Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins.
A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools.
REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal.
Miguel M
MM
de Sousa
REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal; Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain.
Cristian R
CR
Munteanu
Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain.
Alejandro
A
Pazos
CRACS-INESC Porto L.A., R. Campo Alegre 1021/1055, 4169-007 Porto, Portugal.
Nuno A
NA
Fonseca
LIAAD-INESC-Porto, DEI and FEUP, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
Rui
R
Camacho
REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal.
A L
AL
Magalhães
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D030562:Databases, Protein; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
D000596:Amino Acids; D011506:Proteins