Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses

Reddy, Vijay; Natarajan, Padmaja; Okerberg, Brian; Li, Kevin; Damodaran, Komath; Morton, Ryan T.; Brooks, Charles L.; Johnson, John E.

doi:10.1128/jvi.75.24.11943-11947.2001

Cited by 176 publications

(154 citation statements)

References 11 publications

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“…These subunits come together to form a 28-nm T ϭ 3 icosahedral particle both in vivo and in vitro (Fig. 1a) (28,33). In vitro, the assembly of CCMV at neutral pH has been shown to be dependent on the presence of divalent metal ions, such as Ca 2ϩ .…”

Section: Resultsmentioning

confidence: 99%

Paramagnetic viral nanoparticles as potential high‐relaxivity magnetic resonance contrast agents

Allen

Bulte

Liepold

et al. 2005

Magnetic Resonance in Med

191

162

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Section: Resultsmentioning

confidence: 99%

Paramagnetic viral nanoparticles as potential high‐relaxivity magnetic resonance contrast agents

Allen

Bulte

Liepold

et al. 2005

Magnetic Resonance in Med

191

162

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“…The individual contribution of interfacial residues to intersubunit association energies have been theoretically predicted for the MVMi capsid and for other viruses as well, and the results are available from the Virus Particle Explorer (VIPER; available at http:͞͞mmtsb.scripps. edu͞viper͞viper.html) (53). A comparison with our experimental results revealed that four of the seven side chains whose truncation prevented assembly corresponded to residues predicted to be energetically important (association energy Ϫ2.0 to Ϫ4.6 kcal͞mol).…”

Section: Discussionmentioning

confidence: 99%

Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid

Reguera

Carreira

Riolobos

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

126

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Twenty-eight amino acid residues involved in most noncovalent interactions between trimeric protein subunits in the capsid of the parvovirus minute virus of mice were truncated individually to alanine, and the effects on capsid assembly, thermostability, and conformation were analyzed. Only seven side chains were essential for protein subunit recognition. These side chains virtually corresponded with those that either buried a large hydrophobic surface on trimer association or formed buried intertrimer hydrogen bonds or salt bridges. The seven residues are evolutionarily conserved, and they define regularly spaced spots on a thin equatorial belt surrounding each trimer. Truncation of the many side chains that were dispensable for assembly, including those participating in solvent-accessible polar interactions, did not substantially affect capsid thermostability either. However, the interfacial residues located at the base of the pores delineating the capsid five-fold axes participated in a heat-induced conformational rearrangement associated with externalization of the capsid protein N terminus, and they were needed for infectivity. Thus, at the subunit interfaces of this model virus capsid, only key residues involved in the strongest interactions are critical for assembly and stability, but additional residues fulfill other important biological roles. P rotein-protein recognition mediates many fundamental biological processes. A detailed knowledge of these processes requires the determination of the structural, energetic, and functional roles of individual amino acid residues and interactions in protein-protein interfaces. These studies have been generally undertaken by using small protein-ligand complexes or oligomeric proteins of moderate size (reviewed in ref. 1; see also refs. 2-4). In contrast, for multimeric protein complexes, such as viral capsids (5, 6) or large cellular assemblies, little is known about the specific molecular determinants of protein association and stability. Mutational studies of virus capsids, generally focused on a few specific amino acid residues, have provided important insights (7-22). However, exhaustive experimental studies on the relative importance of residues and molecular interactions in viral capsid assembly, disassembly, and͞or stability are still very limited. These studies contribute also to the understanding of protein structure-function relationships and evolution under conflictive selective constraints (22-27), and they could be exploited possibly in the design of thermostable vaccines and antiviral agents promoting capsid disassembly or interfering with assembly (23, 28-31).Many viruses, including viruses of medical or veterinary significance, have capsids of icosahedral symmetry. The icosahedral T ϭ 1 capsids of parvoviruses (32-37) are formed by 60 protein subunits that are contributed by three nonidentical polypeptide chains (VP1, VP2, and VP3). These polypeptides derive, however, from a single gene and show identical fold and core sequence (Fig. 1). In the minut...

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“…It appears that there are even viruses that initiate their "lifecycle" exclusively in combination with some other viruses, often "stealing" the protein material of those viruses and diverting the cellular processes they initiated to their own advantage 6,7 the viruses are thus parasites even of their own kin. Although we know the exact nature (the shape and the genome) of only about a hundred 8 viruses, it seems that they are almost as diverse as life itself, so that they represent a type of index to the library of life forms that they parasitize upon. The viruses are indeed only abbreviated, indexed, crippled representation of life and they can hardly be classified as life.…”

Section: Introductionmentioning

confidence: 99%

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions

Šiber

Božič

Podgornik

2012

Phys. Chem. Chem. Phys.

132

153

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We summarize some aspects of electrostatic interactions in the context of viruses. A simplified but, within well defined limitations, reliable approach is used to derive expressions for electrostatic energies and the corresponding osmotic pressures in single-stranded RNA viruses and double-stranded DNA bacteriophages. The two types of viruses differ crucially in the spatial distribution of their genome charge which leads to essential differences in their free energies, depending on the capsid size and total charge in a quite different fashion. Differences in the free energies are trailed by the corresponding characteristics and variations in the osmotic pressure between the inside of the virus and the external bathing solution.

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Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses

Cited by 176 publications

References 11 publications

Paramagnetic viral nanoparticles as potential high‐relaxivity magnetic resonance contrast agents

Paramagnetic viral nanoparticles as potential high‐relaxivity magnetic resonance contrast agents

Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid

Energies and pressures in viruses: contribution of nonspecific electrostatic interactions

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