title: Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.
abstract: Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical calculations and a Generalized Born continuum solvent model. Starting from its fully extended conformation, our simulation has produced a final structure resembling that of NMR native structure to within 1A main-chain root mean square deviation. Remarkably, the simulated structure stayed in the native state for most part of the simulation after it reached the state. Of greater significance is that our simulation has not only reached the correct main-chain conformation, but also a very high degree of accuracy in side-chain packing conformation. This feat has traditionally been a challenge for ab initio simulation studies. In addition to characterization of the trajectory, comparison of our results to experimental data is also presented. Analysis of the trajectory suggests that the rate-limiting step of folding of this mini-protein is the packing of the Trp side-chain.
authors.affiliation: Department of Chemistry and Biochemistry, Center of Biomedical Research Excellence in Structural and Functional Genomics, University of Delaware, Newark, DE 19716, USA.
authors.forename: Shibasish
authors.initials: S
authors.lastname: Chowdhury
authors.forename: Mathew C
authors.initials: MC
authors.lastname: Lee
authors.forename: Guoming
authors.initials: G
authors.lastname: Xiong
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D019295:Computational Biology; D003198:Computer Simulation; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D012984:Software; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry*
chemical_list: D014364:Tryptophan