A Network Of Conformational Transition In An Unfolding Process Of HP-35 Revealed By High-temperature MD Simulation And A Markov State Model

Protein is one of the fundamental materials,the main bearer of life function.Protein molecule is a kind of macromolecule with three-dimensional structure,to which the amino acids fold according to certain rules.The study of protein folding is one of the most important fields in biophysics.However,the time scale of protein folding is far beyond the existing computer capabilities,and the accuracy of the current force field is far from the required,an alternative way is to study unfolding process using MD simulations at high temperature,and information obtained from studying unfolding can shed light on the mechanism of protein folding.In this paper,the "headpiece" domain of Villin protein(HP-35)was studied by the molecular dynamics,some results were obtained from its unfolding dynamics simulations:Firstly,using the AMBER force field,the protein is completely unfolded under the condition of high temperature(500 K),meaning that the simulated trajectory(1000 ns)has the conformations without any secondary structure.The intactness of the hydrophobic core was analyzed to insure that all conformations were unfolded states.At the beginning 1-2 ns,the unfolding process started and the 18 amino acid of Helix 2 was the first amino acid to unfolded;During the unfolding process,there existed rich unfolded states.Secondly,based on the software MSMBuilder,six intermediate states was found and the transition matrix was build.According to the TPT theory,two pathways was found to be the biggest transition net flux which were microstate 5→microstate 4→microstate 6;microstate 5→microstate2→microstate6.Lastly,using the principle component analysis(PCA)method,Helix 1 and Helix 3 was found to stretched the protein to both sides to make the protein structure extented,which is consistent with the pathways with the biggest transition flux.