A multi-scale-multi-stable model for the rhodopsin photocycle.
نویسندگان
چکیده
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.
منابع مشابه
A New Compromise Decision-making Model based on TOPSIS and VIKOR for Solving Multi-objective Large-scale Programming Problems with a Block Angular Structure under Uncertainty
This paper proposes a compromise model, based on a new method, to solve the multi-objective large-scale linear programming (MOLSLP) problems with block angular structure involving fuzzy parameters. The problem involves fuzzy parameters in the objective functions and constraints. In this compromise programming method, two concepts are considered simultaneously. First of them is that the optimal ...
متن کاملFuzzy Multi-Objective Two-Stage DEA Model for Evaluating the Performance of Companies Listed on Tehran Stock Exchange
The aim of this study is to provide a new two-stage DEA model with fuzzy multi-objective programming approach for evaluating the performance of companies listed in the Tehran Stock Exchange. In this study, a two-stage DEA model, different from the traditional model, we introduce for performance analysis. In this regard, the stable operation of companies, into two sub-process, have divided, whic...
متن کاملBuckling of multi wall carbon nanotube cantilevers in the vicinity of graphite sheets using monotone positive method
In this paper, a monotone positive solution is studied for buckling of a distributed model of multi walled carbon nanotube (MWCNT) cantilevers in the vicinity of thin and thick graphite sheets subject to intermolecular forces. In the modeling of intermolecular forces, Van der Waals forces are taken into account. A hybrid nano-scale continuum model based on Lennard–Jones potential is applied to ...
متن کاملA Compromise Decision-Making Model Based on TOPSIS and VIKOR for Multi-Objective Large- Scale Nonlinear Programming Problems with A Block Angular Structure under Fuzzy Environment
This paper proposes a compromise model, based on a new method, to solve the multiobjectivelarge scale linear programming (MOLSLP) problems with block angular structureinvolving fuzzy parameters. The problem involves fuzzy parameters in the objectivefunctions and constraints. In this compromise programming method, two concepts areconsidered simultaneously. First of them is that the optimal alter...
متن کاملA Compromise Decision-making Model for Multi-objective Large-scale Programming Problems with a Block Angular Structure under Uncertainty
This paper proposes a compromise model, based on the technique for order preference through similarity ideal solution (TOPSIS) methodology, to solve the multi-objective large-scale linear programming (MOLSLP) problems with block angular structure involving fuzzy parameters. The problem involves fuzzy parameters in the objective functions and constraints. This compromise programming method is ba...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Molecules
دوره 19 9 شماره
صفحات -
تاریخ انتشار 2014