Statistical analysis of pair-wise compatibility of spatially nearest neighbor and adjacent residues in alpha-helix and beta-strands: application to a minimal model for secondary structure prediction.
Secondary structural elements like alpha-helix and beta-strands possess distinctly different structural features and thus the relative positioning of the nearest neighbor residues, and also the sequence-wise adjacent residues is important in determining the structural preference. In the present work we have statistically examined the pair-wise compatibility pattern of physically nearest neighbors and separately the adjacent residue pairs along the sequence in between the nearest neighbor partners in alpha-helices and beta-strands. It has been demonstrated that the patterns and hence, the physical basis of the compatibility of adjacent residue pairs and the spatially nearest neighbors are significantly different in most cases. The influence of tertiary contacts on the pair-wise compatibility is shown to be significant for beta-strands while it is small for alpha-helices. Based on the compatibility of physically nearest neighbors and the sequence-wise adjacent residue pairs, a minimal model has been constructed to predict the alpha-helices, beta-strands and coils of a protein from its sequence. Application of this method to 100 sequences shows that it has a predictive capability comparable to that of other more sophisticated statistical methods.
Sen
Srikanta
S
Human Genetics and Gemonics Division, Indian Institute of Chemical Biology, 4, Raja S C Mullick Road, Jadavpur, Calcutta 700032, India. srikanta@chembiotek.com
D020029:Base Pairing; D003627:Data Interpretation, Statistical; D008956:Models, Chemical; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results
D011506:Proteins