AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal.

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ID: 101668
2020
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Abstract
The data described here supports a part of the research article "Effect of 4‑HNE Modification on ZU5-ANK Domain and the Formation of Their Complex with β‑Spectrin: A Molecular Dynamics Simulation Study" [1]. Dataset on Gaff force field parameters of AMBER is provided for the non-standard arginine resulting of reaction with 4-hydroxy-2-nonenal (4-HNE), the major secondary product of lipids peroxidation. Arg-HNE 2-pentilpyrrole adduct is part of the 4-hydroxyalkenals described in various physiopathological disorders related to increased oxidative stress. Data include a framework for derivation of missing bonds, angles and dihedral parameters for modified arginine, alongside optimized partial charges derived with Restrained Electrostatic Potential (RESP) method and the new force field parameters obtained by quantum mechanicals methods (QM) using Hartree-Fock (HF)/6 - 31G** level of theory. Benchmark as a graphics tutorial summary steps to obtained new parameters and the validation of non-standard amino acids is presented. The new residue constructed is put available to the scientific community to perform molecular dynamics simulations of modified 4-HNE proteins on arginine residue and complete the set of data parameters for nucleophilic residues with this reactive aldehyde ADDIN EN.CITE ADDIN EN.CITE.DATA [2]. Data that could be used for the researchers interested in the role of protein oxidation as mediator in cellular pathophysiological.
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alvizamador2020amberdata Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Alviz-Amador, Antistio;Galindo-Murillo, Rodrigo;Pérez-González, Humberto;Rodríguez-Cavallo, Erika;Vivas-Reyes, Ricardo;Méndez-Cuadro, Darío;
Journal Data in brief
Year 2020
DOI
10.1016/j.dib.2020.105294
URL
Keywords
validation molecular dynamics protein carbonylation geometry optimization amber force field parameterization gaff quantum-mechanics

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