dorsal/arxiv
View SchemaEffects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2
| Authors | Pablo Echenique, J. L. Alonso, Ivan Calvo |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0602022 |
| URL | https://arxiv.org/abs/q-bio/0602022 |
| DOI | 10.1063/1.2345627 |
| Journal | in the BIFI 2006 II International Congress Proceedings, edited by J. Clemente-Gallardo et al., vol. 851, pp. 108-116, AIP Conference Proceedings, Melville, New York, 2006 |
Abstract
A general approach to the design of accurate classical potentials for protein folding is described. It includes the introduction of a meaningful statistical measure of the differences between approximations of the same potential energy, the definition of a set of Systematic and Approximately Separable and Modular Internal Coordinates (SASMIC), much convenient for the simulation of general branched molecules, and the imposition of constraints on the most rapidly oscillating degrees of freedom. All these tools are used to study the effects of constraints in the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of the correcting terms to the naive CED based in the Potential Energy Surface (PES) without any simplifying assumption. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.
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"abstract": "A general approach to the design of accurate classical potentials for protein\nfolding is described. It includes the introduction of a meaningful statistical\nmeasure of the differences between approximations of the same potential energy,\nthe definition of a set of Systematic and Approximately Separable and Modular\nInternal Coordinates (SASMIC), much convenient for the simulation of general\nbranched molecules, and the imposition of constraints on the most rapidly\noscillating degrees of freedom. All these tools are used to study the effects\nof constraints in the Conformational Equilibrium Distribution (CED) of the\nmodel dipeptide HCO-L-Ala-NH2. We use ab initio Quantum Mechanics calculations\nincluding electron correlation at the MP2 level to describe the system, and we\nmeasure the conformational dependence of the correcting terms to the naive CED\nbased in the Potential Energy Surface (PES) without any simplifying assumption.\nThese terms are related to mass-metric tensors determinants and also occur in\nthe Fixman\u0027s compensating potential. We show that some of the corrections are\nnon-negligible if one is interested in the whole Ramachandran space. On the\nother hand, if only the energetically lower region, containing the principal\nsecondary structure elements, is assumed to be relevant, then, all correcting\nterms may be neglected up to peptides of considerable length. This is the first\ntime, as far as we know, that the analysis of the conformational dependence of\nthese correcting terms is performed in a relevant biomolecule with a realistic\npotential energy function.",
"arxiv_id": "q-bio/0602022",
"authors": [
"Pablo Echenique",
"J. L. Alonso",
"Ivan Calvo"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"doi": "10.1063/1.2345627",
"journal_ref": "in the BIFI 2006 II International Congress Proceedings, edited by\n J. Clemente-Gallardo et al., vol. 851, pp. 108-116, AIP Conference\n Proceedings, Melville, New York, 2006",
"title": "Effects of constraints in general branched molecules: A quantitative ab initio study in HCO-L-Ala-NH2",
"url": "https://arxiv.org/abs/q-bio/0602022"
},
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