Data mining, ab initio, and molecular mechanics study on conformation of phenylalanine and its interaction with neighboring backbone amide groups in proteins

Data mining results for 1029 X-ray protein structures demonstrate that there are, on average, more than nine phenylalanine residues in a typical protein structure. Moreover, the conformations of these phenylalanine residues are not arbitrary but fall into four regular types. These four phenylalanine conformational types can be related to the interaction between the phenylalanine's phenyl group and its neighboring backbone amide groups. They are designated as "Aphe," "Cphe," "ACphe," and "NACphe," respectively, depending on the presence and absence of such phenyl-amide interactions. It is shown that 96.2% of the phenylalanine residues occurring in proteins fall into the first three types, which involve one or two types of these interactions. The side chain and associated backbone fragment of each phenylalanine type have characteristic conformational regularities. The interaction potential energy surfaces of these interactions were exhaustively and systematically evaluated by means of the validated CHARMm force field. We show that this force field produces interaction energies comparable to BSSE-corrected values calculated using MP2/6-311G(2d,2p) and MP2/6-31+G(2d,p). The phenyl-amide interactions occurring in proteins have configurations corresponding to a stabilization energy of up to 11 kJ/mol in vacuum. None occur that would correspond to a phenyl-amide repulsion. We conclude that the phenyl-amide interaction is one of the factors responsible for the conformational regularity of the phenyalanine in proteins and that it is of significance due to its strength and common occurrence. (C) 2002 Wiley Periodicals, Inc.