dorsal/arxiv
View SchemaAb initio study of alanine polypeptide chains twisting
| Authors | Ilia A. Solov'yov, Alexander V. Yakubovitch, Andrey V. Solov'yov, Walter Greiner |
|---|---|
| Categories | |
| ArXiv ID | physics/0511036 |
| URL | https://arxiv.org/abs/physics/0511036 |
| DOI | 10.1103/PhysRevE.73.021916 |
Abstract
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles Phi and Psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.
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"abstract": "We have investigated the potential energy surfaces for alanine chains\nconsisting of three and six amino acids. For these molecules we have calculated\npotential energy surfaces as a function of the Ramachandran angles Phi and Psi,\nwhich are widely used for the characterization of the polypeptide chains. These\nparticular degrees of freedom are essential for the characterization of\nproteins folding process. Calculations have been carried out within ab initio\ntheoretical framework based on the density functional theory and accounting for\nall the electrons in the system. We have determined stable conformations and\ncalculated the energy barriers for transitions between them. Using a\nthermodynamic approach, we have estimated the times of characteristic\ntransitions between these conformations. The results of our calculations have\nbeen compared with those obtained by other theoretical methods and with the\navailable experimental data extracted from the Protein Data Base. This\ncomparison demonstrates a reasonable correspondence of the most prominent\nminima on the calculated potential energy surfaces to the experimentally\nmeasured angles Phi and Psi for alanine chains appearing in native proteins. We\nhave also investigated the influence of the secondary structure of polypeptide\nchains on the formation of the potential energy landscape. This analysis has\nbeen performed for the sheet and the helix conformations of chains of six amino\nacids.",
"arxiv_id": "physics/0511036",
"authors": [
"Ilia A. Solov\u0027yov",
"Alexander V. Yakubovitch",
"Andrey V. Solov\u0027yov",
"Walter Greiner"
],
"categories": [
"physics.bio-ph",
"physics.chem-ph"
],
"doi": "10.1103/PhysRevE.73.021916",
"title": "Ab initio study of alanine polypeptide chains twisting",
"url": "https://arxiv.org/abs/physics/0511036"
},
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