Cargando…
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
[Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angl...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2015
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504185/ https://www.ncbi.nlm.nih.gov/pubmed/26190950 http://dx.doi.org/10.1021/acs.jctc.5b00356 |
_version_ | 1782381443545038848 |
---|---|
author | Robertson, Michael J. Tirado-Rives, Julian Jorgensen, William L. |
author_facet | Robertson, Michael J. Tirado-Rives, Julian Jorgensen, William L. |
author_sort | Robertson, Michael J. |
collection | PubMed |
description | [Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields. |
format | Online Article Text |
id | pubmed-4504185 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-45041852015-07-17 Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field Robertson, Michael J. Tirado-Rives, Julian Jorgensen, William L. J Chem Theory Comput [Image: see text] The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ(1), and χ(2) potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields. American Chemical Society 2015-06-01 2015-07-14 /pmc/articles/PMC4504185/ /pubmed/26190950 http://dx.doi.org/10.1021/acs.jctc.5b00356 Text en Copyright © 2015 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes. |
spellingShingle | Robertson, Michael J. Tirado-Rives, Julian Jorgensen, William L. Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field |
title | Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field |
title_full | Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field |
title_fullStr | Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field |
title_full_unstemmed | Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field |
title_short | Improved Peptide and Protein Torsional Energetics
with the OPLS-AA Force Field |
title_sort | improved peptide and protein torsional energetics
with the opls-aa force field |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504185/ https://www.ncbi.nlm.nih.gov/pubmed/26190950 http://dx.doi.org/10.1021/acs.jctc.5b00356 |
work_keys_str_mv | AT robertsonmichaelj improvedpeptideandproteintorsionalenergeticswiththeoplsaaforcefield AT tiradorivesjulian improvedpeptideandproteintorsionalenergeticswiththeoplsaaforcefield AT jorgensenwilliaml improvedpeptideandproteintorsionalenergeticswiththeoplsaaforcefield |