Minimal Design Principles for Icosahedral Virus Capsids

ACS Nano ◽  
2021 ◽  
Author(s):  
Manuel Martín-Bravo ◽  
Jose M. Gomez Llorente ◽  
Javier Hernández-Rojas ◽  
David J. Wales
Keyword(s):  
Design Principles ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Minimal Design

A Dissection of the Protein–Protein Interfaces in Icosahedral Virus Capsids

2007 ◽  
Vol 367 (2) ◽  
pp. 574-590 ◽  
Author(s):  
Ranjit Prasad Bahadur ◽  
Francis Rodier ◽  
Joël Janin
Keyword(s):  
Protein Interfaces ◽  
Virus Capsids ◽  
Icosahedral Virus

scholarly journals Dynamics of Icosahedral Viruses: What Does Viral Tiling Theory Teach Us?

2008 ◽  
Vol 9 (3-4) ◽  
pp. 211-220 ◽  
Author(s):  
Kasper Peeters ◽  
Anne Taormina
Keyword(s):  
Vibrational Spectra ◽  
Coarse Graining ◽  
Point Mass ◽  
Inversion Symmetry ◽  
Top Down ◽  
Virus Capsid ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Icosahedral Viruses

We present a top-down approach to the study of the dynamics of icosahedral virus capsids, in which each protein is approximated by a point mass. Although this represents a rather crude coarse-graining, we argue that it highlights several generic features of vibrational spectra which have been overlooked so far. We furthermore discuss the consequences of approximate inversion symmetry as well as the role played by viral tiling theory in the study of virus capsid vibrations.

Organization of dsDNA in icosahedral virus capsids

1992 ◽  
Vol 50 (1) ◽  
pp. 452-453 ◽  
Author(s):  
Frank P. Booy ◽  
Benes L. Trus ◽  
William W. Newcomb ◽  
Jay C. Brown ◽  
Philip Serwer ◽  
...  
Keyword(s):  
Structural Biology ◽  
Viral Capsids ◽  
Viral Genomes ◽  
Nucleic Acid Molecule ◽  
Cryo Electron Microscopy ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Dna Strands ◽  
Simplex Virus

Condensation/decondensation reactions which effect the packaging of viral genomes into their capsids and their subsequent release constitute one of the basic phenomena which structural biology seeks to explain. The appropriate nucleic acid molecule(s) must be selected; then packaged at a high density to allow efficient utilization of the available space; the mutual electrostatic repulsion of DNA strands must somehow be overcome; and the arrangement of the DNA must allow for its ready release upon initiation of infection. Cryo-electron microscopy has emerged as an incisive tool for visualizing the internal organization of packaged DNA inside viral capsids. We illustrate its effectiveness with observations relating to bacteriophages T4, T7, and herpes simplex virus, type 1 (HSV-1).

VIPERdb: A Tool for Virus Research

2018 ◽  
Vol 5 (1) ◽  
pp. 477-488 ◽  
Author(s):  
Phuong T. Ho ◽  
Daniel J. Montiel-Garcia ◽  
Jonathan. J. Wong ◽  
Mauricio Carrillo-Tripp ◽  
Charles L. Brooks ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Contrast Structure ◽  
Web Based ◽  
Web Interfaces ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Derived Properties ◽  
Virus Research ◽  
Data Visualizations ◽  
Compare And Contrast

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.

THE MORPHOGENESIS OF HIGH SYMMETRY: THE SYMMETRIZATION THEOREM

1999 ◽  
Vol 07 (02) ◽  
pp. 159-211 ◽  
Author(s):  
CHRISTOPHER J. MARZEC
Keyword(s):  
Figure Of Merit ◽  
Local Minimum ◽  
Basin Of Attraction ◽  
Three Dimensional ◽  
High Symmetry ◽  
Gradient Dynamics ◽  
Symmetrical Configuration ◽  
Virus Capsids ◽  
Icosahedral Virus ◽  
Local Gradient

A multi-part theorem is presented concerning the morphogenesis of high-symmetry structures made of three-dimensional morphological units (MU's) free to move on the surface of a sphere. All parts of each MU interact non-specifically with the remainder of the structure, via an isotropic function of distance. Summing all interactions gives a net figure of merit, ℐ, that depends upon MU positions and orientations. The structure evolves via gradient dynamics, each MU moving down the local gradient of ℐ. The analysis is reresented with generality in Fourier space, which eases the expression of symmetry. Structures near symmetry, but far from a local minimum of ℐ, are analyzed. For each, a symmetrical configuration can be found, for which ℐ is an extremum with respect to symmetry-breaking perturbations. Under gradient dynamics, a quadratic measure of such deviations from symmetry decreases monotonically, anywhere in the large basin of attraction of a local minimum. Thus: high symmetry is an attractor. Application is made to icosahedral virus capsids. The Symmetrization Theorem shows that a stable capsid, maintained by non-specific interactions among its capsomeres, could arise generically in a "bottom-up" process. For animated evolutions that self-assemble into high symmetry, visit

Mechanical properties of icosahedral virus capsids

2007 ◽  
Vol 14 (S1) ◽  
pp. 111-119 ◽  
Author(s):  
G. A. Vliegenthart ◽  
G. Gompper
Keyword(s):  
Mechanical Properties ◽  
Virus Capsids ◽  
Icosahedral Virus

Specific Labeling of Protein Domains with Antibody Fragments

1981 ◽  
Vol 39 ◽  
pp. 416-417
Author(s):  
U. Aebi ◽  
L.E. Buhle ◽  
W.E. Fowler
Keyword(s):  
Image Processing ◽  
Specific Protein ◽  
Antibody Fragments ◽  
Supramolecular Organization ◽  
Two Dimensional ◽  
Ordered Structures ◽  
Virus Capsids ◽  
Processing Techniques

Many important supramolecular structures such as filaments, microtubules, virus capsids and certain membrane proteins and bacterial cell walls exist as ordered polymers or two-dimensional crystalline arrays in vivo. In several instances it has been possible to induce soluble proteins to form ordered polymers or two-dimensional crystalline arrays in vitro. In both cases a combination of electron microscopy of negatively stained specimens with analog or digital image processing techniques has proven extremely useful for elucidating the molecular and supramolecular organization of the constituent proteins. However from the reconstructed stain exclusion patterns it is often difficult to identify distinct stain excluding regions with specific protein subunits. To this end it has been demonstrated that in some cases this ambiguity can be resolved by a combination of stoichiometric labeling of the ordered structures with subunit-specific antibody fragments (e.g. Fab) and image processing of the electron micrographs recorded from labeled and unlabeled structures.

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