Visual violet light cycle simulation method based on molecular dynamics

Abstract

The invention relates to a molecular dynamics visual purple protein light cycle simulation research method, which is used for carrying out simulation research by using a monopolymer, and belongs to the field of neuroscience and the field of molecular dynamics. The method comprises the following specific steps: (1) twisting a chromophore C12-C13 = C14-C15 dihedral angle by using Gaussian software, and adjusting the angle; (2) embedding a monomer protein in a CHARMM-GUI software embedding cell membrane environment, and carrying out independent force field setting on chromophore small molecules; (3) carrying out equilibrium state molecular dynamics simulation by using NAMD software; (4) analyzing a molecular dynamics track, and carrying out corresponding analysis through a cpptraj module of AMBER and a tcl file of VMD. And (5) calculating the free energy by using a stretching molecular dynamics and umbrella-shaped sampling mode. According to the method disclosed by the invention, the structural change of the rhodopsin in the light circulation process is researched by utilizing molecular dynamics, so that the simulation of light circulation is further realized, and the method plays an important role in clinical application, brain function research and engineering material design of the rhodopsin in the field of neuroscience.

Description

technical field [0001] The invention belongs to the fields of neuroscience and molecular dynamics, and in particular relates to a rhodopsin light cycle simulation system based on molecular dynamics. Background technique [0002] The use of light-sensitive proteins to observe and control cellular activity is considered one of the most ground-breaking innovations in neuroscience in recent years, and this approach is gradually replacing traditional methods of studying neural function. Karl Deisseroth first coined the term optogenetics in 2006. Optogenetics is a combination of genetics and optics that stimulates or inhibits specific events in living tissue or specific cells in behavioral animals. Reversible silencing of neurons has important implications for their dynamics and behavior when isolating the neural circuits of specific neuronal populations. Light-induced functions are controlled by photoreceptor proteins, which contain an embedded light-sensing chromophore molecule...

AI Technical Summary

Problems solved by technology

Classical molecular dynamics cannot accurately obtain the conformation of ion channels, and there is a huge difference between conventional molecular dynamics simulations and real biological process time scales, resulting in insufficient sampling

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