POLYPEPTIDE SEQUENCE PROPERTY RELATIONSHIPS IN ESCHERICHIA-COLI BASEDON AUTO CROSS COVARIANCES

For multivariate classification and quantitative structure activity st udies of proteins, which involve amino acid sequences of different len gth, preprocessing methods are needed which make it possible to transl ate the sequence into a quantitative measure with the same number of v ariables. Here three different preprocessing methods are investigated. Two of the methods are variants of auto cross covariances calculated from a multipositional description of the protein sequence. For the mu ltipositional description three orthogonal scales were used which phys ico-chemically describes the amino acids. The third method is a quanti fication of each sequence by a diamino acid frequency histogram. The m ethods are investigated by a classification of 106 Escherichia coli an d Gramnegative bacteria proteins. The proteins were divided into four classes depending on their location in the cell. The four classes were : cytoplasm, inner membrane, periplasm and outer membrane. For the pro ceeding classification PLS discriminant analysis was used. The results showed that one of the variants of auto cross covariances and the dia mino acid frequency histogram representation contained much informatio n related to the given classification problem. Hence the amino acid se quences for proteins with different final locations in Escherichia col i have significant features related to protein structure and location.