Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations Export

@article{citeulike:2476026, abstract = {Abstract: We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.}, address = {Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea, and Department of Chemistry, Pusan National University, Pusan 609-735, Korea}, author = {Jang, S. and Kim, E. and Shin, S. and Pak, Y.}, citeulike-article-id = {2476026}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ja034701i}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ja034701i}, day = {3}, doi = {10.1021/ja034701i}, journal = {J. Am. Chem. Soc.}, keywords = {implicit\_solvation, protein\_folding}, month = {December}, number = {48}, pages = {14841--14846}, posted-at = {2008-03-06 00:28:00}, priority = {2}, title = {Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations}, url = {http://dx.doi.org/10.1021/ja034701i}, volume = {125}, year = {2003} }

TY - JOUR ID - citeulike:2476026 L3 - citeulike-article-id:2476026 N2 - Abstract: We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins. IS - 48 JF - J. Am. Chem. Soc. AD - Contribution from the School of Chemistry, Seoul National University, Seoul 151-747, Korea, and Department of Chemistry, Pusan National University, Pusan 609-735, Korea EP - 14846 TI - Ab Initio Folding of Helix Bundle Proteins Using Molecular Dynamics Simulations VL - 125 SP - 14841 KW - implicit_solvation KW - protein_folding AU - Jang, S AU - Kim, E AU - Shin, S AU - Pak, Y PY - 2003/12/03/ UR - http://dx.doi.org/10.1021/ja034701i ER -