An inhomogeneous self‐consistent reaction field theory of protein core effects. Towards a quantum scheme for describing enzyme reactions

A quantum chemical framework is described where the electronic properties of model subsystems inside or at the surface of globular proteins (enzymes) can be calculated. Protein and solvent surroundings are incorporated in our effective Schrodinger equation. The theory is a generalization of the SCRF of protein core effects [O. Tapia, F. Sussman, and E. Poulain, J. Theor. Biol. 71, 49 (1978)]. A test has been carried out within the CNDO–INDO approximate scheme on the proton relay system of liver alcohol dehydrogenase. The results have elicited the fundamental role played by the protein core potential and the polarization potential in stabilizing ion‐pair structures against canonical H‐bonded ones. The polarization field introduces a nonlinear dependency on the model system wave function via the field created by its charge density. This fact is instrumental for a proper description of a highly polarized subsystem coupled to a polarizable surrounding medium.

[1]  A. Warshel,et al.  Energetics of enzyme catalysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

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

[3]  Charged particles in polarizable fluids , 1978 .

[4]  O. Tapia,et al.  A quantum chemical study of solvent effects on biomolecules: an application of the virtual charge model and the self-consistent reaction field theory of solvent effect to γ-amino butyric acid, β-alanine and glycine , 1979 .

[5]  G. Johannin,et al.  An estimate of intraproteic electrostatic fields values originated by the peptide groups in -chymotrypsin. , 1972, Biochemical and biophysical research communications.

[6]  O. Tapia,et al.  Environmental effects on H-bond potentials: A SCRF MO CNDO/2 study of some model systems. , 1978, Journal of theoretical biology.

[7]  Harold A. Scheraga,et al.  Energy Parameters in Polypeptides. I. Charge Distributions and the Hydrogen Bond , 1967 .

[8]  G. Corongiu,et al.  Monte Carlo simulations of water clusters around Zn++ and a linear Zn++⋅CO2 complex , 1980 .

[9]  R. Mcweeny,et al.  Methods Of Molecular Quantum Mechanics , 1969 .

[10]  B. Berne,et al.  A monte carlo procedure for the study of solvent effects on quantum molecular degrees of freedom , 1981 .

[11]  E. Clementi,et al.  Preliminary attempt to follow the enthalpy of an enzymatic reaction by ab initio computations: Catalytic action of papain , 1978 .

[12]  Orlando Tapia,et al.  Self-consistent reaction field theory of solvent effects , 1975 .

[13]  A. Warshel A microscopic model for calculations of chemical processes in aqueous solutions , 1978 .

[14]  D. A. Dunnett Classical Electrodynamics , 2020, Nature.

[15]  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.

[16]  Jacopo Tomasi,et al.  Molecular SCF Calculations for the Ground State of Some Three‐Membered Ring Molecules: (CH2)3, (CH2)2NH, (CH2)2NH2+, (CH2)2O, (CH2)2S, (CH)2CH2, and N2CH2 , 1970 .

[17]  S. Yomosa,et al.  Molecular Orbital studies on the Enzymatic Reaction Mechanism of Serine Proteases. I. Charge Relay System in Substrate Free State , 1977 .

[18]  Harel Weinstein,et al.  Analytical calculation of atomic and molecular electrostatic potentials from the Poisson equation , 1973 .

[19]  S. Nordholm,et al.  Theory of solvent effects on the equilibrium properties of a diatomic guest molecule , 1980 .

[20]  A. Kornyshev,et al.  Phenomenological Theory of Polar Systems , 1972 .

[21]  W G Hol,et al.  On the role of the active site helix in papain, an ab initio molecular orbital study. , 1979, Biophysical chemistry.

[22]  D. Oxtoby Local polarization theory for field‐induced molecular multipoles , 1980 .

[23]  C. Jameson,et al.  Molecular electronic property density functions: The nuclear magnetic shielding density , 1980 .

[24]  David L. Beveridge,et al.  Approximate molecular orbital theory , 1970 .

[25]  E. Clementi,et al.  Monte carlo simulation of water solvent with biomolecules. Glycine and the corresponding zwitterion , 1978 .

[26]  R. Daudel,et al.  Quantum Theory of Chemical Reactivity , 1973 .

[27]  H. Eklund,et al.  Three-dimensional structure of horse liver alcohol dehydrogenase at 2-4 A resolution. , 1976, Journal of molecular biology.

[28]  L R Pratt,et al.  Relation between the local field at large distances from a charge or dipole and the dielectric constant. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[29]  H. Umeyama,et al.  Enzymic dynamics and molecular orbital study on the roles of arginines in carboxypeptidase A, a sliding mechanism , 1978 .

[30]  P A Kollman,et al.  Electrostatic potentials of proteins. 2. Role of electrostatics in a possible catalytic mechanism for carboxypeptidase A. , 1976, Journal of the American Chemical Society.

[31]  I. West,et al.  The proton‐translocating ATPase of Escherichia coli , 1974, FEBS letters.

[32]  O. Tapia,et al.  Towards a quantum-chemical representation of enzyme activity. A scrf pce cndo/2 study of the ladh proton relay system , 1980 .

[33]  D. Rees Experimental evaluation of the effective dielectric constant of proteins. , 1980, Journal of molecular biology.

[34]  B. Roos,et al.  Ab initio molecular orbital calculations on the water-carbon dioxide system. Reaction pathway for water + carbon dioxide .fwdarw. carbonic acid , 1977 .

[35]  R. Bonaccorsi,et al.  An approximate expression of the electrostatic molecular potential in terms of completely transferable group contributions , 1977 .

[36]  B. Ninham Long-range vs. short-range forces. The present state of play , 1980 .

[37]  H. Mcconnell,et al.  Intramolecular Charge Transfer in Aromatic Free Radicals , 1961 .

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

[39]  M. A. Vorotyntsev,et al.  Electrostatic models in the theory of solutions , 1976 .

[40]  O. Tapia,et al.  Medium polarization effect on proton potential shape S.A SCRF--MO CNDO/2 study of methanol and methanethiol H-bonded to imidazol. , 1978, Biochemical and biophysical research communications.

[41]  W. G. Laidlaw,et al.  On the application of the variational principle to a type of nonlinear ’’Schrödinger equation’’ , 1979 .

[42]  J. Sipe,et al.  Limitations of the concept of polarizability density as applied to atoms and molecules , 1978 .

[43]  G. N. Ramachandran,et al.  Conformation of polypeptides and proteins. , 1968, Advances in protein chemistry.

[44]  D. Oxtoby The calculation of pair polarizabilities through continuum electrostatic theory , 1978 .

[45]  P. Becker Electron and Magnetization Densities in Molecules and Crystals , 1980 .

[46]  J. A. Yoffe Electric polarizabilities using point charge models , 1979 .

[47]  M. Karplus,et al.  Molecular dynamics of ferrocytochrome c , 1980, Nature.

[48]  Arieh Warshel,et al.  Calculations of chemical processes in solutions , 1979 .

[49]  H. Schaefer Methods of Electronic Structure Theory , 1977 .

[50]  E. Bertaut The equivalent charge concept and its application to the electrostatic energy of charges and multipoles , 1978 .

[51]  Alberte Pullman,et al.  Anab initio theoretical study of the binding of ZnII with biologically significant ligands: CO2, H2O, OH−, imidazole, and imidazolate , 1978 .

[52]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1977, Journal of molecular biology.

[53]  S. Yomosa On the Basic Equation for the Equilibrium Electronic States in Polar Solvents —Broken Symmetry— , 1978 .

[54]  J. Kraut Serine proteases: structure and mechanism of catalysis. , 1977, Annual review of biochemistry.

[55]  H. Berendsen,et al.  The α-helix dipole and the properties of proteins , 1978, Nature.