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Molecules 2014, 19(9), 14961-14978; doi:10.3390/molecules190914961

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

1
NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy
2
Department of Physics "E. Fermi", University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa, Italy
3
Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
*
Author to whom correspondence should be addressed.
Received: 21 July 2014 / Revised: 28 August 2014 / Accepted: 8 September 2014 / Published: 18 September 2014
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Abstract

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. View Full-Text
Keywords: rhodopsin; multi-scale modeling; classical molecular dynamics; coarse grained models; computer simulations rhodopsin; multi-scale modeling; classical molecular dynamics; coarse grained models; computer simulations
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Tavanti, F.; Tozzini, V. A Multi-Scale–Multi-Stable Model for the Rhodopsin Photocycle. Molecules 2014, 19, 14961-14978.

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