Empirical energy functions for energy minimization and dynamics of nucleic acids

An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems. Among the properties studied and used for parameter optimization are base pairing interactions, sugar and phosphate energy surfaces, small crystal heats of sublimation, base, phosphate and sugar analogue vibration spectra, and the overall behavior of a DNA hexamer duplex in vacuum molecular dynamics simulations. The results obtained are compared with those from two other energy functions that have been used recently for nucleic acids. Parameters for two energy functions are given; one includes heavy atoms and only polar hydrogens and the other includes all atoms.

[1]  Arieh Warshel,et al.  Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings , 1970 .

[2]  Y. Kyōgoku,et al.  The crystal structure of barium diethyl phosphate , 1966 .

[3]  M. Sundaralingam,et al.  Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. , 1972, Journal of the American Chemical Society.

[4]  Yonezo Morino,et al.  A Note on the Classification of Normal Vibrations of Molecules , 1952 .

[5]  Andrew Dearing,et al.  Studies of nucleotide conformations and interactions. The relative stabilities of double‐helical B‐DNA sequence isomers , 1981, Biopolymers.

[6]  K. Breslauer,et al.  Calorimetric determination of base‐stacking enthalpies in double‐helical DNA molecules , 1982, Biopolymers.

[7]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[8]  M. Levitt,et al.  Energy refinement of hen egg-white lysozyme. , 1974, Journal of molecular biology.

[9]  L. Sukhodub,et al.  Experimental studies of molecular interactions between nitrogen bases of nucleic acids , 1979, Biopolymers.

[10]  J. Duchesne.  Physico-chemical properties of nucleic acids , 1973 .

[11]  E. R. Bissell,et al.  THE INFRARED SPECTRA OF DEUTERATED TETRAHYDROFURANS , 1960 .

[12]  M Levitt,et al.  How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Marquardt.  An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[14]  A. Warshel,et al.  Consistent Force Field Calculations. II. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes , 1970 .

[15]  M Karplus,et al.  Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. , 1979, Biochemistry.

[16]  R. E. Marsh,et al.  A refinement of the crystal structure of diketopiperazine (2,5-piperazinedione) , 1959 .

[17]  D. Cremer,et al.  General definition of ring puckering coordinates , 1975 .

[18]  A. Warshel,et al.  Consistent Force Field for Calculations of Conformations, Vibrational Spectra, and Enthalpies of Cycloalkane and n‐Alkane Molecules , 1968 .

[19]  M Karplus,et al.  Dynamics of DNA oligomers. , 1983, Journal of biomolecular structure & dynamics.

[20]  H. Scheraga,et al.  Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids , 1975 .

[21]  N C Seeman,et al.  RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate. , 1976, Journal of molecular biology.

[22]  M Levitt,et al.  Computer simulation of DNA double-helix dynamics. , 1983, Cold Spring Harbor symposia on quantitative biology.

[23]  W. Person,et al.  MATRIX ISOLATION STUDIES OF NUCLEIC ACID CONSTITUENTS. I. INFRARED SPECTRA OF URACIL MONOMERS , 1983 .

[24]  E. Freire,et al.  Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid , 1977, Biopolymers.

[25]  S. Lifson,et al.  Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. , 1974, Journal of the American Chemical Society.

[26]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[27]  S H Kim,et al.  Determinations of atomic partial charges for nucleic acid constituents from x‐ray diffraction data. I. 2′‐Deoxycytidine‐5′‐monophosphate , 1985, Biopolymers.

[28]  M. Karplus,et al.  A model for the simulation of an aqueous dipeptide solution , 1979 .

[29]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[30]  W. Olson,et al.  How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies , 1982 .

[31]  M Karplus,et al.  Structure refinement of oligonucleotides by molecular dynamics with nuclear Overhauser effect interproton distance restraints: application to 5' d(C-G-T-A-C-G)2. , 1986, Journal of molecular biology.

[32]  J. Scherer,et al.  Transferability of Urey‐Bradley Force Constants. I. Calculation of Force Constants on a Digital Computer , 1960 .

[33]  L. Ehrenberg,et al.  The Crystal Structure of Lower Paraffins. IV. Refinement of the Crystal Structures of Pentane and Octane. , 1967 .

[34]  J A McCammon,et al.  Phenylalanine transfer RNA: molecular dynamics simulation. , 1984, Science.

[35]  D. Gorenstein,et al.  The torsional potential for phosphate diesters. The effect of geometry optimization in CNDO and ab initio molecular orbital calculations. , 1977, Biochimica et biophysica acta.

[36]  Z. Shakked,et al.  Base-stacking interactions in double-helical DNA structures: experiment versus theory. , 1984, Journal of biomolecular structure & dynamics.

[37]  Wilma K. Olson.  How flexible is the furanose ring? 2. An updated potential energy estimate , 1982 .

[38]  W. Olson.  Theoretical studies of nucleic acid conformation: potential energies, chain statistics, and model building , 1982 .

[39]  E. Brown,et al.  Conformational geometry and vibrational frequencies of nucleic acid chains , 1975, Biopolymers.

[40]  J. M. Eyster,et al.  The normal vibrations of tetrahydrofuran and its deuterated derivatives , 1974 .

[41]  M Karplus,et al.  Dynamics of proteins: elements and function. , 1983, Annual review of biochemistry.

[42]  Peter A. Kollman,et al.  AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .

[43]  R. Ornstein,et al.  An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking , 1978, Biopolymers.

[44]  John C. Slater,et al.  The Van Der Waals Forces in Gases , 1931 .

[45]  D. Turner,et al.  Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. , 1983, Biochemistry.

[46]  Structures and properties of organic liquids: n-alkyl ethers and their conformational equilibriums , 1981 .

[47]  N C Seeman,et al.  RNA double-helical fragments at atomic resolution. II. The crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. , 1976, Journal of molecular biology.