Computer simulations of membrane protein folding: structure and dynamics.
A lattice model of membrane proteins with a composite energy function is proposed to study their folding dynamics and native structures using Monte Carlo simulations. This model successfully predicts the seven helix bundle structure of sensory rhodopsin I by practicing a three-stage folding. Folding dynamics of a transmembrane segment into a helix is further investigated by varying the cooperativity in the formation of alpha helices for both random folding and assisted folding. The chain length dependence of the folding time of a hydrophobic segment to a helical state is studied for both free and anchored chains. An unusual length dependence in the folding time of anchored chains is observed.
Chen
C-M
CM
Physics Department, National Taiwan Normal University, Taipei, Republic of China. cchen@phy.ntnu.edu.tw
Chen
C-C
CC
D000465:Algorithms; D001436:Bacteriorhodopsins / Q000737:chemistry*; D003198:Computer Simulation; D004735:Energy Transfer; D025602:Halorhodopsins; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry; D008958:Models, Molecular; D009038:Motion; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D025603:Sensory Rhodopsins
D025602:Halorhodopsins; D008565:Membrane Proteins; C061497:SRI protein, Halobacterium; D025603:Sensory Rhodopsins; D001436:Bacteriorhodopsins