Molecular Dynamics Simulations of Channelrhodopsin Chimera, C1C2

Molecular dynamics (MD) simulations have been successfully used for modeling dynamic behavior of biologically relevant systems, such as ion channels in representative environments to decode protein structure-function relationships. Protocol presented here describes steps for generating input files and modeling a monomer of transmembrane cation channel, channelrhodopsin chimera (C1C2), in representative environment of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) planar lipid bilayer, TIP3P water and ions (Na⁺ and Cl^-) using molecular dynamics package NAMD, molecular graphics/analysis tool VMD, and other relevant tools. MD simulations of C1C2 were performed at 303.15 K and in constant particle number, isothermal-isobaric (NpT) ensemble. The results of modeling have helped understand how key interactions in the center of the C1C2 channel contribute to channel gating and subsequent solvent transport across the membrane.