Dependence of positive binding energies on side chains - A theoretical prediction on the origin of regular ordering for the amino acid residues in the selectivity filter

作者：Ai Hongqi^*; Zhang Chong; Li Yun; Zhang Liang; Li Fang

来源：Journal of Physical Chemistry B, 2007, 111(49): 13786-13796.

DOI：10.1021/jp074198m

The side-chain effects of metalated and protonated dipeptides, including GGH(+)M(+), GAH(+)M(+), AGH(+)M(+), AAH(+)M(+), GWH(+)M(+), GSH(+)M(+), GTH(+)M(+), GFH(+)M(+), GYH(+)M(+), and GVH(+)M(+) (G = glycine, A = alanine, W = tryptophan, S = serine, T = threonine, F = phenylalanine, and V = valine; M = Li, Na, and K), are theoretically explored in this paper on their positive binding energies (PBEs), which are derived from interactions of M+ with the carboxyl oxygen(s). The B3LYP/6-311++G B3LYP/6-31G* calculations suggest that the PBEs of dipeptides with side chain(s) are much smaller than those with no side chain (GGH(+)M(+)). Generally, larger side chains and smaller M+ radii would lead to fewer PBEs for the M+ involved systems. On the basis of the direct dependence of PBE on the electrostatic repulsion between two kinds of cations (H+ and M+) in these dipeptide models, it could be reasonably expected that the side-chain effect on the electrostatic repulsion and consequently on the PBEs could offer one good insight, on a chemical-physical basis, into the origin of regular ordering of the amino acids when they form a filter in the K+ channel protein (MacKinnon, et al. Science 1998, 280, 106).

• 出版日期2007-12-13
• 单位山东大学; 济南大学; 聊城大学