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Article: Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution

TitleComparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
Authors
Issue Date2003
Citation
Proteins: Structure, Function And Genetics, 2003, v. 50 n. 3, p. 451-463 How to Cite?
AbstractWe compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, β and α separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of β of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between α and β at values of ψ near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio β/α varies between 1.5 and 2.2, the easy pass lies at ψ near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around φ = π and ψ = 0, whereas the amber force field gives two additional densely sampled states near φ = ±100° and ψ = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in highresolution protein structures than is the case for any of the MM simulations. © 2003 Wiley-Liss, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/167783
ISSN
2015 Impact Factor: 2.499
2015 SCImago Journal Rankings: 1.383
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHu, Hen_US
dc.contributor.authorElstner, Men_US
dc.contributor.authorHermans, Jen_US
dc.date.accessioned2012-10-08T03:11:31Z-
dc.date.available2012-10-08T03:11:31Z-
dc.date.issued2003en_US
dc.identifier.citationProteins: Structure, Function And Genetics, 2003, v. 50 n. 3, p. 451-463en_US
dc.identifier.issn0887-3585en_US
dc.identifier.urihttp://hdl.handle.net/10722/167783-
dc.description.abstractWe compare the conformational distributions of Ace-Ala-Nme and Ace-Gly-Nme sampled in long simulations with several molecular mechanics (MM) force fields and with a fast combined quantum mechanics/molecular mechanics (QM/MM) force field, in which the solute's intramolecular energy and forces are calculated with the self-consistent charge density functional tight binding method (SCCDFTB), and the solvent is represented by either one of the well-known SPC and TIP3P models. All MM force fields give two main states for Ace-Ala-Nme, β and α separated by free energy barriers, but the ratio in which these are sampled varies by a factor of 30, from a high in favor of β of 6 to a low of 1/5. The frequency of transitions between states is particularly low with the amber and charmm force fields, for which the distributions are noticeably narrower, and the energy barriers between states higher. The lower of the two barriers lies between α and β at values of ψ near 0 for all MM simulations except for charmm22. The results of the QM/MM simulations vary less with the choice of MM force field; the ratio β/α varies between 1.5 and 2.2, the easy pass lies at ψ near 0, and transitions between states are more frequent than for amber and charmm, but less frequent than for cedar. For Ace-Gly-Nme, all force fields locate a diffuse stable region around φ = π and ψ = 0, whereas the amber force field gives two additional densely sampled states near φ = ±100° and ψ = 0, which are also found with the QM/MM force field. For both solutes, the distribution from the QM/MM simulation shows greater similarity with the distribution in highresolution protein structures than is the case for any of the MM simulations. © 2003 Wiley-Liss, Inc.en_US
dc.languageengen_US
dc.relation.ispartofProteins: Structure, Function and Geneticsen_US
dc.subject.meshAlanine - Chemistryen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshDatabases, Proteinen_US
dc.subject.meshDipeptides - Chemistryen_US
dc.subject.meshGlycine - Chemistryen_US
dc.subject.meshModels, Molecularen_US
dc.subject.meshProtein Conformationen_US
dc.subject.meshProtein Foldingen_US
dc.subject.meshProteins - Chemistryen_US
dc.subject.meshQuantum Theoryen_US
dc.subject.meshSolutions - Chemistryen_US
dc.subject.meshWater - Chemistryen_US
dc.titleComparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solutionen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1002/prot.10279en_US
dc.identifier.pmid12557187-
dc.identifier.scopuseid_2-s2.0-0037441479en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-0037441479&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume50en_US
dc.identifier.issue3en_US
dc.identifier.spage451en_US
dc.identifier.epage463en_US
dc.identifier.isiWOS:000180691300007-
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridElstner, M=7004554960en_US
dc.identifier.scopusauthoridHermans, J=7201896483en_US
dc.identifier.citeulike1007761-

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