Keeping the shape but changing the charges: A simulation study of urea and its iso-steric analogs

As a first step in simulating solvent denaturation, we compare two possible potentials for urea; one based directly on a parameterization for proteins and another generated from ab initio, quantum calculations. Our results, which are derived from numerous, 1 ns simulations, indicate that both potentials reproduce essentially the same observed water structure (as evident in radial distribution functions). However, even though the quantum potential better approximates dimer energies, it is unable to simulate the dynamic behavior of water (as evident in measurements of diffusion) as well as the potential based on protein parameters. To understand its behavior in aqueous solution, we compare the urea simulations with those of solute molecules that possess the same planar, Y‐shape as urea but are progressively more hydrophobic. We find that adding urea to a solution increases the number of hydrogen bonds, while adding any of the Y‐shaped analogs decreases the number of hydrogen bonds. Moreover, in contrast to ...

[1]  V. Daggett,et al.  Testing the Modified Hydration-Shell Hydrogen-Bond Model of Hydrophobic Effects Using Molecular Dynamics Simulation , 1996 .

[2]  M. Levitt,et al.  Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution , 1995 .

[3]  M. Levitt,et al.  The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. , 1995, Journal of molecular biology.

[4]  V. Daggett,et al.  pH-dependent conformations of the amyloid beta(1-28) peptide fragment explored using molecular dynamics. , 1995, Biochemistry.

[5]  J. Pranata.  Nature of Denaturing Agents: Monte Carlo Simulations of Bimolecular Complexes Involving Urea and N-Methylacetamide in Aqueous Solution , 1995 .

[6]  P. Kollman,et al.  Molecular dynamics free energy simulations: Influence of the truncation of long‐range nonbonded electrostatic interactions on free energy calculations of polar molecules , 1994 .

[7]  G. Karlstroem,et al.  Molecular Dynamics Simulations of 2 m Aqueous Urea Solutions , 1994 .

[8]  M Gerstein,et al.  Volume changes on protein folding. , 1994, Structure.

[9]  P. Åstrand,et al.  NONEMPIRICAL INTERMOLECULAR POTENTIALS FOR UREA-WATER SYSTEMS , 1994 .

[10]  I. Ortega‐Blake,et al.  A refined Monte Carlo study of aqueous urea solutions , 1993 .

[11]  G. Turrell,et al.  Raman spectroscopic investigation of the dynamics of urea–water complexes , 1993 .

[12]  E. Boek,et al.  Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r , 1993 .

[13]  J. Simons,et al.  Ab initio study of the internal rotation barrier of formamide and the formamide–H2O complex , 1993 .

[14]  P. Privalov,et al.  Protein interactions with urea and guanidinium chloride. A calorimetric study. , 1992, Journal of molecular biology.

[15]  B. Coussens,et al.  The molecular structure of the urea molecule: is the minimum energy structure planar? , 1992 .

[16]  M. Levitt,et al.  A molecular dynamics simulation of the C-terminal fragment of the L7/L12 ribosomal protein in solution , 1991 .

[17]  P. Åstrand,et al.  Properties of urea–water solvation calculated from a new ab initio polarizable intermolecular potential , 1991 .

[18]  A. Soper,et al.  Neutron Diffraction Studies of Structure in Aqueous Solutions of Urea and Tetramethylammonium Chloride and in Methanol , 1991 .

[19]  W. M. Haynes.  CRC Handbook of Chemistry and Physics , 1990 .

[20]  C. Breneman,et al.  Determining atom‐centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis , 1990 .

[21]  Y. Mizutani,et al.  Effect of urea on hydrophobic interaction: Raman difference spectroscopy on the carbon-hydrogen stretching vibration of acetone and the carbon-nitrogen stretching vibration of urea , 1989 .

[22]  A. Soper,et al.  HH correlations in a solution of urea , 1989 .

[23]  R. Sharon,et al.  Accurate simulation of protein dynamics in solution. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Finney,et al.  Neutron scattering studies of molecular hydration in solution , 1988 .

[25]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[26]  V. Barone,et al.  A molecular dynamics study of associations in solution: an NPT simulation of the urea dimer in water , 1987 .

[27]  L. E. Chirlian,et al.  Atomic charges derived from electrostatic potentials: A detailed study , 1987 .

[28]  J. Finney,et al.  Neutron Diffraction Studies of Aqueous Solutions of Molecules of Biological Importance: An Approach to Liquid‐State Structural Chemistry , 1986, Annals of the New York Academy of Sciences.

[29]  U. Kaatze,et al.  Dielectric relaxation in aqueous solutions of urea and some of its derivatives , 1986 .

[30]  H. Piekarski,et al.  Enthalpies of solution of urea in water-alkanol mixtures and the enthalpic pair interaction coefficients of urea and several nonelectrolytes in water , 1986 .

[31]  Hideki Tanaka,et al.  Computer experiments on aqueous solutions. VII. Potential energy function for urea dimer and molecular dynamics calculation of 8 mol % aqueous solution of urea , 1985 .

[32]  M. Bloemendal,et al.  Properties of some protein denaturants in N,N-dimethylformamide. Enthalpic interaction coefficients of urea and substituted urea compounds , 1985 .

[33]  F. Grieser,et al.  Excited-state torsional relaxation in 1,1'-dihexyl-3,3,3',3'-tetramethylindocarbocyanine iodide: application to the probing of micelle structure , 1985 .

[34]  R. A. Kuharski,et al.  Molecular dynamics study of solvation in urea-water solution , 1984 .

[35]  R. A. Kuharski,et al.  Solvation of Hydrophobic Species in Aqueous Urea Solution: A Molecular Dynamics Study , 1984 .

[36]  Hideki Tanaka,et al.  Computer experiment on aqueous solution. IV. Molecular dynamics calculation on the hydration of urea in an infinitely dilute aqueous solution with a new urea–water pair potential , 1984 .

[37]  M. Levitt,et al.  Molecular dynamics of native protein. I. Computer simulation of trajectories. , 1983, Journal of molecular biology.

[38]  Michael L. Klein,et al.  Intermolecular potential functions and the properties of water , 1982 .

[39]  G. L. Hofacker.  B. Pullman (Ed.): Intermolecular Interactions: From Diatomics to Biopolymers. John Wiley & Sons, Chichester, New York, Brisbane, Toronto 1978. 447 Seiten, Preis: £ 19.50 , 1979 .

[40]  Barry Robson,et al.  Intermolecular Interactions: from diatomics to biopolymers , 1978 .

[41]  Bernard Pullman,et al.  Intermolecular interactions, from diatomics to biopolymers , 1978 .

[42]  R. Burge,et al.  X‐ray diffraction studies of aqueous solutions of urea , 1977 .

[43]  W. Jencks,et al.  INTERACTIONS OF UREA AND OTHER POLAR COMPOUNDS IN WATER , 1975 .

[44]  P. Kollman,et al.  Hydrogen bonding ability of the amide group , 1974 .

[45]  G. Perron,et al.  Apparent Molal Volumes and Heat Capacities of Urea and Methyl-Substituted Ureas in H2O and D2O at 25 °C , 1974 .

[46]  P. C. Hariharan,et al.  The influence of polarization functions on molecular orbital hydrogenation energies , 1973 .

[47]  E. G. Finer,et al.  Nuclear magnetic resonance studies of aqueous urea solutions , 1972 .

[48]  Felix Franks,et al.  Structural Approach to the Solvent Power of Water for Hydrocarbons; Urea as a Structure Breaker , 1968 .

[49]  J. Brandts,et al.  Thermodynamics of protein denaturation. III. Denaturation of ribonuclease in water and in aqueous urea and aqueous ethanol mixtures , 1967 .

[50]  R. Stokes.  Thermodynamics of aqueous urea solutions , 1967 .

[51]  C. Swenson.  Effects of protein denaturants of the urea-guanidinium class on bulk water structure: An infrared study☆ , 1966 .

[52]  R. Mills,et al.  A Study of Diffusion in the Ternary System, Labeled Urea-Urea-Water, at 25° by Measurements of the Intradiffusion Coefficients1 of Urea2 , 1965 .

[53]  W. Jencks,et al.  THE EFFECT OF COMPOUNDS OF THE UREA-GUANIDINIUM CLASS ON THE ACTIVITY COEFFICIENT OF ACETYLTETRAGLYCINE ETHYL ESTER AND RELATED COMPOUNDS. , 1965, Journal of the American Chemical Society.

[54]  Harold A. Scheraga,et al.  The Temperature Dependence of the Enthalpy of Formation of the Amide Hydrogen Bond; the Urea Model1 , 1965 .

[55]  S. Malik,et al.  Nonpolar Group Participation in the Denaturation of Proteins by Urea and Guanidinium Salts. Model Compound Studies , 1964 .

[56]  C. Tanford,et al.  THE SOLUBILITY OF AMINO ACIDS AND RELATED COMPOUNDS IN AQUEOUS UREA SOLUTIONS. , 1963, The Journal of biological chemistry.

[57]  G. Kegeles,et al.  The Diffusion Coefficients, Densities, and Viscosities of Solutions of Acetamide in Water , 1963 .

[58]  A. Holtzer,et al.  THE EFFECT OF UREA ON HYDROPHOBIC BONDS: THE CRITICAL MICELLE CONCENTRATION OF n-DODECYLTRIMETHYLAMMONIUM BROMIDE IN AQUEOUS SOLUTIONS OF UREA1 , 1961 .

[59]  S. Gill,et al.  SOLUBILITY OF DIKETOPIPERAZINE IN AQUEOUS SOLUTIONS OF UREA1 , 1961 .

[60]  L. J. Gosting,et al.  A Study of the Diffusion of Urea in Water at 25° with the Gouy Interference Method1 , 1952 .