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Díaz-Valle A, Falcón-González JM, Carrillo-Tripp M. Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis. Int J Mol Sci 2019; 20:E5966. [PMID: 31783519 PMCID: PMC6928768 DOI: 10.3390/ijms20235966] [Citation(s) in RCA: 6] [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: 10/12/2019] [Revised: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 02/06/2023] Open
Abstract
The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein-protein interaction, decreasing the absolute value of the binding free energy, without altering the protein's secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid's thermodynamic properties.
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Affiliation(s)
- Armando Díaz-Valle
- Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, C.P. 66600 Apodaca, Nuevo León, Mexico;
| | - José Marcos Falcón-González
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato, Instituto Politécnico Nacional, Av. Mineral de Valenciana No. 200, Col. Fraccionamiento Industrial Puerto Interior, C.P. 36275 Silao de la Victoria, Guanajuato, Mexico;
| | - Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, C.P. 66600 Apodaca, Nuevo León, Mexico;
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Ho PT, Montiel-Garcia DJ, Wong JJ, Carrillo-Tripp M, Brooks CL, Johnson JE, Reddy VS. VIPERdb: A Tool for Virus Research. Annu Rev Virol 2019; 5:477-488. [PMID: 30265627 DOI: 10.1146/annurev-virology-092917-043405] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.
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Affiliation(s)
- Phuong T Ho
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA;
| | - Daniel J Montiel-Garcia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA; .,Department of Information Technologies, Instituto Tecnológico Superior de Irapuato, 36300 Irapuato, Guanajuato, Mexico
| | - Jonathan J Wong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA;
| | - Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, 66600 Apodaca, Nuevo León, Mexico
| | - Charles L Brooks
- Department of Computational Medicine and Bioinformatics, Department of Chemistry, and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA;
| | - Vijay S Reddy
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA;
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Alonzo-Velázquez JL, Botello-Rionda S, Herrera-Guzmán R, Carrillo-Tripp M. CapsidMesh: Atomic-detail structured mesh representation of icosahedral viral capsids and the study of their mechanical properties. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2018; 34:e2991. [PMID: 29603677 DOI: 10.1002/cnm.2991] [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: 10/27/2017] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Viruses are the most abundant pathogens affecting all forms of life. A major component of a virus is a protein shell, known as the viral capsid, that encapsulates the genomic material. The fundamental functions of the capsid are to protect and transport the viral genome and recognize the host cell. Descriptions of this macromolecular complex have been proposed at different scales of approximation. Here, we introduce a methodology to generate a structured volumetric mesh of icosahedral viral capsids (CapsidMesh) based on the atomic positions of their constituents. Material properties of the capsid proteins can be set on every mesh element individually. Hence, we have control over all levels of protein structure (atoms, amino acids, subunits, oligomers, and capsid). The CapsidMesh models are suitable for numerical simulations and analysis of a physical process using a third-party package. In particular, we used our methodology to generate a CapsidMesh of several capsids previously characterized by atomic force microscopy experiments and then simulated the mechanical nanoindentation through the finite element method. By fitting to the experimental linear elastic response, we estimated the elastic modulus and mechanical stresses produced on the capsids. Our results show that the atomic detail of the CapsidMesh is sufficient to reproduce anisotropic properties of the particle.
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Affiliation(s)
- José Luis Alonzo-Velázquez
- Ciencias de la Computación, Centro de Investigación en Matemáticas, A.C., Jalisco S/N, Col. Valenciana,, C.P. 36023, Guanajuato, Guanajuato, México
| | - Salvador Botello-Rionda
- Ciencias de la Computación, Centro de Investigación en Matemáticas, A.C., Jalisco S/N, Col. Valenciana,, C.P. 36023, Guanajuato, Guanajuato, México
| | - Rafael Herrera-Guzmán
- Ciencias de la Computación, Centro de Investigación en Matemáticas, A.C., Jalisco S/N, Col. Valenciana,, C.P. 36023, Guanajuato, Guanajuato, México
| | - Mauricio Carrillo-Tripp
- Laboratorio de la Diversidad Biomolecular, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT,, C.P. 66600, Apodaca, Nuevo León, México
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Abstract
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This article presents a statistical-ensemble-based approach that samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations. Further, instead of using larger capsomers (trimers, pentamers) as building blocks, we allow all possible subassemblies to bind in all possible combinations. We represent the resulting assembly graph in two different ways: First, we use the Wilcoxon signed-rank measure to compare the distributions of binding free energy computed on the sampled conformations to predict likely pathways. Second, we represent chemical equilibrium aspects of the transitions as a Bayesian Factor graph where both associations and dissociations are modeled based on concentrations and the binding free energies. We applied these protocols on the feline panleukopenia virus and the Nudaurelia capensis virus. Results from these experiments showed a significant departure from those that one would obtain if only the static configurations of the proteins were considered. Hence, we establish the importance of an uncertainty-aware protocol for pathway analysis, and we provide a statistical framework as an important first step toward assembly pathway prediction with high statistical confidence.
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Affiliation(s)
- Nathan Clement
- Department of Computer Science, The University of Texas at Austin , Austin, Texas
| | - Muhibur Rasheed
- Department of Computer Science, The University of Texas at Austin , Austin, Texas
| | - Chandrajit Lal Bajaj
- Department of Computer Science, The University of Texas at Austin , Austin, Texas
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Clement N, Rasheed M, Bajaj C. Uncertainty Quantified Computational Analysis of the Energetics of Virus Capsid Assembly. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2016; 2016:1706-1713. [PMID: 28936368 PMCID: PMC5604467 DOI: 10.1109/bibm.2016.7822775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Most of the existing research in assembly pathway prediction/analysis of viral capsids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire capsid. This assumption does not take into account the conformational changes of the constituent proteins as well as minor changes to the binding interfaces that continue throughout the assembly process until stabilization. This paper presents a statistical-ensemble based approach which samples the configurational space for each monomer with the relative local orientation between monomers, to capture the uncertainties in binding and conformations. Furthermore, instead of using larger capsomers (trimers, pentamers) as building blocks, we allow all possible subassemblies to bind in all possible combinations. We represent the resulting assembly graph in two different ways: First, we use the Wilcoxon signed rank measure to compare the distributions of binding free energy computed on the sampled conformations to predict likely pathways. Second, we represent chemical equilibrium aspects of the transitions as a Bayesian Factor graph where both associations and dissociations are modeled based on concentrations and the binding free energies. We applied these protocols on the feline panleukopenia virus and the Nudaurelia capensis virus. Results from these experiments showed significant departure from those one would obtain if only the static configurations of the proteins were considered. Hence, we establish the importance of an uncertainty-aware protocol for pathway analysis, and provide a statistical framework as an important first step towards assembly pathway prediction with high statistical confidence.
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Affiliation(s)
- N Clement
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
| | - M Rasheed
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
| | - C Bajaj
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712
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Carrillo-Tripp M, Montiel-García DJ, Brooks CL, Reddy VS. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. J Struct Biol 2015; 190:47-55. [PMID: 25697908 DOI: 10.1016/j.jsb.2015.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/20/2015] [Accepted: 02/10/2015] [Indexed: 11/16/2022]
Abstract
Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.
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Affiliation(s)
- Mauricio Carrillo-Tripp
- Biomolecular Diversity Laboratory, Unidad de Genómica Avanzada (Langebio) CINVESTAV, Irapuato, Mexico.
| | | | - Charles L Brooks
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI, USA; Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Vijay S Reddy
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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Rasheed M, Bajaj C. Highly Symmetric and Congruently Tiled Meshes for Shells and Domes. PROCEDIA ENGINEERING 2015; 124:213-225. [PMID: 27563368 PMCID: PMC4994975 DOI: 10.1016/j.proeng.2015.10.134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We describe the generation of all possible shell and dome shapes that can be uniquely meshed (tiled) using a single type of mesh face (tile), and following a single meshing (tiling) rule that governs the mesh (tile) arrangement with maximal vertex, edge and face symmetries. Such tiling arrangements or congruently tiled meshed shapes, are frequently found in chemical forms (fullerenes or Bucky balls, crystals, quasi-crystals, virus nano shells or capsids), and synthetic shapes (cages, sports domes, modern architectural facades). Congruently tiled meshes are both aesthetic and complete, as they support maximal mesh symmetries with minimal complexity and possess simple generation rules. Here, we generate congruent tilings and meshed shape layouts that satisfy these optimality conditions. Further, the congruent meshes are uniquely mappable to an almost regular 3D polyhedron (or its dual polyhedron) and which exhibits face-transitive (and edge-transitive) congruency with at most two types of vertices (each type transitive to the other). The family of all such congruently meshed polyhedra create a new class of meshed shapes, beyond the well-studied regular, semi-regular and quasi-regular classes, and their duals (platonic, Catalan and Johnson). While our new mesh class is infinite, we prove that there exists a unique mesh parametrization, where each member of the class can be represented by two integer lattice variables, and moreover efficiently constructable.
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Affiliation(s)
- Muhibur Rasheed
- Computational Visualization Center, Department of Computer Science and Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78731, USA
| | - Chandrajit Bajaj
- Computational Visualization Center, Department of Computer Science and Institute of Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78731, USA
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Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL, Reddy VS. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res 2008; 37:D436-42. [PMID: 18981051 PMCID: PMC2686430 DOI: 10.1093/nar/gkn840] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb(2), we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Phi-Psi (Phi-Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence-structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.
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Affiliation(s)
- Mauricio Carrillo-Tripp
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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