Paper Citing NAMD - Abstract
Cheng, Xiaolin; Ivanov, Ivaylo; Wang, Hailong; Sine, Steven M.; McCammon, J. Andrew
Nanosecond-timescale conformational dynamics of the human alpha 7 nicotinic acetylcholine receptor
BIOPHYSICAL JOURNAL, 93:2622-2634, OCT 2007
We explore the conformational dynamics of a homology model of the human alpha 7 nicotinic acetylcholine receptor using molecular dynamics simulation and analyses of root mean-square fluctuations, block partitioning of segmental motion, and principal component analysis. The results reveal flexible regions and concerted global motions of the subunits encompassing extracellular and transmembrane domains of the subunits. The most relevant motions comprise a bending, hinged at the beta 10-M1 region, accompanied by concerted tilting of the M2 helices that widens the intracellular end of the channel. Despite the nanosecond timescale, the observations suggest that tilting of the M2 helices may initiate opening of the pore. The results also reveal direct coupling between a twisting motion of the extracellular domain and dynamic changes of M2. Covariance analysis of interresidue motions shows that this coupling arises through a network of residues within the Cys and M2-M3 loops where Phe(135) is stabilized within a hydrophobic pocket formed by Leu(270) and Ile(271). The resulting concerted motion causes a downward shift of the M2 helices that disrupts a hydrophobic girdle formed by 9' and 13' residues.
