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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Molecular Diversity Preservation International (MDPI)
2013
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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. |
format | Online Article Text |
id | pubmed-3645717 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Molecular Diversity Preservation International (MDPI) |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT johanssonmariau recurrentstructuralmotifsinnonhomologousproteinstructures AT zoetevincent recurrentstructuralmotifsinnonhomologousproteinstructures AT guexnicolas recurrentstructuralmotifsinnonhomologousproteinstructures |