Next Article in Journal
Plant bZIP Transcription Factors Responsive to Pathogens: A Review
Next Article in Special Issue
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
Previous Article in Journal
Oxidative Stress in Complex Regional Pain Syndrome (CRPS): No Systemically Elevated Levels of Malondialdehyde, F2-Isoprostanes and 8OHdG in a Selected Sample of Patients
Previous Article in Special Issue
Adsorption and Orientation of Human Islet Amyloid Polypeptide (hIAPP) Monomer at Anionic Lipid Bilayers: Implications for Membrane-Mediated Aggregation
Open AccessArticle

Recurrent Structural Motifs in Non-Homologous Protein Structures

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.
Int. J. Mol. Sci. 2013, 14(4), 7795-7814; https://doi.org/10.3390/ijms14047795
Received: 8 March 2013 / Revised: 27 March 2013 / Accepted: 1 April 2013 / Published: 10 April 2013
(This article belongs to the Collection Protein Folding)
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. View Full-Text
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
Show Figures

Graphical abstract

MDPI and ACS Style

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

Show more citation formats Show less citations formats

Article Access Map by Country/Region

1
Only visits after 24 November 2015 are recorded.
Back to TopTop