dorsal/arxiv
View SchemaQuantitative Protein Dynamics from Dominant Folding Pathways
| Authors | M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, H. Orland |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0701028 |
| URL | https://arxiv.org/abs/q-bio/0701028 |
| DOI | 10.1103/PhysRevLett.99.118102 |
Abstract
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details using existing computers becomes feasible. In addition, this formalism provides a natural framework to investigate the relationships between thermodynamical and kinetic aspects of the folding. For example, it is possible to show that, in order to have a large probability to remain unchanged under Langevin diffusion, the native state has to be characterized by a small conformational entropy. We discuss how to determine the most probable folding pathway, to identify configurations representative of the transition state and to compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine di-peptide, within an all-atom model based on the empiric GROMOS96 force field.
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"abstract": "We develop a theoretical approach to the protein folding problem based on\nout-of-equilibrium stochastic dynamics. Within this framework, the\ncomputational difficulties related to the existence of large time scale gaps in\nthe protein folding problem are removed and simulating the entire reaction in\natomistic details using existing computers becomes feasible. In addition, this\nformalism provides a natural framework to investigate the relationships between\nthermodynamical and kinetic aspects of the folding. For example, it is possible\nto show that, in order to have a large probability to remain unchanged under\nLangevin diffusion, the native state has to be characterized by a small\nconformational entropy. We discuss how to determine the most probable folding\npathway, to identify configurations representative of the transition state and\nto compute the most probable transition time. We perform an illustrative\napplication of these ideas, studying the conformational evolution of alanine\ndi-peptide, within an all-atom model based on the empiric GROMOS96 force field.",
"arxiv_id": "q-bio/0701028",
"authors": [
"M. Sega",
"P. Faccioli",
"F. Pederiva",
"G. Garberoglio",
"H. Orland"
],
"categories": [
"q-bio.QM",
"cond-mat.soft",
"q-bio.BM"
],
"doi": "10.1103/PhysRevLett.99.118102",
"title": "Quantitative Protein Dynamics from Dominant Folding Pathways",
"url": "https://arxiv.org/abs/q-bio/0701028"
},
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