dorsal/arxiv
View SchemaNative geometry and the dynamics of protein folding
| Authors | P. F. N. Faisca, M. M. Telo da Gama |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0411044 |
| URL | https://arxiv.org/abs/q-bio/0411044 |
| DOI | 10.1016/j.bpc.2004.12.022 |
| Journal | Biophysical Chemistry 115, 169-175 (2005) |
Abstract
In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the G\={o} model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.
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"abstract": "In this paper we investigate the role of native geometry on the kinetics of\nprotein folding based on simple lattice models and Monte Carlo simulations.\nResults obtained within the scope of the Miyazawa-Jernigan indicate the\nexistence of two dynamical folding regimes depending on the protein chain\nlength. For chains larger than 80 amino acids the folding performance is\nsensitive to the native state\u0027s conformation. Smaller chains, with less than 80\namino acids, fold via two-state kinetics and exhibit a significant correlation\nbetween the contact order parameter and the logarithmic folding times. In\nparticular, chains with N=48 amino acids were found to belong to two broad\nclasses of folding, characterized by different cooperativity, depending on the\ncontact order parameter. Preliminary results based on the G\\={o} model show\nthat the effect of long range contact interaction strength in the folding\nkinetics is largely dependent on the native state\u0027s geometry.",
"arxiv_id": "q-bio/0411044",
"authors": [
"P. F. N. Faisca",
"M. M. Telo da Gama"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1016/j.bpc.2004.12.022",
"journal_ref": "Biophysical Chemistry 115, 169-175 (2005)",
"title": "Native geometry and the dynamics of protein folding",
"url": "https://arxiv.org/abs/q-bio/0411044"
},
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