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Int. J. Mol. Sci. 2013, 14(4), 7795-7814; doi:10.3390/ijms14047795
Article

Recurrent Structural Motifs in Non-Homologous Protein Structures

1,* , 2
 and
1,*
1 Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland 2 Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
* Authors to whom correspondence should be addressed.
Received: 8 March 2013 / Revised: 27 March 2013 / Accepted: 1 April 2013 / Published: 10 April 2013
(This article belongs to the Special Issue Protein Folding 2015)
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Abstract

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.
Keywords: Delaunay triangulation; protein fragments; long-range contacts; protein folding; protein structure; structural motifs; structure comparison/similarity; structure prediction Delaunay triangulation; protein fragments; long-range contacts; protein folding; protein structure; structural motifs; structure comparison/similarity; structure prediction
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Johansson, M.U.; Zoete, V.; Guex, N. Recurrent Structural Motifs in Non-Homologous Protein Structures. Int. J. Mol. Sci. 2013, 14, 7795-7814.

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