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Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations
dc.contributor.author | Rubio Martínez, Jaime |
dc.contributor.author | Tomás Belenguer, María Santos |
dc.contributor.author | Pérez González, Juan Jesús |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament de Tecnologia de l'Arquitectura |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament d'Enginyeria Química |
dc.date.accessioned | 2017-11-17T18:35:42Z |
dc.date.available | 2017-11-17T18:35:42Z |
dc.date.issued | 2017-11-01 |
dc.identifier.citation | Rubio, J., Tomas, M., Perez, J. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations. "Journal of Molecular Graphics and Modelling", 1 Novembre 2017, vol. 78, núm. November, p. 1-11. |
dc.identifier.issn | 1873-4243 10933263 |
dc.identifier.uri | http://hdl.handle.net/2117/110882 |
dc.description.abstract | In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra- and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetamide. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C7 eq only sampled in chloroform; the C5 or extended conformation; the polyproline (PII) conformation and the right-handed a-helix conformation (aR). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed. |
dc.format.extent | 11 p. |
dc.language.iso | eng |
dc.rights | Attribution-NonCommercial-NoDerivs 3.0 Spain |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/3.0/es/ |
dc.subject | Àrees temàtiques de la UPC::Enginyeria química::Química física |
dc.subject.lcsh | Peptides |
dc.subject.other | Alanine dipeptide |
dc.subject.other | Amino acid conformations |
dc.subject.other | Chloroform |
dc.subject.other | Dimethyl sulfoxide |
dc.subject.other | Intermolecular interactions |
dc.subject.other | Intramolecular interactions |
dc.subject.other | MD simulations |
dc.subject.other | Methanol |
dc.subject.other | N-methylacetamide |
dc.subject.other | Solvent effects |
dc.title | Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations |
dc.type | Article |
dc.subject.lemac | Pèptids |
dc.contributor.group | Universitat Politècnica de Catalunya. GBMI - Grup de Biotecnologia Molecular i Industrial |
dc.identifier.doi | 10.1016/j.jmgm.2017.10.005 |
dc.relation.publisherversion | http://www.sciencedirect.com/science/article/pii/S1093326317306101?via%3Dihub |
dc.rights.access | Open Access |
local.identifier.drac | 21592047 |
dc.description.version | Postprint (published version) |
local.citation.author | Rubio, J.; Tomas, M.; Perez, J. |
local.citation.publicationName | Journal of Molecular Graphics and Modelling |
local.citation.volume | 78 |
local.citation.number | November |
local.citation.startingPage | 1 |
local.citation.endingPage | 11 |
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