Comparison of different statistical methods for calculations of amino acid propensities toward certain secondary structure types

Abstract

The conformational preferences of amino acids are very important for understanding conformational interactions in proteins. Moreover, when used as propensities they can be helpful in predicting secondary and tertiary structures of proteins. Propensity for secondary structures represents an intrinsic property of amino acid, and it is now known that different amino acids have distinct propensities for the adoption of helical, strand, and random coil conformations. Several statistical studies were performed in order to calculate amino acid propensities [1-3]. In our previous work we carried out study of propensities using statistical method [4]. Clear preferences of amino acids towards certain secondary structures based on the study, classify amino acids into four groups: α-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cβ and Cγ atoms that predict their preference for a particular secondary structure. Here we compare other statistical methods for amino acid propensities with the statistical method which we used in our previous work. Comparison was made on the basis of correlation coefficients (ρ(s,p)). As a source of protein data we used structures archived in Protein Data Bank (PDB). The secondary structure assignment was performed by the program DSSP.