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Title: On the use of the discrete constant pH molecular dynamics to describe the conformational space of peptides
Author: Privat, Cristian
Madurga Díez, Sergio
Mas i Pujadas, Francesc
Rubio Martínez, Jaime
Keywords: Pèptids
Dinàmica molecular
Equilibri àcid-base
Molecular dynamics
Acid-base equilibrium
Issue Date: 29-Dec-2020
Publisher: MDPI
Abstract: Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.
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It is part of: Polymers, 2020, vol. 13, num. 1, p. 99
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ISSN: 2073-4360
Appears in Collections:Articles publicats en revistes (Ciència dels Materials i Química Física)

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