Development and benchmark to obtain AMBER parameters dataset for non-standard amino acids modified with 4-hydroxy-2-nonenal

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

doi:10.1016/j.dib.2018.11.102

Development and benchmark to obtain AMBER parameters dataset for non-standard amino acids modified with 4-hydroxy-2-nonenal

Data Brief. 2018 Nov 27:21:2581-2589. doi: 10.1016/j.dib.2018.11.102. eCollection 2018 Dec.

Authors

Antistio Alviz-Amador¹, Rodrigo Galindo-Murillo², Rafael Pineda-Alemán³, Humberto Pérez-González⁴, Erika Rodríguez-Cavallo¹, Ricardo Vivas-Reyes⁵, Darío Méndez-Cuadro³

Affiliations

¹ Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia.
² Department of Medicinal Chemistry, University of Utah, Salt Lake, USA.
³ Analytical Chemistry and Biomedicine Group, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia.
⁴ Department of Mathematical, Exact and Natural Sciences Faculty, University of Cartagena, Cartagena, Colombia.
⁵ Grupo de Química Cuántica y Teórica, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena, Colombia.

Abstract

The data described here support the research article "4-HNE carbonylation induces local conformational changes on bovine serum albumin and thioredoxin. A molecular dynamics study" (Alviz-Amador et al., 2018) . Dataset on Gaff force field parameters of AMBER is provided for assembled three non-standard amino acids resulting of the 4-HNE Michael addition, the main end product of lipids peroxidation. Data include a framework for derivation of missing bonds, angles and dihedral parameters for Cys, His, and Lys modified amino acids, alongside optimized partial charges derived with Restrained Electrostatic Potential (RESP) method and the new force field parameters obtained by quantic mechanical (QM) using 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 residues constructed are put available to the scientific community to perform molecular dynamics simulations of modified 4-HNE proteins.

Keywords: AMBER; Force field parameterization; Gaff; Geometry optimization; Mechanical quantic; Molecular dynamics; Validation.