FOLDING A MINI-PROTEIN (TRPCAGE) USING WEIGHTED ENSEMBLE PATH SAMPLING

点击翻译按钮获取中文摘要

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Folding a mini-protein (trpcage) via the Weighted Ensemble Path Sampling Method How proteins fold is a matter of scientific interest because the folding pathway must cover a broad and rough configurational landscape, and overcome large entropic barriers to reach the folded state. Besides the scientific interest, there are direct and practical reasons to understand protein folding: Diseases like Alzheimers, Huntingtons and Parkinsons are proposed to be caused by protein mis-folding. Attempts to use computer simulations to probe protein-folding span the past 50 years, and is quite challenging. Therefore computational folding of mini-proteins is used to probe the accuracy and effectiveness of computational models and methods. Here we present folding the trpcage mini-protein via the Weighted Ensemble Path Sampling method. The Weighted Ensemble method was previously applied to the protein Camodulin, to investigate transitions of a two state system. There, the method demonstrated its usefulness to make tractable rare transitions that require the system to climb over prohibitive energy barriers. Here, we adapt and apply the method for protein-folding, where the protein model must overcome a manifold of energy barriers to reach the folded state. We compare the efficiency of this method to brute force folding via conventional molecular dynamics.