ArticleMolecules (Basel, Switzerland)2014
A multi-scale-multi-stable model for the rhodopsin photocycle.
Article in Molecules (Basel, Switzerland), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering.Frontiers in chemistry · 2022Review
- Aggregation behavior of nanoparticles: Revisiting the phase diagram of colloids.Frontiers in molecular biosciences · 2022Review
- Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.The Journal of membrane biology · 2019Review
- Multiscale Molecular Dynamics Simulation of Multiple Protein Adsorption on Gold Nanoparticles.International journal of molecular sciences · 2019Article
- Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin.Frontiers in molecular biosciences · 2019Article
- Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2.Physical chemistry chemical physics : PCCP · 2016Article
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Authors and funding
2 authors.
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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.
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