dorsal/arxiv
View SchemaEnergetics of Protein-DNA Interactions
| Authors | Jason E Donald, William W Chen, Eugene I Shakhnovich |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611095 |
| URL | https://arxiv.org/abs/q-bio/0611095 |
Abstract
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that theoretical models describe the macromolecular interaction energetics accurately. While several methods have been proposed, there has not been a careful comparison of how well the different methods are able to predict biologically important quantities such as the correct DNA binding sequence, total binding free energy, and free energy changes caused by DNA mutation. In addition to carrying out the comparison, we present two important theoretical models developed initially in protein folding that have not yet been tried on protein-DNA interactions. In the process, we find that the results of these knowledge-based potentials show a strong dependence on the interaction distance and the derivation method. Finally, we present a knowledge-based potential that gives comparable or superior results to the best of the other methods, including the molecular mechanics force field AMBER99.
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"abstract": "Protein-DNA interactions are vital for many processes in living cells,\nespecially transcriptional regulation and DNA modification. To further our\nunderstanding of these important processes on the microscopic level, it is\nnecessary that theoretical models describe the macromolecular interaction\nenergetics accurately. While several methods have been proposed, there has not\nbeen a careful comparison of how well the different methods are able to predict\nbiologically important quantities such as the correct DNA binding sequence,\ntotal binding free energy, and free energy changes caused by DNA mutation. In\naddition to carrying out the comparison, we present two important theoretical\nmodels developed initially in protein folding that have not yet been tried on\nprotein-DNA interactions. In the process, we find that the results of these\nknowledge-based potentials show a strong dependence on the interaction distance\nand the derivation method. Finally, we present a knowledge-based potential that\ngives comparable or superior results to the best of the other methods,\nincluding the molecular mechanics force field AMBER99.",
"arxiv_id": "q-bio/0611095",
"authors": [
"Jason E Donald",
"William W Chen",
"Eugene I Shakhnovich"
],
"categories": [
"q-bio.BM"
],
"title": "Energetics of Protein-DNA Interactions",
"url": "https://arxiv.org/abs/q-bio/0611095"
},
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