AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal
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 re...
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| Format: | Article |
| Language: | English |
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Elsevier
2020-04-01
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| Series: | Data in Brief |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340920301888 |
| _version_ | 1819139272904540160 |
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| author | Antistio Alviz-Amador Rodrigo Galindo-Murillo Humberto Pérez-González Erika Rodríguez-Cavallo Ricardo Vivas-Reyes Darío Méndez-Cuadro |
| author_facet | Antistio Alviz-Amador Rodrigo Galindo-Murillo Humberto Pérez-González Erika Rodríguez-Cavallo Ricardo Vivas-Reyes Darío Méndez-Cuadro |
| author_sort | Antistio Alviz-Amador |
| collection | DOAJ |
| description | 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, Gaff, Force field parameterization, Quantum-mechanics, Molecular dynamics, Geometry optimization, Validation, Protein carbonylation |
| first_indexed | 2024-12-22T11:20:02Z |
| format | Article |
| id | doaj.art-9375e7bc580e4b7fbd4171b7c7be6842 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-22T11:20:02Z |
| publishDate | 2020-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-9375e7bc580e4b7fbd4171b7c7be68422022-12-21T18:27:54ZengElsevierData in Brief2352-34092020-04-0129AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenalAntistio Alviz-Amador0Rodrigo Galindo-Murillo1Humberto Pérez-González2Erika Rodríguez-Cavallo3Ricardo Vivas-Reyes4Darío Méndez-Cuadro5Analytical 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, ColombiaDepartment of Medicinal Chemistry, Skaggs Pharmacy Research Building, University of Utah, 257 1400 E, Salt Lake City, UT 84112, USAAnalytical 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, ColombiaAnalytical 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, ColombiaGrupo 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, ColombiaAnalytical 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; Corresponding author.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, Gaff, Force field parameterization, Quantum-mechanics, Molecular dynamics, Geometry optimization, Validation, Protein carbonylationhttp://www.sciencedirect.com/science/article/pii/S2352340920301888 |
| spellingShingle | Antistio Alviz-Amador Rodrigo Galindo-Murillo Humberto Pérez-González Erika Rodríguez-Cavallo Ricardo Vivas-Reyes Darío Méndez-Cuadro AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal Data in Brief |
| title | AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal |
| title_full | AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal |
| title_fullStr | AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal |
| title_full_unstemmed | AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal |
| title_short | AMBER parameters and topology data of 2-pentylpyrrole adduct of arginine with 4-hydroxy-2-nonenal |
| title_sort | amber parameters and topology data of 2 pentylpyrrole adduct of arginine with 4 hydroxy 2 nonenal |
| url | http://www.sciencedirect.com/science/article/pii/S2352340920301888 |
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