Possible sources of error in the computer simulation of protein structures and interactions

Publisher Summary The significance of the results to be obtained from the simulation of protein structures and interactions, abetted by the availability of software packages and of powerful workstations with superb graphic capabilities, is encouraging a proliferation of published material. Unfortunately, the quality of the predictions may be affected by a number of possible sources of error so that, unless the information obtained from the simulation is contrasted with experimental data, the danger exists that the unaware user of a software package may be offering a discussion based on a biased and/or wrongly characterized structure. It is important to be aware of the quality of the parameters in use. The role of perturbation theory is to suggest the use of 1/R- xpansions for the evaluation of the interaction energy between non-bonded atoms. The actual expressions of the expansions may be obtained from theoretical results but also with some semi-empirical considerations.

[1]  Robert S. Mulliken,et al.  Comparison of Two Atomic Charge Definitions, as Applied to the Hydrogen Fluoride Molecule , 1971 .

[2]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[3]  Andrey A. Bliznyuk,et al.  A combined quantum chemical/molecular mechanical study of hydrogen-bonded systems , 1992 .

[4]  Arieh Warshel,et al.  An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .

[5]  M Karplus,et al.  Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. , 1991, Biochemistry.

[6]  Harold A. Scheraga,et al.  Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 1. Application to neutral molecules as models for polypeptides , 1990 .

[7]  Ji-Min Yan,et al.  Point-Charge Models for Molecules Derived from Least-Squares Fitting of the Electric Potential , 1988 .

[8]  Robert J. Woods,et al.  Derivation of net atomic charges from molecular electrostatic potentials , 1990 .

[9]  H. Scheraga,et al.  Modeling amino acid side chains. 3. Influence of intra- and intermolecular environment on point charges , 1993 .

[10]  Ernest R. Davidson,et al.  Electronic Population Analysis of Molecular Wavefunctions , 1967 .

[11]  Enrico Clementi,et al.  Computational Aspects for Large Chemical Systems , 1980 .

[12]  F. Weinhold,et al.  Natural population analysis , 1985 .

[13]  Frank A. Momany,et al.  Determination of partial atomic charges from ab initio molecular electrostatic potentials. Application to formamide, methanol, and formic acid , 1978 .

[14]  F. L. Hirshfeld.  Bonded-atom fragments for describing molecular charge densities , 1977 .

[15]  A. Brünger,et al.  Torsion angle dynamics: Reduced variable conformational sampling enhances crystallographic structure refinement , 1994, Proteins.

[16]  A. T. Hagler,et al.  Determination of atomic point charges and point dipoles from the Cartesian derivatives of the molecular dipole moment and second moments, and from energy second derivatives of planar dimers. I. Theory , 1989 .

[17]  S. Tsuzuki,et al.  Comparison of atomic charge distributions obtained from different procedures: basis set and electron correlation effects , 1996 .

[18]  W. Thiel,et al.  Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches , 1996, J. Comput. Chem..

[19]  Jiali Gao.  Comparison of the hybrid AM1/TIP3P and the OPLS functions through Monte Carlo simulations of acetic acid in water , 1992 .

[20]  V. Vasilyev,et al.  Tetrahedral intermediate formation in the acylation step of acetylcholinesterases. A combined quantum chemical and molecular mechanical model , 1994 .

[21]  M. Paniagua,et al.  Atomic partitioning of two-center potentials for slater basis , 1986 .

[22]  P. Politzer,et al.  Properties of atoms in molecules. IV. Atomic charges in some linear polyatomic molecules , 1972 .

[23]  K. Jug.  Charge distributions and multipole moments in molecules , 1975 .

[24]  K. Merz,et al.  Analysis of a large data base of electrostatic potential derived atomic charges , 1992 .

[25]  I. H. Hillier,et al.  On partitioning the overlap charge density in self-consistent charge molecular-orbital calculations , 1969 .

[26]  János G. Ángyán,et al.  Modelling the electric field of water obtained from accurate SCF wave functions , 1990 .

[27]  Peter Politzer,et al.  Properties of atoms in molecules. I. Proposed definition of the charge on an atom in a molecule , 1970 .

[28]  K. Roby.  Quantum theory of chemical valence concepts: II. Hybrid atomic orbitals and localized molecular orbitals studied by projection operator techniques , 1974 .

[29]  Keith R. Roby,et al.  Quantum theory of chemical valence concepts , 1974 .

[30]  S. Huzinaga,et al.  Mulliken Population Analysis and Point Charge Model of Molecules , 1980 .

[31]  R. Dovesi,et al.  Multiple expansion of molecular charge distribution , 1974 .

[32]  J. D. L. Vega,et al.  Atomic partitioning of long-range two-center potentials , 1985 .

[33]  Donald E. Williams,et al.  Representation of the molecular electrostatic potential by a net atomic charge model , 1981 .

[34]  Paul G. Mezey,et al.  Molecular electron density lego approach to molecule building , 1993 .

[35]  György G. Ferenczy,et al.  Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values , 1989 .

[36]  J. Noell.  Modified electronic population analysis for transition-metal complexes , 1982 .

[37]  Christophe Chipot,et al.  Modeling amino acid side chains. 1. Determination of net atomic charges from ab initio self-consistent-field molecular electrostatic properties , 1992 .

[38]  R. S. Mulliken.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[39]  Jiali Gao,et al.  Optimization of the Lennard‐Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3‐21G basis set , 1996 .

[40]  Ronald M. Levy,et al.  Helix–coil transitions in a simple polypeptide model , 1980 .

[41]  Transformation of the ϕ‐ψ plot for proteins to a new representation with local helicity and peptide torsional angles as variables , 1980 .

[42]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[43]  R. Bader,et al.  Partitioning and characterization of molecular charge distributions , 1971 .

[44]  Robert S. Mulliken,et al.  Electronic Population Analysis on LCAO‐MO Molecular Wave Functions. III. Effects of Hybridization on Overlap and Gross AO Populations , 1955 .

[45]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[46]  R. Naaman,et al.  The structure of small molecules and ions , 1988 .

[47]  Peter A. Kollman,et al.  Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..

[48]  M. Paniagua,et al.  1.1.1 electrostatic description of molecular systems , 1985 .

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

[50]  E. Shakhnovich,et al.  Pseudodihedrals: Simplified protein backbone representation with knowledge‐based energy , 1994, Protein science : a publication of the Protein Society.

[51]  Robert S. Mulliken,et al.  Electronic Population Analysis on LCAO‐MO Molecular Wave Functions. IV. Bonding and Antibonding in LCAO and Valence‐Bond Theories , 1955 .

[52]  Kenneth M. Merz,et al.  An examination of a density functional/molecular mechanical coupled potential , 1995, J. Comput. Chem..

[53]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[54]  Ulrich Sternberg,et al.  New approach to the semiempirical calculation of atomic charges for polypeptides and large molecular systems , 1994, J. Comput. Chem..

[55]  F. J. Luque,et al.  Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction , 1990 .

[56]  J. M. Pocock,et al.  Computer Simulations of Protein Structures and Interactions , 1995 .

[57]  A. Elofsson,et al.  Local moves: An efficient algorithm for simulation of protein folding , 1995, Proteins.

[58]  S. Fraga,et al.  Computational chemistry : structure, interactions, and reactivity , 1992 .

[59]  Harold A. Scheraga,et al.  Analytical intermolecular potential functions from ab initio SCF calculations for hydration of methylamine and methylammonium ion , 1990 .

[60]  Johann Gasteiger,et al.  Extension of the method of iterative partial equalization of orbital electronegativity to small ring systems , 1983 .

[61]  Serafin Fraga,et al.  A semiempirical formulation for the study of molecular interactions , 1982 .

[62]  Arieh Warshel,et al.  Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches , 1993 .

[63]  Harold A. Scheraga,et al.  Analytic intermolecular potential functions from ab initio SCF calculations of interaction energies between methane, methanol, acetic acid, and acetate and water , 1988 .

[64]  Uwe Koch,et al.  An improved description of the molecular charge density in force fields with atomic multipole moments , 1995, J. Comput. Chem..

[65]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[66]  K. Jug.  Effects of polarization on charge distributions and integral approximations , 1973 .

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

[68]  J. Maruani.  Molecules in Physics, Chemistry, and Biology , 1988 .

[69]  K. Jug.  A new definition of atomic charges in molecules , 1973 .

[70]  M. Paniagua,et al.  Transferability of atomic descriptions in molecules , 1986 .

[71]  György G. Ferenczy,et al.  Transferable net atomic charges from a distributed multipole analysis for the description of electrostatic properties: a case study of saturated hydrocarbons , 1993 .

[72]  R. Rein,et al.  Molecular-orbital studies of intermolecular interaction energies. II. Approximations concerned with Coulomb interactions and comparison of the two London schemes. , 1967, The Journal of chemical physics.

[73]  Robert Rein,et al.  On Physical Properties and Interactions of Polyatomic Molecules: With Application to Molecular Recognition in Biology , 1973 .

[74]  ed. Et al. Woolf,et al.  Webster's New Collegiate Dictionary , 1973 .

[75]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[76]  Robert S. Mulliken,et al.  Electronic Population Analysis on LCAO–MO Molecular Wave Functions. II. Overlap Populations, Bond Orders, and Covalent Bond Energies , 1955 .

[77]  G. Gallup,et al.  Population analyses of valence-bond wavefunctions and BeH2 , 1973 .

[78]  K. Gundertofte,et al.  A comparison of conformational energies calculated by several molecular mechanics methods , 1996 .

[79]  H. H. Jaffé,et al.  Electronegativity. I. Orbital Electronegativity of Neutral Atoms , 1962 .

[80]  L. Curtiss,et al.  Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint , 1988 .

[81]  M. Levitt.  A simplified representation of protein conformations for rapid simulation of protein folding. , 1976, Journal of molecular biology.

[82]  Ralph E. Christoffersen,et al.  Electron population analysis. Gross atomic charges in molecules , 1971 .

[83]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[84]  T. Fueno,et al.  Electronic Population Analysis Based on the Electron Pair Concept , 1976 .

[85]  Christophe Chipot,et al.  Modeling amino acid side chains. 2. Determination of point charges from electrostatic properties: toward transferable point charge models , 1993 .

[86]  György G. Ferenczy,et al.  Quantum mechanical computations on very large molecular systems: The local self‐consistent field method , 1994, J. Comput. Chem..

[87]  S. Iwata.  An alternative way to analyze the electron distribution in ab initio calculations , 1980 .