Novel scoring function for modeling structures of oligomers of transmembrane α‐helices

• DOI: 10.1002/prot.20229
• Publication Date: 2004-07-12T21:04:43Z
• Authors: Yungki Park; Markus Elsner; Rene Staritzbichler; Volkhard Helms
• Keywords: Interaction energy

Abstract 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 play an role the tight packing TM α‐helices, although polar can also be some instances. Based on assumption interaction alone is sufficient for meso‐scale (residue‐scale) description we designed novel residue‐scale scoring function modeling structures oligomers α‐helices. We first calculated atomistic energies two amino acids, X Y , pair parallel glycine‐ ‐glycine compiled them according to three variables, distance C α atoms rotational angles about their helical axes. Upon averaging over angles, obtained one‐dimensional energy profiles functions only. Each was fitted with generic fitting atoms, yielding analytical all possible acid pairs. For glycophorin A, neu/erbB‐2, phospholamban, lowest‐energy conformations through exhaustive scanning entire conformational space using were compatible available experimental data. Proteins 2004. © 2004 Wiley‐Liss, Inc.