Computational Approaches to Biochemical Reactivity
Gábor Náray-Szabó, Arieh Warshel
Kluwer Academic, Jan 1, 1997 - Science - 379 pages
This work summarises recent results in the rapidly developing discipline of the computational aspects of biochemical reactivity. It presents a comprehensive and critical treatise on the subject, with numerous references covering all relevant and recent work. The chapters, written by experts in the field, deal with quantum mechanical models for reactions in solution, ab initio molecular orbital studies on enzymatic reactions, combined quantum-classical models for proteins, force field approaches for modelling enzymes, electrostatic effects in proteins, electrostatic basis of enzyme catalysis, the mechanism of proteases, modelling of proton transfer reactions in enzymes and protein-ligand interactions.
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Free energy perturbation calculations within quantum mechanical
Hybrid potentials for molecular systems in the condensed phase
Molecular mechanics and dynamics simulations of enzymes
5 other sections not shown
acid active active site approach approximation Aqvist aspartate binding Biochemistry Biol calculations carbonyl Carboxypeptidase catalysis catalytic cavity charge distribution Chem chemical reactions Comp complex computational conformational continuum contribution density dielectric constant dipoles electronic electrostatic effects electrostatic interactions enzymatic enzyme equation experimental Fersht free energy perturbation function geometry H-bond Hamiltonian histidine Honig hydrogen bonds hydrolysis inhibitor initio intermediate ionized Karplus kcal/mol Kollman ligand lysozyme matrix McCammon methods molecular dynamics molecular dynamics simulations molecular mechanics mutations negatively charged nucleophilic orbitals oxyanion oxyanion hole oxygen parameters peptide phosphate Phys polarizability polarization procedure proteases protein proton proton transfer QM atoms QM/MM quantum mechanical reaction coordinate reaction field reaction mechanism residues role semiempirical serine serine proteases side chain solute solvation solvent solvent molecules stabilisation stabilization step structure substrate subtilisin surface theoretical Tomasi transition Truhlar values Warshel water molecule wavefunction