A Structural interpretation of the sequential preferences

J. Vondrášek

Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6

It will be shown that probability of amino acids occurrence in proteins (P1) differs across organisms and species. Based on these propensities a difference between the real occurrence and a level of expectancy for sequential motifs of di- (P2), tri- (P3) and tetrapeptides (P4) will be demonstrated. The connection between structural representations of the over or under-populated motifs will be discussed in terms of their phi/psi distribution in proteins from PDB. Potential utilization of the findings will be discussed including protein design and ligand engineering.