1
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Gresh N, Perahia D. Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry. J Comput Chem 2021; 42:1430-1446. [PMID: 34101861 DOI: 10.1002/jcc.26555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
Dimethyl phosphate (DMP- ) is a model for the phosphodiester backbone of DNA, RNA, and phospholipids. It is central for the binding of divalent cations and water along the backbone of nucleic acids. Significant polarization and charge-transfer contributions and nonadditivity come into play in the multimolecular complexes organized around phosphate. Prior to large-scale molecular dynamics (MD) with advanced polarizable potentials, it is essential to evaluate how well the values and trends of intermolecular interaction energies (ΔE) from ab initio quantum chemistry (QC) and their individual contributions are reproduced in a diversity of such complexes. These differ by the starting binding modes of a divalent cation, Zn(II), namely direct, bi- or mono-dentate to anionic and/or ester oxygens, versus through-water binding. We present first the results from automated refinements of the individual contributions of the SIBFA potential with respect to their QC counterparts using a Zn(II) or a water probe. This is followed by validations on eight relaxed multimolecular complexes of DMP- with Zn(II) or Mg(II) and seven waters, then on sixteen complexes of DMP- with Zn(II) and eight waters in arrangements extracted from MD or energy-minimization on a droplet of sixty-four waters. This monitors the compared evolutions of SIBFA and QC ΔE and their individual contributions in the competing arrangements. Some waters, bridging Zn(II) and DMP- , were found to have exceptionally large dipole moments, of up to 3.8 Debye. The perspectives of extension to a flexible phosphodiester backbone are discussed in the context of the SIBFA potential for DNA and RNA.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, Paris, France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
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2
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Kwapien K, Gavara L, Docquier J, Berthomieu D, Hernandez J, Gresh N. Intermolecular interactions of the extended recognition site of
VIM
‐2
metallo‐β‐lactamase
with 1,2,4‐triazole‐3‐thione inhibitors. Validations of a polarizable molecular mechanics potential by ab initio
QC. J Comput Chem 2020; 42:86-106. [DOI: 10.1002/jcc.26437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Karolina Kwapien
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques Université de Paris UMR 8601 Paris France
- Laboratoire de Chimie Théorique Paris France
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | | | - Dorothée Berthomieu
- Institut Charles Gerhardt, UMR 5253, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Jean‐François Hernandez
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier, ENSCM, Faculté de Pharmacie Montpellier France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique Paris France
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3
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Jing Z, Qi R, Liu C, Ren P. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field. J Chem Phys 2018; 147:161733. [PMID: 29096462 DOI: 10.1063/1.4985921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
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4
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Ahlstrand E, Hermansson K, Friedman R. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations. J Phys Chem A 2017; 121:2643-2654. [DOI: 10.1021/acs.jpca.6b12969] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emma Ahlstrand
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Kersti Hermansson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden
| | - Ran Friedman
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
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5
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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6
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Gresh N, Perahia D, de Courcy B, Foret J, Roux C, El-Khoury L, Piquemal JP, Salmon L. Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. J Comput Chem 2016; 37:2770-2782. [DOI: 10.1002/jcc.24503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/31/2016] [Accepted: 09/04/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées (LBPA), UMR 8113; Ecole Normale Supérieure Cachan France
| | - Benoit de Courcy
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale; Paris France
| | - Johanna Foret
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
| | - Lea El-Khoury
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Centre d'Analyses et de Recherche; UR EGFEM, LSIM, Faculté de Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique; Sorbonne Universités; UPMC, UMR 7616 CNRS Paris France
- Department of Biomolecular Engineering; The University of Texas at Austin; Texas 78712
| | - Laurent Salmon
- Laboratoire de Chimie Bioorganique et Bioinorganique; Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), Univ Paris-Saclay, Univ Paris-Sud, UMR 8182 CNRS; rue du Doyen Georges Poitou Orsay F-91405 France
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Dudev T, Devereux M, Meuwly M, Lim C, Piquemal JP, Gresh N. Quantum-chemistry based calibration of the alkali metal cation series (Li+Cs+) for large-scale polarizable molecular mechanics/dynamics simulations. J Comput Chem 2014; 36:285-302. [DOI: 10.1002/jcc.23801] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/05/2014] [Accepted: 11/10/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Todor Dudev
- Faculty of Chemistry and Pharmacy; University of Sofia; 1164 Sofia Bulgaria
| | - Mike Devereux
- Department of Chemistry; University of Basel; Basel Switzerland
| | - Markus Meuwly
- Department of Chemistry; University of Basel; Basel Switzerland
| | - Carmay Lim
- Institute of Biomedical Sciences; Academia Sinica; Taipei 115 Taiwan
- Department of Chemistry; National Tsing Hua University; Hsinchu 300 Taiwan
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités; UPMC, UMR7616 CNRS Paris France
| | - Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale; 45 rue des Saints-Pères, 75270 Paris Cedex 06 France
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