2011; 174:333-43. [PMID: 21296161 DOI: 10.1016/j.jsb.2011.01.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/22/2011] [Accepted: 01/31/2011] [Indexed: 10/18/2022]
Abstract
In fitting atomic structures into cryoEM density maps of macromolecular assemblies, the cross-correlation function (CCF) is the most prevalent method of scoring the goodness-of-fit. However, there are still many possible, less studied ways of scoring fits. In this paper, we introduce four scores new to cryoEM fitting and compare their performance to three known scores. Our benchmark consists of (a) 4 protein assemblies with simulated maps at 5-20 Å resolution, including the heptameric ring of GroEL; and (b) 4 experimental maps of GroEL at ∼6-23 Å resolution with corresponding fitted atomic models. We perturb each fit 1000 times and assess each new fit with each score. The correlation between a score and the Cα RMSD of each fit from the "correctly" fitted structure shows that the CCF is one of the best scores, but in certain situations could be augmented or even replaced by other scores. For instance, our implementation of a score based on mutual information outperforms or is comparable to the CCF in almost all test cases, and our new "envelope score" works as well as the CCF at sub-nanometer resolution but is an order of magnitude faster to calculate. The results also suggest that the width of the Gaussian function used to blur the atomic structure into a density map can significantly affect the fitting process. Finally, we show that our score-testing method, when combined with the Laplacian CCF or the mutual information scores, can be used as a statistical tool for improving cryoEM density fitting.
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Affiliation(s)
- Daven Vasishtan
- Institute of Structural and Molecular Biology, Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London WC1E7HX, UK
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Tang Y, Pan X, Chen Y, Tai PC, Sui SF. Dimeric SecA couples the preprotein translocation in an asymmetric manner. PLoS One 2011; 6:e16498. [PMID: 21304597 PMCID: PMC3029384 DOI: 10.1371/journal.pone.0016498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 12/20/2010] [Indexed: 12/01/2022] Open
Abstract
The Sec translocase mediates the post-translational translocation of a number of preproteins through the inner membrane in bacteria. In the initiatory translocation step, SecB targets the preprotein to the translocase by specific interaction with its receptor SecA. The latter is the ATPase of Sec translocase which mediates the post-translational translocation of preprotein through the protein-conducting channel SecYEG in the bacterial inner membrane. We examined the structures of Escherichia coli Sec intermediates in solution as visualized by negatively stained electron microscopy in order to probe the oligomeric states of SecA during this process. The symmetric interaction pattern between the SecA dimer and SecB becomes asymmetric in the presence of proOmpA, and one of the SecA protomers predominantly binds to SecB/proOmpA. Our results suggest that during preprotein translocation, the two SecA protomers are different in structure and may play different roles.
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Affiliation(s)
- Ying Tang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xijiang Pan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yong Chen
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Phang C. Tai
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Sen-Fang Sui
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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48
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Birmanns S, Rusu M, Wriggers W. Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes. J Struct Biol 2010; 173:428-35. [PMID: 21078392 DOI: 10.1016/j.jsb.2010.11.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/31/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
Abstract
We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colors tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colors. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0.
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Affiliation(s)
- Stefan Birmanns
- University of Texas School of Biomedical Informatics at Houston, 7000 Fannin St. UCT 600, Houston, TX 77030, USA.
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The amino-terminal disease hotspot of ryanodine receptors forms a cytoplasmic vestibule. Nature 2010; 468:585-8. [DOI: 10.1038/nature09471] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 09/03/2010] [Indexed: 11/08/2022]
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Wriggers W, Alamo L, Padrón R. Matching structural densities from different biophysical origins with gain and bias. J Struct Biol 2010; 173:445-50. [PMID: 20854911 DOI: 10.1016/j.jsb.2010.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 09/09/2010] [Accepted: 09/14/2010] [Indexed: 11/26/2022]
Abstract
The registration of volumetric structures in real space involves geometric and density transformations that align a target map and a probe map in the best way possible. Many computational docking strategies exist for finding the geometric transformations that superimpose maps, but the problem of finding an optimal density transformation, for the purposes of difference calculations or segmentation, has received little attention in the literature. We report results based on simulated and experimental electron microscopy maps, showing that a single scale factor (gain) may be insufficient when it comes to minimizing the density discrepancy between an aligned target and probe. We propose an affine transformation, with gain and bias, that is parameterized by known surface isovalues and by an interactive centering of the "cancellation peak" in the surface thresholded difference map histogram. The proposed approach minimizes discrepancies across a wide range of interior densities. Owing to having only two parameters, it avoids overfitting and requires only minimal knowledge of the probe and target maps. The linear transformation also preserves phases and relative amplitudes in Fourier space. The histogram matching strategy was implemented in the newly revised volhist tool of the Situs package, version 2.6.
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Affiliation(s)
- Willy Wriggers
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10065, USA.
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