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

Antistio Alviz-Amador; Rodrigo Galindo-Murillo; Humberto Pérez-González; Erika Rodríguez-Cavallo; Ricardo Vivas-Reyes; Darío Méndez-Cuadro

doi:10.1016/j.dib.2020.105294

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

Data Brief. 2020 Feb 19:29:105294. doi: 10.1016/j.dib.2020.105294. eCollection 2020 Apr.

Authors

Antistio Alviz-Amador¹, Rodrigo Galindo-Murillo², Humberto Pérez-González¹, Erika Rodríguez-Cavallo³, Ricardo Vivas-Reyes⁴, Darío Méndez-Cuadro¹

Affiliations

¹ Analytical Chemistry and Biomedicine Group, Faculty of Exact and Natural Sciences, Campus of San Pablo, University of Cartagena, First Floor Lab.109. Cra. 50 #24-120, PA 130015, Cartagena, Colombia.
² Department of Medicinal Chemistry, Skaggs Pharmacy Research Building, University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA.
³ Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, Campus of Zaragocilla, Ancient Building CREAD, University of Cartagena, Lab 103. Cra. 50 #24-120, PA 130015, Cartagena, Colombia.
⁴ Grupo de Química Cuántica y Teórica, Faculty of Exact and Natural Sciences, Campus of San Pablo, University of Cartagena, Second Floor # 202. Cra. 50 #24-120, PA 130015, Cartagena, Colombia.

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.

Keywords: AMBER; Force field parameterization; Gaff; Geometry optimization; Molecular dynamics; Protein carbonylation; Quantum-mechanics; Validation.