Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.

The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold sp...

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Autores principales:	Moitrayee Bhattacharyya, Roopali Upadhyay, Saraswathi Vishveshwara
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/37b8ce3e3313430082003dd354aff6ab
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spelling	oai:doaj.org-article:37b8ce3e3313430082003dd354aff6ab2021-11-18T08:04:49ZInteraction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.1932-620310.1371/journal.pone.0051676https://doaj.org/article/37b8ce3e3313430082003dd354aff6ab2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284738/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a "spatial motif" and several "fold specific hot spots" that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.Moitrayee BhattacharyyaRoopali UpadhyaySaraswathi VishveshwaraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 12, p e51676 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Moitrayee Bhattacharyya Roopali Upadhyay Saraswathi Vishveshwara Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
description	The fidelity of the folding pathways being encoded in the amino acid sequence is met with challenge in instances where proteins with no sequence homology, performing different functions and no apparent evolutionary linkage, adopt a similar fold. The problem stated otherwise is that a limited fold space is available to a repertoire of diverse sequences. The key question is what factors lead to the formation of a fold from diverse sequences. Here, with the NAD(P)-binding Rossmann fold domains as a case study and using the concepts of network theory, we have unveiled the consensus structural features that drive the formation of this fold. We have proposed a graph theoretic formalism to capture the structural details in terms of the conserved atomic interactions in global milieu, and hence extract the essential topological features from diverse sequences. A unified mathematical representation of the different structures together with a judicious concoction of several network parameters enabled us to probe into the structural features driving the adoption of the NAD(P)-binding Rossmann fold. The atomic interactions at key positions seem to be better conserved in proteins, as compared to the residues participating in these interactions. We propose a "spatial motif" and several "fold specific hot spots" that form the signature structural blueprints of the NAD(P)-binding Rossmann fold domain. Excellent agreement of our data with previous experimental and theoretical studies validates the robustness and validity of the approach. Additionally, comparison of our results with statistical coupling analysis (SCA) provides further support. The methodology proposed here is general and can be applied to similar problems of interest.
format	article
author	Moitrayee Bhattacharyya Roopali Upadhyay Saraswathi Vishveshwara
author_facet	Moitrayee Bhattacharyya Roopali Upadhyay Saraswathi Vishveshwara
author_sort	Moitrayee Bhattacharyya
title	Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
title_short	Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
title_full	Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
title_fullStr	Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
title_full_unstemmed	Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.
title_sort	interaction signatures stabilizing the nad(p)-binding rossmann fold: a structure network approach.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/37b8ce3e3313430082003dd354aff6ab
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Interaction signatures stabilizing the NAD(P)-binding Rossmann fold: a structure network approach.

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