THE STUDY OF TENDENCY FOR AMINO ACID NEIGHBORS IN ALPHA HELICES

In order to study the tendency of amino acid neighbors in helical structures, proteins with known structures were carefully analyzed. The studied helical positions: N, Ncap, N1, N2, N3, N4, M, C4, C3, C2, C1, Ccap, C and their doublet counterparts: N Ncap, NcapN1, N1N2, N2N3, N3N4, M1M2, M2M3, C4C3, C3C2, C2C1, C1Ccap, CcapC were carefully analyzed. The propensity for all amino acids in different helical positions and also the propensity for all 400 different doublet positions were calculated and compared. For this purpose, a databank of 3705 helices was designed and used. In this database helices were longer than 7 amino acid residues and were derived from 696 non-homologous proteins with less than 25% identity. SLP(Single Local Propensity) for each 20 amino acid in different helical positions was calculated. Furthermore, DLPo or the observed Doublet Local Propencity which is based upon prefered occurrence of paired amino acids in different doublet positions of alpha helices and DLPe or the expected Doublet Local Propensity calculated directly using SLPs was also calculated. If the propensity of a particular doublet in a specific alpha helical positon or DLPo becomes more than the calculated single positions in alpha helices, in other words, DLPo>>DLPe it indicates that this particular doublet has a tendency in staying as neighbors in that particular helical position. Results showed that doublets in which DLPo>>DLPe are as follows: Met-Thr for N’Ncap position, Glu-Pro in NcapN1, Pro-Arg at N1N2, Lys-His in C2C1, Thr-Gly in C1Ccap, and Gln-Pro in CcapC’. It was also seen that Gly in Ccap position has a tendency to neighbor on a hydrophobic amino acid at C’ position. Studying the tendency of amino acids in neighboring each other in alpha helices can be used in designing novel helical structures and can also be used in modifying existing helical structures in proteins.