Ab initio Folding Simulation of the Trp-cage Mini-protein Approaches NMR Resolution
| Autor: | Mathew C. Lee, Shibasish Chowdhury, Yong Duan, Guoming Xiong |
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| Rok vydání: | 2003 |
| Předmět: |
Models
Molecular Protein Folding Magnetic Resonance Spectroscopy Time Factors Protein Conformation Biophysics Ab initio Biophysical Phenomena Force field (chemistry) Molecular dynamics Protein structure Structural Biology Native state Computer Simulation Molecular Biology Root-mean-square deviation Quantitative Biology::Biomolecules Chemistry Tryptophan Computational Biology Hydrogen Bonding Nuclear magnetic resonance spectroscopy Crystallography Chemical physics Protein folding Software Protein Binding |
| Zdroj: | Journal of Molecular Biology. 327:711-717 |
| ISSN: | 0022-2836 |
| DOI: | 10.1016/s0022-2836(03)00177-3 |
| Popis: | 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 1 A 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. |
| Databáze: | OpenAIRE |
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