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Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent
Rodríguez García, Alejandro; Mokoema, Pol; Corcho Sánchez, Francisco José; Bisetty, Krishna; Pérez González, Juan Jesús
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química; Universitat Politècnica de Catalunya. IMEM - Innovació, Modelització i Enginyeria en (BIO) Materials
The prediction capabilities of atomistic simulations of peptides are hampered by different difficulties, including the reliability of force fields, the treatment of the solvent or the adequate sampling of the conformational space. In this work, we have studied the conformational profile of the 10 residue miniprotein CLN025 known to exhibit a β-hairpin in its native state to understand the limitations of implicit methods to describe solvent effects and how these may be compensated by using different force fields. For this purpose, we carried out a thorough sampling of the conformational space of CLN025 in explicit solvent using the replica exchange molecular dynamics method as a sampling technique and compared the results with simulations of the system modeled using the analytical linearized Poisson-Boltzmann (ALPB) method with three different AMBER force fields: parm94, parm96, and parm99SB. The results show the peptide to exhibit a funnel-like free energy landscape with two minima in explicit solvent. In contrast, the higher minimum nearly disappears from the energy surface when the system is studied with an implicit representation of the solvent. Moreover, the different force fields used in combination with the ALPB method do not describe the system in the same manner. The results of this work suggest that the balance between intra- and intermolecular interactions is the cause of the differences between implicit and explicit solvent simulations in this system, stressing the role of the environment to define properly the conformational profile of a peptide in solution.
Peer Reviewed
Àrees temàtiques de la UPC::Matemàtiques i estadística
Peptides
Pèptids
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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