Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

The last in a set of units by the same authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. The unit describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories. Curr. Protoc. Nucleic Acid Chem. 56:7.10.1‐7.10.21. © 2014 by John Wiley & Sons, Inc.

[1]  D. Case,et al.  Twenty-five years of nucleic acid simulations. , 2013, Biopolymers.

[2]  Adrian E. Roitberg,et al.  Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide , 2013, Journal of chemical theory and computation.

[3]  W. V. van Gunsteren,et al.  Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations. , 2013, Biochemistry.

[4]  Angel E García,et al.  High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations , 2013, Proceedings of the National Academy of Sciences.

[5]  S. Le Grand,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[6]  Daniel R Roe,et al.  PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. , 2013, Journal of chemical theory and computation.

[7]  Stefan Grimme,et al.  Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. , 2013, Journal of the American Chemical Society.

[8]  Pengfei Li,et al.  Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. , 2013, Journal of chemical theory and computation.

[9]  Niel M. Henriksen,et al.  Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations. , 2013, The journal of physical chemistry. B.

[10]  Shintaro Fujimoto,et al.  Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution , 2013, Science China Chemistry.

[11]  Damien Larivière,et al.  Easy DNA Modeling and More with GraphiteLifeExplorer , 2013, PloS one.

[12]  Maarten G. Wolf,et al.  Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform‐to‐water partition coefficients , 2012, J. Comput. Chem..

[13]  Daniel Svozil,et al.  The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. , 2012, Physical chemistry chemical physics : PCCP.

[14]  Holger Gohlke,et al.  MMPBSA.py: An Efficient Program for End-State Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[15]  Michal Otyepka,et al.  Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration. , 2012, The journal of physical chemistry. B.

[16]  Niel M. Henriksen,et al.  Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure , 2012, Journal of biomolecular NMR.

[17]  L. Nilsson,et al.  Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations. , 2012, Journal of chemical theory and computation.

[18]  M. Orozco,et al.  Frontiers in molecular dynamics simulations of DNA. , 2012, Accounts of chemical research.

[19]  Alexander D. MacKerell,et al.  Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. , 2012, Journal of chemical theory and computation.

[20]  Thomas Gaillard,et al.  Evaluation of DNA Force Fields in Implicit Solvation. , 2011, Journal of chemical theory and computation.

[21]  C. Simmerling,et al.  Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase. , 2011, Journal of the American Chemical Society.

[22]  J. Šponer,et al.  Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles , 2011, Journal of chemical theory and computation.

[23]  Alexander D. MacKerell,et al.  Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA , 2011, J. Comput. Chem..

[24]  D. Turner,et al.  Benchmarking AMBER Force Fields for RNA: Comparisons to NMR Spectra for Single-Stranded r(GACC) Are Improved by Revised χ Torsions , 2011, The journal of physical chemistry. B.

[25]  Brian N. Dominy,et al.  Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions , 2011, J. Comput. Chem..

[26]  Modesto Orozco,et al.  Toward a consensus view of duplex RNA flexibility. , 2010, Biophysical journal.

[27]  Clarisse G. Ricci,et al.  Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions. , 2010, The journal of physical chemistry. B.

[28]  J. P. Grossman,et al.  Millisecond-scale molecular dynamics simulations on Anton , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.

[29]  M. Orozco,et al.  Nucleic acid simulations themed issue. , 2009, Physical Chemistry, Chemical Physics - PCCP.

[30]  D. Case,et al.  A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA , 2009, Nucleic acids research.

[31]  Thomas E. Cheatham,et al.  Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters , 2009, The journal of physical chemistry. B.

[32]  Alexander D. MacKerell,et al.  CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields , 2009, J. Comput. Chem..

[33]  P. Auffinger,et al.  A short guide for molecular dynamics simulations of RNA systems. , 2009, Methods.

[34]  Daniel Svozil,et al.  Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. , 2008, The journal of physical chemistry. B.

[35]  F. Javier Luque,et al.  Towards a molecular dynamics consensus view of B-DNA flexibility , 2008, Nucleic acids research.

[36]  F. J. Luque,et al.  Dynamics of B-DNA on the microsecond time scale. , 2007, Journal of the American Chemical Society.

[37]  T. Cheatham,et al.  Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue? , 2007, Journal of chemical theory and computation.

[38]  John L. Klepeis,et al.  Anton, a special-purpose machine for molecular dynamics simulation , 2007, ISCA '07.

[39]  M. Zacharias.  Minor groove deformability of DNA: a molecular dynamics free energy simulation study. , 2006, Biophysical journal.

[40]  C. Sagui,et al.  Molecular dynamics simulations of DNA with polarizable force fields: convergence of an ideal B-DNA structure to the crystallographic structure. , 2006, The journal of physical chemistry. B.

[41]  Jiří Šponer,et al.  Molecular dynamics simulations of sarcin–ricin rRNA motif , 2006, Nucleic acids research.

[42]  Xiangdong Liu,et al.  The effect of salt concentration on DNA conformation transition: a molecular-dynamics study , 2006, Journal of molecular modeling.

[43]  Manju Bansal,et al.  Sequence Preference for BI/BII Conformations in DNA: MD and Crystal Structure Data Analysis , 2005, Journal of biomolecular structure & dynamics.

[44]  Chris Oostenbrink,et al.  An improved nucleic acid parameter set for the GROMOS force field , 2005, J. Comput. Chem..

[45]  W. V. Gunsteren,et al.  Validation of the 53A6 GROMOS force field , 2005, European Biophysics Journal.

[46]  Heinz Sklenar,et al.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. , 2004, Biophysical journal.

[47]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[48]  Jaroslav Koca,et al.  Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. , 2004, Biophysical journal.

[49]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[50]  E. Westhof,et al.  Anion binding to nucleic acids. , 2004, Structure.

[51]  Krystyna Zakrzewska.  DNA deformation energetics and protein binding. , 2003, Biopolymers.

[52]  Martin Karplus,et al.  DNA polymorphism: a comparison of force fields for nucleic acids. , 2003, Biophysical journal.

[53]  Pavel Hobza,et al.  Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution. , 2003, Journal of the American Chemical Society.

[54]  Chunlin Wang,et al.  Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking , 2003, J. Comput. Chem..

[55]  Alexander D. MacKerell,et al.  Free energy and structural pathways of base flipping in a DNA GCGC containing sequence. , 2002, Journal of molecular biology.

[56]  D. Beveridge,et al.  Molecular dynamics simulations of B '-DNA: sequence effects on A-tract-induced bending and flexibility. , 2001, Journal of molecular biology.

[57]  Ioan Andricioaei,et al.  On the calculation of entropy from covariance matrices of the atomic fluctuations , 2001 .

[58]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[59]  Junmei Wang,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..

[60]  D. Case,et al.  Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model , 2000 .

[61]  Alexander D. MacKerell,et al.  All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data , 2000 .

[62]  P. Kollman,et al.  A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. , 1999, Journal of biomolecular structure & dynamics.

[63]  D. Langley,et al.  Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results. , 1998, Journal of biomolecular structure & dynamics.

[64]  David A. Case,et al.  Modeling Unusual Nucleic Acid Structures , 1998 .

[65]  Bernard R. Brooks,et al.  Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution , 1998 .

[66]  D. Beveridge,et al.  Molecular dynamics simulations of an oligonucleotide duplex with adenine tracts phased by a full helix turn. , 1998, Journal of molecular biology.

[67]  Wilfred F. van Gunsteren,et al.  Validation of molecular dynamics simulation , 1998 .

[68]  M Feig,et al.  Structural equilibrium of DNA represented with different force fields. , 1998, Biophysical journal.

[69]  G G Hu,et al.  The B-DNA dodecamer at high resolution reveals a spine of water on sodium. , 1998, Biochemistry.

[70]  S. Harvey,et al.  The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition , 1998, J. Comput. Chem..

[71]  H. Sklenar,et al.  Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions. , 1997, Biophysical journal.

[72]  Alexander D. MacKerell.  Observations on the A versus B Equilibrium in Molecular Dynamics Simulations of Duplex DNA and RNA , 1997 .

[73]  D. Beveridge,et al.  A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. , 1997, Biophysical journal.

[74]  P A Kollman,et al.  Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III). , 1997, Structure.

[75]  B. Pettitt,et al.  Experiment vs force fields: DNA conformation from molecular dynamics simulations , 1997 .

[76]  P. Kollman,et al.  A molecular level picture of the stabilization of A-DNA in mixed ethanol-water solutions. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[77]  Tami I. Spector,et al.  Unrestrained Molecular Dynamics of Photodamaged DNA in Aqueous Solution , 1997 .

[78]  P. Kollman,et al.  Molecular Dynamics Simulations Find That 3‘ Phosphoramidate Modified DNA Duplexes Undergo a B to A Transition and Normal DNA Duplexes an A to B Transition , 1997 .

[79]  O. Tapia,et al.  Molecular Dynamics Simulations of DNA with Protein's Consistent GROMOS Force Field and the Role of Counterions' Symmetry , 1997 .

[80]  Richard Lavery,et al.  Internal coordinate modeling of DNA: Force field comparisons , 1997, J. Comput. Chem..

[81]  J. Feigon,et al.  Localization of Divalent Metal Ions in the Minor Groove of DNA A-Tracts , 1997 .

[82]  David A. Case,et al.  A computational study of the role of solvation effects in reverse turn formation in the tetrapeptides APGD and APGN , 1997 .

[83]  Peter A. Kollman,et al.  Molecular dynamics simulations highlight the structural differences among DNA: DNA, RNA:RNA, and DNA:RNA hybrid duplexes , 1997 .

[84]  Alexander D. MacKerell.  Influence of Magnesium Ions on Duplex DNA Structural, Dynamic, and Solvation Properties , 1997 .

[85]  Bhyravabhotla Jayaram,et al.  Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA: Fractional Occupancy of Electronegative Pockets , 1997 .

[86]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[87]  R. Osman,et al.  Computational Simulations of DNA Distortions by a cis,syn-Cyclobutane Thymine Dimer Lesion† , 1996 .

[88]  L. Nilsson,et al.  Glass transition in DNA from molecular dynamics simulations. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[89]  P A Kollman,et al.  Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. , 1996, Journal of molecular biology.

[90]  R Lavery,et al.  Modelling extreme stretching of DNA. , 1996, Nucleic acids research.

[91]  Lennart Nilsson,et al.  Constant pressure molecular dynamics simulations of the dodecamers: d(GCGCGCGCGCGC)2 and r(GCGCGCGCGCGC)2 , 1996 .

[92]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

[93]  Shankar Kumar,et al.  Multidimensional free‐energy calculations using the weighted histogram analysis method , 1995, J. Comput. Chem..

[94]  B. Roux.  The calculation of the potential of mean force using computer simulations , 1995 .

[95]  Heinz Sklenar,et al.  JUMNA (junction minimisation of nucleic acids) , 1995 .

[96]  C. Brooks,et al.  First-principles calculation of the folding free energy of a three-helix bundle protein. , 1995, Science.

[97]  P. Kollman,et al.  A second generation force field for the simulation of proteins , 1995 .

[98]  Vitaly Buckin,et al.  Mg2+ recognizes the sequence of DNA through its hydration shell , 1994 .

[99]  David E. Smith,et al.  Computer simulations of NaCl association in polarizable water , 1994 .

[100]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[101]  P. Kollman,et al.  A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .

[102]  B. Brooks,et al.  Protein hydration elucidated by molecular dynamics simulation. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[103]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[104]  R L Jernigan,et al.  Static and statistical bending of DNA evaluated by Monte Carlo simulations. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[105]  J. Åqvist,et al.  Ion-water interaction potentials derived from free energy perturbation simulations , 1990 .

[106]  M. Karplus,et al.  Active site dynamics in protein molecules: A stochastic boundary molecular‐dynamics approach , 1985, Biopolymers.

[107]  M. Karplus,et al.  Method for estimating the configurational entropy of macromolecules , 1981 .

[108]  V. Zhurkin,et al.  [Atom--atomic potential functions for conformational calculations of nucleic acids]. , 1980, Molekuliarnaia biologiia.

[109]  C. Bugg,et al.  Interactions of hydrated metal ions with nucleotides: the crystal structure of barium adenosine 5'-monophosphate heptahydrate. , 1976, Biochemistry.

[110]  Daniel Svozil,et al.  Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. , 2007, Biophysical journal.

[111]  Filip Rázga,et al.  Structure , Dynamics , and Elasticity of Free 16 S rRNA Helix 44 Studied by Molecular Dynamics Simulations , 2006 .

[112]  Jiří Šponer,et al.  Computational studies of RNA and DNA , 2006 .

[113]  J. Šponer,et al.  Interaction of Metal Cations with Nucleic Acids and their Building Units , 2006 .

[114]  P. Kollman,et al.  Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. , 2001, Annual review of biophysics and biomolecular structure.

[115]  Alexey K. Mazur,et al.  Molecular dynamics of minimal B-DNA , 2001, J. Comput. Chem..

[116]  Alexander D. MacKerell,et al.  Development and current status of the CHARMM force field for nucleic acids , 2000, Biopolymers.

[117]  Alexander D. MacKerell,et al.  All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution , 2000, J. Comput. Chem..

[118]  D. Case,et al.  Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.

[119]  P A Kollman,et al.  Molecular dynamics simulation of nucleic acids. , 2000, Annual review of physical chemistry.

[120]  P A Kollman,et al.  Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. , 1998, Journal of biomolecular structure & dynamics.

[121]  D. Beveridge,et al.  Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.

[122]  C. Brooks.  Computer simulation of liquids , 1989 .