Viral capsid proteins are segregated in structural fold space.

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 a...

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Autores principales:	Shanshan Cheng, Charles L Brooks
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/fc8b757ec4564f03bce21261ca8ae670
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spelling	oai:doaj.org-article:fc8b757ec4564f03bce21261ca8ae6702021-11-18T05:52:27ZViral capsid proteins are segregated in structural fold space.1553-734X1553-735810.1371/journal.pcbi.1002905https://doaj.org/article/fc8b757ec4564f03bce21261ca8ae6702013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23408879/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Viral 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.Shanshan ChengCharles L BrooksPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 2, p e1002905 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Shanshan Cheng Charles L Brooks Viral capsid proteins are segregated in structural fold space.
description	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.
format	article
author	Shanshan Cheng Charles L Brooks
author_facet	Shanshan Cheng Charles L Brooks
author_sort	Shanshan Cheng
title	Viral capsid proteins are segregated in structural fold space.
title_short	Viral capsid proteins are segregated in structural fold space.
title_full	Viral capsid proteins are segregated in structural fold space.
title_fullStr	Viral capsid proteins are segregated in structural fold space.
title_full_unstemmed	Viral capsid proteins are segregated in structural fold space.
title_sort	viral capsid proteins are segregated in structural fold space.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/fc8b757ec4564f03bce21261ca8ae670
work_keys_str_mv	AT shanshancheng viralcapsidproteinsaresegregatedinstructuralfoldspace AT charleslbrooks viralcapsidproteinsaresegregatedinstructuralfoldspace
_version_	1718424766285611008

Viral capsid proteins are segregated in structural fold space.

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