A Multi-Scale–Multi-Stable Model for the Rhodopsin Photocycle

Molecules

Francesco Tavanti¹ 

[1] NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy

关键词: rhodopsin;    multi-scale modeling;    classical molecular dynamics;    coarse grained models;    computer simulations;   

DOI  :  10.3390/molecules190914961

来源: mdpi

【 摘 要 】

We report a multi-scale simulation study of the photocycle of the rhodopsins. The quasi-atomistic representation (“united atoms” UA) of retinal is combined with a minimalist coarse grained (CG, one-bead-per amino acid) representation of the protein, in a hybrid UA/CG approach, which is the homolog of QM/MM, but at lower resolution. An accurate multi-stable parameterization of the model allows simulating each state and transition among them, and the combination of different scale representation allows addressing the entire photocycle. We test the model on bacterial rhodopsin, for which more experimental data are available, and then also report results for mammalian rhodopsins. In particular, the analysis of simulations reveals the spontaneous appearance of meta-stable states in quantitative agreement with experimental data.

【 授权许可】

CC BY   
© 2014 by the authors; licensee MDPI, Basel, Switzerland.