dorsal/arxiv
View SchemaCan contact potentials reliably predict stability of proteins?
| Authors | Jainab Kahtun, Sagar D. Khare, Nikolay V. Dokholyan |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0402039 |
| URL | https://arxiv.org/abs/q-bio/0402039 |
| Journal | J. Mol. Biol. 336: 1223-1238 (2004) |
Abstract
The simplest approximation of interaction potential between amino-acids in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting free energies of protein states across a variety of protein families will aid protein folding and engineering in silico on a computationally tractable time-scale. We test the ability of contact potentials to accurately and transferably (across various protein families) predict stability changes of proteins upon mutations. We develop a new methodology to determine the contact potentials in proteins from experimental measurements of changes in protein thermodynamic stabilities (ddG) upon mutations. We apply our methodology to derive sets of contact interaction parameters for a hierarchy of interaction models including solvation and multi-body contact parameters. We test how well our models reproduce experimental measurements by statistical tests. We evaluate the maximum accuracy of predictions obtained by using contact potentials and the correlation between parameters derived from different data-sets of experimental ddG values. We argue that it is impossible to reach experimental accuracy and derive fully transferable contact parameters using the contact models of potentials. However, contact parameters can yield reliable predictions of ddG for datasets of mutations confined to specific amino-acid positions in the sequence of a single protein.
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"abstract": "The simplest approximation of interaction potential between amino-acids in\nproteins is the contact potential, which defines the effective free energy of a\nprotein conformation by a set of amino acid contacts formed in this\nconformation. Finding a contact potential capable of predicting free energies\nof protein states across a variety of protein families will aid protein folding\nand engineering in silico on a computationally tractable time-scale. We test\nthe ability of contact potentials to accurately and transferably (across\nvarious protein families) predict stability changes of proteins upon mutations.\nWe develop a new methodology to determine the contact potentials in proteins\nfrom experimental measurements of changes in protein thermodynamic stabilities\n(ddG) upon mutations. We apply our methodology to derive sets of contact\ninteraction parameters for a hierarchy of interaction models including\nsolvation and multi-body contact parameters. We test how well our models\nreproduce experimental measurements by statistical tests. We evaluate the\nmaximum accuracy of predictions obtained by using contact potentials and the\ncorrelation between parameters derived from different data-sets of experimental\nddG values. We argue that it is impossible to reach experimental accuracy and\nderive fully transferable contact parameters using the contact models of\npotentials. However, contact parameters can yield reliable predictions of ddG\nfor datasets of mutations confined to specific amino-acid positions in the\nsequence of a single protein.",
"arxiv_id": "q-bio/0402039",
"authors": [
"Jainab Kahtun",
"Sagar D. Khare",
"Nikolay V. Dokholyan"
],
"categories": [
"q-bio.BM"
],
"journal_ref": "J. Mol. Biol. 336: 1223-1238 (2004)",
"title": "Can contact potentials reliably predict stability of proteins?",
"url": "https://arxiv.org/abs/q-bio/0402039"
},
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