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PMID:23408879

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Citation

Cheng, S and Brooks, CL 3rd (2013) Viral capsid proteins are segregated in structural fold space. PLoS Comput. Biol. 9:e1002905

Abstract

Viral capsid proteins assemble into large, symmetrical architectures that are not found in complexes formed by their cellular counterparts. Given the prevalence of the signature jelly-roll topology in viral capsid proteins, we are interested in whether these functionally unique capsid proteins are also structurally unique in terms of folds. To explore this question, we applied a structure-alignment based clustering of all protein chains in VIPERdb filtered at 40% sequence identity to identify distinct capsid folds, and compared the cluster medoids with a non-redundant subset of protein domains in the SCOP database, not including the viral capsid entries. This comparison, using Template Modeling (TM)-score, identified 2078 structural "relatives" of capsid proteins from the non-capsid set, covering altogether 210 folds following the definition in SCOP. The statistical significance of the 210 folds shared by two sets of the same sizes, estimated from 10,000 permutation tests, is less than 0.0001, which is an upper bound on the p-value. We thus conclude that viral capsid proteins are segregated in structural fold space. Our result provides novel insight on how structural folds of capsid proteins, as opposed to their surface chemistry, might be constrained during evolution by requirement of the assembled cage-like architecture. Also importantly, our work highlights a guiding principle for virus-based nanoplatform design in a wide range of biomedical applications and materials science.

Links

PubMed PMC3567143 Online version:10.1371/journal.pcbi.1002905

Keywords

Capsid Proteins/chemistry; Cluster Analysis; Computational Biology; Databases, Protein; Models, Molecular; Protein Conformation; Protein Folding; Sequence Alignment; Sequence Analysis, Protein

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

9CAUD:A0A024B0W1

GO:0098017: viral capsid, major subunit

ECO:0000315:

C

The viral capsid allows for protection of a genome by formation of a protein shell around the genome. The protein allows for a large complex to form as a covering and allow for additional folding in space.

complete
CACAO 11645

Notes

See also

References

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