Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-Path Algorithm Export

@article{citeulike:2966809, abstract = {To predict a protein-folding pathway, we present an alternative to the time-consuming dynamic simulation of atomistic models. We replace the actual dynamic simulation with variational optimization of a reaction path connecting known initial and final protein conformations in such a way as to maximize an estimate of the reactive flux or minimize the mean first passage time at a given temperature, referred to as MaxFlux. We solve the MaxFlux global optimization problem with an efficient graph-theoretic approach, the probabilistic roadmap method (PRM). We employed CHARMM19 and the EEF1 implicit solvation model to describe the protein solution. The effectiveness of our MaxFlux-PRM is demonstrated in our promising simulation results on the folding pathway of the engrailed homeodomain. Our MaxFlux-PRM approach provides the direct evidence to support that the previously reported intermediate state is a genuine on-pathway intermediate, and the demand of CPU power is moderate. 10.1529/biophysj.107.119214}, author = {Li, Da-Wei and Yang, Haijun and Han, Li and Huo, Shuanghong}, citeulike-article-id = {2966809}, citeulike-linkout-0 = {http://dx.doi.org/10.1529/biophysj.107.119214}, citeulike-linkout-1 = {http://www.biophysj.org/cgi/content/abstract/94/5/1622}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18024496}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18024496}, day = {1}, doi = {10.1529/biophysj.107.119214}, journal = {Biophys. J.}, keywords = {protein-folding}, month = {March}, number = {5}, pages = {1622--1629}, posted-at = {2008-07-06 06:31:37}, priority = {3}, title = {Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-Path Algorithm}, url = {http://dx.doi.org/10.1529/biophysj.107.119214}, volume = {94}, year = {2008} }

TY - JOUR ID - citeulike:2966809 L3 - citeulike-article-id:2966809 N2 - To predict a protein-folding pathway, we present an alternative to the time-consuming dynamic simulation of atomistic models. We replace the actual dynamic simulation with variational optimization of a reaction path connecting known initial and final protein conformations in such a way as to maximize an estimate of the reactive flux or minimize the mean first passage time at a given temperature, referred to as MaxFlux. We solve the MaxFlux global optimization problem with an efficient graph-theoretic approach, the probabilistic roadmap method (PRM). We employed CHARMM19 and the EEF1 implicit solvation model to describe the protein solution. The effectiveness of our MaxFlux-PRM is demonstrated in our promising simulation results on the folding pathway of the engrailed homeodomain. Our MaxFlux-PRM approach provides the direct evidence to support that the previously reported intermediate state is a genuine on-pathway intermediate, and the demand of CPU power is moderate. 10.1529/biophysj.107.119214 IS - 5 JF - Biophys. J. EP - 1629 TI - Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-Path Algorithm VL - 94 SP - 1622 KW - protein-folding AU - Li, Da-Wei AU - Yang, Haijun AU - Han, Li AU - Huo, Shuanghong PY - 2008/03/01/ UR - http://dx.doi.org/10.1529/biophysj.107.119214 ER -