title: Ideal amino acid exchange forms for approximating substitution matrices.
abstract: We have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, 'classical' SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9. The BLOSUM62 is the central element of this group. A second group includes SMs derived from alignments of remote homologs or transmembrane proteins. These matrices correlate better with classical SMs (0.8) than among themselves (0.7). A third group consists of intermediate links between SMs and CPs - matrices and potentials that exhibit mutual correlations of at least 0.8. Next, we show that SMs can be approximated with a correlation of 0.9 by expressions c(0) + x(i)x(j) + y(i)y(j) + z(i)z(j), 1<or= i, j <or= 20, where c(0) is a constant and the vectors (x(i)), (y(i)), (z(i)) correlate highly with hydrophobicity, molecular volume and coil preferences of amino acids, respectively. The present paper is the continuation of our work (Pokarowski et al., Proteins 2005;59:49-57), where similar approximation were used to derive ideal amino acid interaction forms from CPs. Both approximations allow us to understand general trends in amino acid similarity and can help improve multiple sequence alignments using the fast Fourier transform (MAFFT), fast threading or another methods based on alignments of physicochemical profiles of protein sequences. The use of this approximation in sequence alignments instead of a classical SM yields results that differ by less than 5%. Intermediate links between SMs and CPs, new formulas for approximating these matrices, and the highly significant dependence of classical SMs on coil preferences are new findings.
authors.affiliation: Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, Warsaw University, 02-097 Warsaw, Poland. pokar@mimuw.edu.pl
authors.forename: Piotr
authors.initials: P
authors.lastname: Pokarowski
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kloczkowski
authors.forename: Szymon
authors.initials: S
authors.lastname: Nowakowski
authors.forename: Maria
authors.initials: M
authors.lastname: Pokarowska
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kolinski
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics*; D011237:Predictive Value of Tests; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins