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Computational investigation of the conformational profile of the four stereomers of Ac-L-Pro-c(3)Phe-NHMe (c(3)Phe= 2,3-methanophenylalanine)
Rodríguez García, Alejandro; Cantó Silva, Josep; Corcho Sánchez, Francisco José; Pérez González, Juan Jesús
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química; Universitat Politècnica de Catalunya. IMEM - Innovació en Materials i Enginyeria Molecular
The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace-Pro-c3Phe-NMe, previously reported to exhibit b-turn structures in dichloromethane with different type I/type II b-turn profiles. Molecular systems were represented at the molecular mechanics level using the parm96 parameterization of the AMBER force field. Calculations were carried out in dichloromethane using an implicit solvent approach. Characterization of the conformational features of the peptide analogs was carried out using simulated annealing (SA), molecular dynamics (MD) and replica exchange molecular dynamics (REMD). Present results show that MD calculations do not provide a reasonable sampling after 300 ns. In contrast, both SA and REMD provide similar results and agree well with experimental observations.
Peer Reviewed
Àrees temàtiques de la UPC::Enginyeria química
Pèptids
Estructura molecular
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
info:eu-repo/semantics/publishedVersion
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