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Novel scoring function for modeling structures of oligomers of transmembrane α‐helices
Author(s) -
Park Yungki,
Elsner Markus,
Staritzbichler Rene,
Helms Volkhard
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20229
Subject(s) - van der waals force , chemistry , van der waals surface , crystallography , interaction energy , van der waals radius , molecule , organic chemistry
Specific non‐covalent interactions between transmembrane (TM) α‐helices are important in a variety of biological processes. Experimental and computational studies have shown that van der Waals interactions play an important role in the tight packing between TM α‐helices, although polar interactions can also be important in some instances. Based on the assumption that van der Waals interaction alone is sufficient for a meso‐scale (residue‐scale) description of the interaction between TM α‐helices, we have designed a novel residue‐scale scoring function for modeling structures of oligomers of TM α‐helices. We first calculated atomistic van der Waals interaction energies between two amino acids, X and Y , of a pair of parallel α‐helices, glycine‐ X ‐glycine and glycine‐ Y ‐glycine and compiled them according to three variables, the distance between the two C α atoms and the rotational angles of X and Y about their helical axes. Upon averaging over the rotational angles, we obtained one‐dimensional interaction energy profiles that are functions of the distance between C α atoms only. Each of the interaction energy profiles was fitted with a generic fitting function of the distance between C α atoms, yielding analytical scoring functions for all possible amino acid pairs. For glycophorin A, neu/erbB‐2, and phospholamban, lowest‐energy conformations obtained through exhaustive scanning of the entire conformational space using the scoring functions were compatible with available experimental data. Proteins 2004. © 2004 Wiley‐Liss, Inc.