1
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Sarkar R, Mainan A, Roy S. Influence of ion and hydration atmospheres on RNA structure and dynamics: insights from advanced theoretical and computational methods. Chem Commun (Camb) 2024. [PMID: 38501190 DOI: 10.1039/d3cc06105a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation. In addition to investigating the RNA's ion environment, we note that the RNA's hydration environment is relatively underexplored. Our study delves into its profound interplay with the structural dynamics of RNA, employing state-of-the-art atomistic simulation techniques. Through examples, we illustrate how specific ions and water molecules are associated with RNA functions, leveraging atomistic simulations to identify preferential ion binding and hydration sites. However, understanding their impact(s) on the RNA structure remains challenging due to the involvement of large length and long time scales associated with RNA's dynamic nature. Nevertheless, our contributions and recent advances in coarse-grained simulation techniques offer insights into large-scale structural changes dynamically linked to the RNA ion atmosphere. In this connection, we also review how different cutting-edge computational simulation methods provide a microscopic lens into the influence of ions and hydration on RNA structure and dynamics, elucidating distinct ion atmospheric components and specific hydration layers and their individual and collective impacts.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Avijit Mainan
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata, West Bengal 741246, India.
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2
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Sengul MY, MacKerell AD. Accurate Modeling of RNA Hairpins Through the Explicit Treatment of Electronic Polarizability with the Classical Drude Oscillator Force Field. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022; 21:461-471. [DOI: 10.1142/s2737416521420060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular dynamics (MD) simulations play a crucial role in modeling biomolecular systems in which the electrostatic interactions are critical in dictating the structural and dynamical properties. Thus, the treatment of the electrostatic interactions defined in the underlying force field (FF) strongly affects the simulation accuracy. Most FFs use fixed partial atomic charges to include electrostatic interactions, and therefore lack the electronic polarization response, representing an intrinsic limitation. To address this limitation, polarizable FFs have been developed that treat atomic polarizabilities explicitly. Here we present the application of the all-atom polarizable (Drude) and non-polarizable (CHARMM) nucleic acid FFs in RNA hairpin systems to investigate the impact of polarization on structural properties, dipole moment distributions, and cation interactions. Results show that the presence of polarizability in the FF significantly improves the stabilization of RNA hairpin structure. As expected, the distributions of dipole moments show more fluctuations when simulated using the polarizable FF, with the variation in dipoles contributing to the stabilization of the structures of the loop regions of the RNAs. Contact map analyses between the bases and cations show that the variation of the ion distribution around the entire hairpin is larger for the polarizable FF and the cations occupy the outer hydration shell to a greater extent. The presented results indicate the importance of the explicit treatment of electronic polarizability in molecular simulations of RNA, including in non-canonical regions.
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Affiliation(s)
- Mert Y. Sengul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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3
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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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4
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Melidis L, Styles IB, Hannon MJ. Targeting structural features of viral genomes with a nano-sized supramolecular drug. Chem Sci 2021; 12:7174-7184. [PMID: 34123344 PMCID: PMC8153246 DOI: 10.1039/d1sc00933h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022] Open
Abstract
RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.
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Affiliation(s)
- Lazaros Melidis
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Iain B Styles
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Computer Science, University of Birmingham Edgbaston Birmingham B15 2TT UK
- Centre of Membrane Proteins and Receptors, The Universities of Birmingham and Nottingham The Midlands UK
- Alan Turing Institute London UK
| | - Michael J Hannon
- Physical Sciences for Health Centre, University of Birmingham Edgbaston Birmingham B15 2TT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
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5
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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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6
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Devillers M, Piquemal J, Salmon L, Gresh N. Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase. J Comput Chem 2020; 41:839-854. [DOI: 10.1002/jcc.26134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/28/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Marion Devillers
- Equipe 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 F‐91405 Orsay France
| | - Jean‐Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS Paris France
- Department of Biomolecular EngineeringThe University of Texas at Austin Texas 78712
| | - Laurent Salmon
- Equipe 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 F‐91405 Orsay France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Université, UMR 7616 CNRS Paris France
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7
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Kruse H, Šponer J. Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking. J Phys Chem A 2019; 123:9209-9222. [PMID: 31560201 DOI: 10.1021/acs.jpca.9b05940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleobase stacking interactions are crucial for the stability of nucleic acids. This study investigates base stacking energies of the cytosine homodimer in different configurations, including intermolecular separation plots, detailed twist dependence, and displaced structures. Highly accurate ab initio quantum chemical single point energies using an energy function based on MP2 complete basis set extrapolation ([6 → 7]ZaPa-NR) and a CCSD(T)/cc-pVTZ-F12 high-level correction are presented as new reference data, providing the most accurate stacking energies of nucleobase dimers currently available. Accurate SAPT2+(3)δMP2 energy decomposition is used to obtain detailed insights into the nature of base stacking interactions at varying vertical distances and twist values. The ab initio symmetry adapted perturbation theory (SAPT) energy decomposition suggests that the base stacking originates from an intricate interplay between dispersion attraction, short-range exchange-repulsion, and Coulomb interaction. The interpretation of the SAPT data is a complex issue as key energy terms vary substantially in the region of optimal (low energy) base stacking geometries. Thus, attempts to highlight one leading stabilizing SAPT base stacking term may be misleading and the outcome strongly depends on the used geometries within the range of geometries sampled in nucleic acids upon thermal fluctuations. Modern dispersion-corrected density functional theory (among them DSD-BLYP-D3, ωB97M-V, and ωB97M-D3BJ) is benchmarked and often reaches up to spectroscopic accuracy (below 1 kJ/mol). The classical AMBER force field is benchmarked with multiple different sets of point-charges (e.g. HF, DFT, and MP2-based) and is found to produce reasonable agreement with the benchmark data.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Královopolská 135 , CZ-61265 Brno , Czech Republic.,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , 62500 Brno , Czech Republic
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8
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Jing Z, Liu C, Cheng SY, Qi R, Walker BD, Piquemal JP, Ren P. Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications. Annu Rev Biophys 2019; 48:371-394. [PMID: 30916997 DOI: 10.1146/annurev-biophys-070317-033349] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics, including electronic polarization. Due to recent advances in physical models, simulation algorithms, and computing hardware, biomolecular simulations with advanced force fields at biologically relevant timescales are becoming increasingly promising. These advancements have not only led to new biophysical insights but also afforded opportunities to advance our understanding of fundamental intermolecular forces. This article describes the recent advances and applications, as well as future directions, of polarizable force fields in biomolecular simulations.
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Affiliation(s)
- Zhifeng Jing
- 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;
| | - Sara Y Cheng
- 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;
| | - Brandon D Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA; .,Sorbonne Université, CNRS, Laboratoire de Chimie Theórique, 75252 Paris CEDEX 05, France.,Institut Universitaire de France, 75005 Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
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9
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Zhang C, Lu C, Jing Z, Wu C, Piquemal JP, Ponder JW, Ren P. AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. J Chem Theory Comput 2018; 14:2084-2108. [PMID: 29438622 PMCID: PMC5893433 DOI: 10.1021/acs.jctc.7b01169] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and χ-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states, 3 J-coupling, nuclear Overhauser effect, and residual dipolar coupling data were compared with NMR results. Starting from a totally unstacked/unfolding state, the rCAAU tetranucleotide was folded into A-form-like structures during ∼1 μs molecular dynamics simulations.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Chao Lu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Zhifeng Jing
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Chuanjie Wu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
| | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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10
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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11
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Kwapien K, Damergi M, Nader S, El Khoury L, Hobaika Z, Maroun RG, Piquemal JP, Gavara L, Berthomieu D, Hernandez JF, Gresh N. Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry. J Phys Chem B 2017; 121:6295-6312. [DOI: 10.1021/acs.jpcb.7b01053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Karolina Kwapien
- Chemistry
and Biology, Nucléo(s)tides and Immunology for Therapy (CBNIT),
UMR 8601, CNRS, UFR Biomédicale, Paris, France
- Institut Charles-Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Mirna Damergi
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Serge Nader
- Chemistry
and Biology, Nucléo(s)tides and Immunology for Therapy (CBNIT),
UMR 8601, CNRS, UFR Biomédicale, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Léa El Khoury
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Zeina Hobaika
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des Sciences, Saint Joseph University of Beirut, BP 11-514, Riad El Solh, Beirut 1116-2050, Lebanon
| | - Richard G. Maroun
- Centre
d’Analyses et de Recherche, UR EGFEM, LSIM, Faculté
des 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, UMR7616 CNRS, Paris, France
- Institut Universitaire de France, Paris Cedex 05, 75231, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Laurent Gavara
- Institut des Biomolécules Max Mousseron,
UMR 5247 CNRS, Faculté de Pharmacie, Université de Montpellier, ENSCM, 15 avenue Charles Flahault, 34093 Montpellier, France
| | - Dorothée Berthomieu
- Institut Charles-Gerhardt, MACS, UMR 5253 CNRS-ENSCM-UM, 8 rue de l’Ecole Normale, 34296 Montpellier Cedex 5, France
| | - Jean-François Hernandez
- Institut des Biomolécules Max Mousseron,
UMR 5247 CNRS, Faculté de Pharmacie, Université de Montpellier, ENSCM, 15 avenue Charles Flahault, 34093 Montpellier, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC, UMR7616 CNRS, Paris, France
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12
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El Khoury L, Naseem-Khan S, Kwapien K, Hobaika Z, Maroun RG, Piquemal JP, Gresh N. Importance of explicit smeared lone-pairs in anisotropic polarizable molecular mechanics. Torture track angular tests for exchange-repulsion and charge transfer contributions. J Comput Chem 2017; 38:1897-1920. [DOI: 10.1002/jcc.24830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/18/2017] [Accepted: 04/03/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Léa El Khoury
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
| | - Karolina Kwapien
- Chemistry and Biology, Nucleo(s)tides and Immunology for Therapy (CBNIT); UMR 8601 CNRS, UFR Biomédicale Paris France
- Institut Charles-Gerhardt, UMR 5253, CNRS-UM2-UM1-ENSM; Montpellier France
| | - Zeina Hobaika
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des Sciences, Saint Joseph University of Beirut; BP 11-514, Riad El Solh Beirut 1116-2050 Lebanon
| | - Richard G. Maroun
- Centre d'Analyses et de Recherche, UR EGFEM, LSIM, Faculté des 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; UMR7616 CNRS Paris France
- Institut Universitaire de France; Paris Cedex 05 75231 France
- Department of Biomedical Engineering; The University of Texas at Austin; Texas 78712
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC; UMR7616 CNRS Paris France
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13
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Lemkul JA, MacKerell AD. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA. J Chem Theory Comput 2017; 13:2072-2085. [PMID: 28398748 PMCID: PMC5485260 DOI: 10.1021/acs.jctc.7b00068] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The structure and dynamics of DNA are governed by a sensitive balance between base stacking and pairing, hydration, and interactions with ions. Force-field models that include explicit representations of electronic polarization are capable of more accurately modeling the subtle details of these interactions versus commonly used additive force fields. In this work, we validate our recently refined polarizable force field for DNA based on the classical Drude oscillator model, in which electronic degrees of freedom are represented as negatively charged particles attached to their parent atoms via harmonic springs. The previous version of the force field, called Drude-2013, produced stable A- and B-DNA trajectories on the order of hundreds of nanoseconds, but deficiencies were identified that included weak base stacking ultimately leading to distortion of B-DNA duplexes and unstable Z-DNA. As a result of extensive refinement of base nonbonded terms and bonded parameters in the deoxyribofuranose sugar and phosphodiester backbone, we demonstrate that the new version of the Drude DNA force field is capable of simulating A- and B-forms of DNA on the microsecond time scale and the resulting conformational ensembles agree well with a broad set of experimental properties, including solution X-ray scattering profiles. In addition, simulations of Z-form duplex DNA in its crystal environment are stable on the order of 100 ns. The revised force field is to be called Drude-2017.
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Affiliation(s)
- Justin A. Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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14
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Lemkul JA, MacKerell AD. Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics. J Chem Theory Comput 2017; 13:2053-2071. [PMID: 28399366 DOI: 10.1021/acs.jctc.7b00067] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments. Recent hardware and software developments make polarizable simulations feasible, and to this end, polarizable force fields represent the next generation of molecular dynamics simulation technology. In this work, we describe the refinement of a polarizable force field for DNA based on the classical Drude oscillator model by targeting quantum mechanical interaction energies and conformational energy profiles of model compounds necessary to build a complete DNA force field. The parametrization strategy employed in the present work seeks to correct weak base stacking in A- and B-DNA and the unwinding of Z-DNA observed in the previous version of the force field, called Drude-2013. Refinement of base nonbonded terms and reparametrization of dihedral terms in the glycosidic linkage, deoxyribofuranose rings, and important backbone torsions resulted in improved agreement with quantum mechanical potential energy surfaces. Notably, we expand on previous efforts by explicitly including Z-DNA conformational energetics in the refinement.
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Affiliation(s)
- Justin A Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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15
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Gresh N, Naseem-Khan S, Lagardère L, Piquemal JP, Sponer JE, Sponer J. Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li +, Na +, K +, and Rb + Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential. J Phys Chem B 2017; 121:3997-4014. [PMID: 28363025 DOI: 10.1021/acs.jpcb.7b01836] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K+ and Na+, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the method's accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li+, Na+, K+, or Rb+) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within ΔE is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K+ or two Rb+ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Sehr Naseem-Khan
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Louis Lagardère
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, Sorbonne Universités , UPMC, UMR7616 CNRS, 75006Paris, France.,Institut Universitaire de France, Paris Cedex 05, 75231, France.,Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas, 78712, United States
| | - Judit E Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovpolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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16
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Zhang C, Bell D, Harger M, Ren P. Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases. J Chem Theory Comput 2017; 13:666-678. [PMID: 28030769 PMCID: PMC5312700 DOI: 10.1021/acs.jctc.6b00918] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Aromatic molecules with π electrons
are commonly involved
in chemical and biological recognitions. For example, nucleobases
play central roles in DNA/RNA structure and their interactions with
proteins. The delocalization of the π electrons is responsible
for the high polarizability of aromatic molecules. In this work, the
AMOEBA force field has been developed and applied to 5 regular nucleobases
and 12 aromatic molecules. The permanent electrostatic energy is expressed
as atomic multipole interactions between atom pairs, and many-body
polarization is accounted for by mutually induced atomic dipoles.
We have systematically investigated aromatic ring stacking and aromatic-water
interactions for nucleobases and aromatic molecules, as well as base–base
hydrogen-bonding pair interactions, all at various distances and orientations.
van der Waals parameters were determined by comparison to the quantum
mechanical interaction energy of these dimers and fine-tuned using
condensed phase simulation. By comparing to quantum mechanical calculations,
we show that the resulting classical potential is able to accurately
describe molecular polarizability, molecular vibrational frequency,
and dimer interaction energy of these aromatic systems. Condensed
phase properties, including hydration free energy, liquid density,
and heat of vaporization, are also in good overall agreement with
experimental values. The structures of benzene liquid phase and benzene-water
solution were also investigated by simulation and compared with experimental
and PDB structure derived statistical results.
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Affiliation(s)
- Changsheng Zhang
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - David Bell
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Matthew Harger
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin , Austin, Texas 78712, United States
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17
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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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