Paper Citing NAMD - Abstract
Lin, Ying-Wu; Wang, Zhong-Hua; Ni, Feng-Yun; Huang, Zhong-Xian
Forced unfolding of apocytochrome b(5) by steered molecular dynamics simulation
PROTEIN JOURNAL, 27:197-203, APR 2008
Apocytochrome b(5) (apocyt b(5)), a small b-type cytochrome with heme prosthetic group removal, has been subjected to steered molecular dynamics (SMD) simulations for investigating the consequences of mechanical force-induced unfolding. Both constant velocity (0.5 and 1.0 angstrom/ps) and constant force (500, 750 and 1000 pN) stretching have been employed to model forced unfolding of apocyt b(5). The results of SMD simulations elucidate that apocyt b(5) is protected against external stress mainly through the interstrand hydrogen bonding between its beta 1-beta 2 and beta 2-beta 3 strands, highlighting the importance of hydrophobic core 2 in stabilization of apocyt b(5). The existence of intermediate states manifested by current simulations in the forced unfolding pathway of apocyt b(5) is different from the observations in pervious thermal or chemical unfolding studies in the absence of force. The present Study could thus provide insights into the relationship between the two cooperative functional modules of apocyt b(5) and also guide the rational molecular design of heme proteins.
