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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

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Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
§ Department of Medicinal Chemistry, University of Utah, 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
Cite this: J. Chem. Theory Comput. 2015, 11, 12, 5723–5736
Publication Date (Web):November 3, 2015
https://doi.org/10.1021/acs.jctc.5b00716
Copyright © 2015 American Chemical Society

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    Abstract

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    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar–phosphate backbone torsion angle β. We suggest a refinement of this potential, βOL1, which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using βOL1 in combination with our previously introduced corrections, εζOL1 and χOL4, (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.5b00716.

    • βOL1 torsion parameters, list of MD simulations, and time series and distributions of selected structural parameters in MD simulations and X-ray data (PDF)

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    78. Jianbo Zhao, Scott D. Kennedy, Kyle D. Berger, Douglas H. Turner. Nuclear Magnetic Resonance of Single-Stranded RNAs and DNAs of CAAU and UCAAUC as Benchmarks for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2020, 16 (3) , 1968-1984. https://doi.org/10.1021/acs.jctc.9b00912
    79. Ho Shin Kim, Nathanael A. Brown, Stefan Zauscher, Yaroslava G. Yingling. Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces. Langmuir 2020, 36 (4) , 931-938. https://doi.org/10.1021/acs.langmuir.9b02926
    80. Vishal Minhas, Tiedong Sun, Alexander Mirzoev, Nikolay Korolev, Alexander P. Lyubartsev, Lars Nordenskiöld. Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels. The Journal of Physical Chemistry B 2020, 124 (1) , 38-49. https://doi.org/10.1021/acs.jpcb.9b09106
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    92. George M. Giambaşu, David A. Case, Darrin M. York. Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory. Journal of the American Chemical Society 2019, 141 (6) , 2435-2445. https://doi.org/10.1021/jacs.8b11474
    93. Karla F. Andriani, Germano Heinzelmann, Giovanni F. Caramori. Shedding Light on the Hydrolysis Mechanism of cis, trans-[Ru(dmso)4Cl2] Complexes and Their Interactions with DNA—A Computational Perspective. The Journal of Physical Chemistry B 2019, 123 (2) , 457-467. https://doi.org/10.1021/acs.jpcb.8b11287
    94. Kara K. Grotz, Mark F. Nueesch, Erik D. Holmstrom, Marcel Heinz, Lukas S. Stelzl, Benjamin Schuler, Gerhard Hummer. Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments. The Journal of Physical Chemistry B 2018, 122 (49) , 11626-11639. https://doi.org/10.1021/acs.jpcb.8b07537
    95. Holli-Joi Sullivan, Carolyn Readmond, Christina Radicella, Victoria Persad, Thomas J. Fasano, Chun Wu. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex–Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS Omega 2018, 3 (11) , 14788-14806. https://doi.org/10.1021/acsomega.8b01574
    96. Barira Islam, Petr Stadlbauer, Miroslav Krepl, Marek Havrila, Shozeb Haider, Jiri Sponer. Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations. Journal of Chemical Theory and Computation 2018, 14 (10) , 5011-5026. https://doi.org/10.1021/acs.jctc.8b00543
    97. Maciej Jasiński, Michael Feig, Joanna Trylska. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. Journal of Chemical Theory and Computation 2018, 14 (7) , 3603-3620. https://doi.org/10.1021/acs.jctc.8b00291
    98. Evan T. Walters, Mohamad Mohebifar, Erin R. Johnson, Christopher N. Rowley. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. The Journal of Physical Chemistry B 2018, 122 (26) , 6690-6701. https://doi.org/10.1021/acs.jpcb.8b02814
    99. Gregory A. Ross, Ariën S. Rustenburg, Patrick B. Grinaway, Josh Fass, John D. Chodera. Biomolecular Simulations under Realistic Macroscopic Salt Conditions. The Journal of Physical Chemistry B 2018, 122 (21) , 5466-5486. https://doi.org/10.1021/acs.jpcb.7b11734
    100. Yuan Zhang, Christopher Roland, Celeste Sagui. Structural and Dynamical Characterization of DNA and RNA Quadruplexes Obtained from the GGGGCC and GGGCCT Hexanucleotide Repeats Associated with C9FTD/ALS and SCA36 Diseases. ACS Chemical Neuroscience 2018, 9 (5) , 1104-1117. https://doi.org/10.1021/acschemneuro.7b00476
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