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Recurrent Structural Motifs in Non-Homologous Protein Structures

We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4–6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in ou...

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Autores principales: Johansson, Maria U., Zoete, Vincent, Guex, Nicolas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645717/
https://www.ncbi.nlm.nih.gov/pubmed/23574940
http://dx.doi.org/10.3390/ijms14047795
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author Johansson, Maria U.
Zoete, Vincent
Guex, Nicolas
author_facet Johansson, Maria U.
Zoete, Vincent
Guex, Nicolas
author_sort Johansson, Maria U.
collection PubMed
description We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4–6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them, describe recurrent structural patterns that are important for protein stability. In view of their properties, such structural motifs are potentially useful for inter-residue contact prediction and protein structure refinement.
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spelling pubmed-36457172013-05-13 Recurrent Structural Motifs in Non-Homologous Protein Structures Johansson, Maria U. Zoete, Vincent Guex, Nicolas Int J Mol Sci Article We have extracted an extensive collection of recurrent structural motifs (RSMs), which consist of sequentially non-contiguous structural motifs (4–6 residues), each of which appears with very similar conformation in three or more mutually unrelated protein structures. We find that the proteins in our set are covered to a substantial extent by the recurrent non-contiguous structural motifs, especially the helix and strand regions. Computational alanine scanning calculations indicate that the average folding free energy changes upon alanine mutation for most types of non-alanine residues are higher for amino acids that are present in recurrent structural motifs than for amino acids that are not. The non-alanine amino acids that are most common in the recurrent structural motifs, i.e., phenylalanine, isoleucine, leucine, valine and tyrosine and the less abundant methionine and tryptophan, have the largest folding free energy changes. This indicates that the recurrent structural motifs, as we define them, describe recurrent structural patterns that are important for protein stability. In view of their properties, such structural motifs are potentially useful for inter-residue contact prediction and protein structure refinement. Molecular Diversity Preservation International (MDPI) 2013-04-10 /pmc/articles/PMC3645717/ /pubmed/23574940 http://dx.doi.org/10.3390/ijms14047795 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland http://creativecommons.org/licenses/by/3.0 This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Johansson, Maria U.
Zoete, Vincent
Guex, Nicolas
Recurrent Structural Motifs in Non-Homologous Protein Structures
title Recurrent Structural Motifs in Non-Homologous Protein Structures
title_full Recurrent Structural Motifs in Non-Homologous Protein Structures
title_fullStr Recurrent Structural Motifs in Non-Homologous Protein Structures
title_full_unstemmed Recurrent Structural Motifs in Non-Homologous Protein Structures
title_short Recurrent Structural Motifs in Non-Homologous Protein Structures
title_sort recurrent structural motifs in non-homologous protein structures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645717/
https://www.ncbi.nlm.nih.gov/pubmed/23574940
http://dx.doi.org/10.3390/ijms14047795
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