dorsal/arxiv
View SchemaDo theoretical physicists care about the protein-folding problem?
| Authors | Jose Luis Alonso, Gregory A. Chass, Imre G. Csizmadia, Pablo Echenique, Alfonso Tarancon |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0407024 |
| URL | https://arxiv.org/abs/q-bio/0407024 |
Abstract
The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.
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"abstract": "The prediction of the biologically active native conformation of a protein is\none of the fundamental challenges of structural biology. This problem remains\nyet unsolved mainly due to three factors: the partial knowledge of the\neffective free energy function that governs the folding process, the enormous\nsize of the conformational space of a protein and, finally, the relatively\nsmall differences of energy between conformations, in particular, between the\nnative one and the ones that make up the unfolded state.\n Herein, we recall the importance of taking into account, in a detailed\nmanner, the many interactions involved in the protein folding problem (such as\nsteric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar\ninteractions, coulombic energy or hydrophobic attraction) and we propose a\nstrategy to effectively construct a free energy function that, including the\neffects of the solvent, could be numerically tractable. It must be pointed out\nthat, since the internal free energy function that is mainly described does not\ninclude the constraints of the native conformation, it could only help to reach\nthe \u0027molten globule\u0027 state. We also discuss about the limits and the lacks from\nwhich suffer the simple models that we, physicists, love so much.",
"arxiv_id": "q-bio/0407024",
"authors": [
"Jose Luis Alonso",
"Gregory A. Chass",
"Imre G. Csizmadia",
"Pablo Echenique",
"Alfonso Tarancon"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"title": "Do theoretical physicists care about the protein-folding problem?",
"url": "https://arxiv.org/abs/q-bio/0407024"
},
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