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The free energy surface for the nucleotide transfer reaction of T7 polymerase is evaluated by free energy pertubation/empirical valence bond (FEP/EVB) calculations. A key aspect of the enzyme simulation is a comparison of enzymatic free energy profiles with the corresponding reference reactions in water using the same computational methodology, thereby enabling a quantitative estimate for the free energy of the nucleotide insertion reaction.

Detailed calculations of the reduction potentials of the blue copper proteins plastocyanin and rusticyanin using the QM/MM all-atom frozen density functional theory, FDFT method is reported.By using a classical reference potential, the relevant ab initio free energies are evaluated.

Empirical valence bond simulations were carried out to determine the origin of the enormous catalytic power of ribonuclease A, an enzyme belonging to a class that catalyzes the cleavage of phosphodiester bonds in RNA. A general acid-general base mechanism with a dianionic transition state and a triester-like mechanism with a monoionic transition state were analyzed. In the former, a catalytic effect of ~18 +/- 6 kcal/mol was established, while in the latter mechanism, a value of ~12 +/- 6 kcal/mol was calculated.

Conformational studies were performed on the dimethyl phosphate anion, dimethyl phosphorothioate anion, dimethyl methylphosphonate and methyl ethylphosphonate anion in the gas phase and in aqueous solution. Results showed that the aqueous solvation effects have an important role in conformational stability and kinetics of conformationalf transitions of these esters. Also, the substitution of either O3' or O5' oxygen in the phosphodiester bonds enhances the local flexibility of the resulting DNA linkage.

Computer simulation approaches are employed in relating the structure of acetylcholinesterase to its total catalytic effect. Specifically, microscopic and semimicroscopic techniques are used to determine how the enzyme lowers the energy barrier of the acylation step of acetylcholine hydrolysis, as against the reference reaction in water. From the results, it is concluded that the most important catalytic effects are associated with nearby residues rather than distant ionized residues.

The importance of quantum mechanical nuclear movements in enzymatic reactions was studied by realistic simulations that consider the fluctuations of an entire enzyme-substrate complex. The quantized classical path method was employed based on Feynman's path integral equation. The computations analyze the quantum mechanical activation free energy and deuterium isotope effect for the proton transfer step in the catalytic reaction of carbonic anhydrase. The possible catalytic advantage of quantum mechanical nuclear motions was studied.

The free energies of the radical-pair states are calculated for the photosynthetic bacterial reaction centers from Rhodopseudomonas viridis. The radical pair states are P+B-H and P+BH-, where P is a bacteriochlorophyll dimer acting as an electron donor, H is the bacteriopheophytin acting as the acceptor and B is a bacteriochlorophyll representing an intermediary. During the charge-separation reaction, P+B-H acts as an intermediate. The dielectric effects of the protein, membrane and solvent are considered.

The two divalent metal ions present in the exo site of DNA pol I exert an electrostatic influence during the phosphodiester bond hydrolysis. The first metal ion facilitates electrostatic stabilization to the OH- nucleophile and the second metal ion stabilizes the negative charge on the phosphate. The second metal ion is not involved in the strain mechanism. Sites that bound to the metal ion in a rigid environment decreases the capacity of the metal toward the phosphate center during the nucleophilic attack.

The linear free energy relationships for a series of six adiabatic reactions in solutions were analyzed by computer simulation methods. The simulations evaluated the hydride transfer reactions within a class of NAD+ analogues. Quantum mechanical nuclear corrections of the activation energies of the solute and solvent were analyzed by the quantized classical path method. The solute and solvent energies obtained from the microscopic parameter are different than those obtained by the phenomenological approach.

A theoretical study of the reaction of tyrosyl-tRNA-synthetase (TTS) to examine the basis of linear free energy relationships (LFER) in enzymatic reactions proves the efficiency of pure valence band (VB) resonance structures in analyzing LFER. This VB representation uses Marcus-type concepts to determine LFER in proteins and to analyze reaction mechanisms. This approach helps determine the value of beta in the equation relating changes in activation free energies due to perturbations and free energy difference between reactants and products.

Experimental 19F chemical shifts of the fluorine nuclear magnetic resonance spectrum of the galactose binding protein from Escherichia coli are controlled by weak or long-range electrical interactions. These can be derived by using the responses of the shielding tensor elements to the uniform field components and the non uniform or gradient terms, along with the mean values of the fields (Ex) and field gradients (Vii) obtained from molecular dynamics (MD) trajectories. The 19F NMR shielding of the pentapeptide Gly-Gly(5-F) Trp-Gly-Gly in water is close to that of the denatured protein. Van der Waals interactions are not significant for fluorine shielding non equivalence in proteins, as the experimental outcomes can be acquired by using the computed field and field gradient terms. The ability to predict protein NMR shielding patterns and ranges may be useful for structural analysis and for verifying the varying techniques of deriving protein electrostatics.

The computer simulations of the CO2/HCO3-interconversion step in human carbonic anhydrase are repoprted. The reaction potential energy surface and reaction free energy profiles are constructed using the empirical valence method and a combination of the free energy perturbation technique and molecular dynamics, respectively. The simulated results are found to be in good agreement with experimental estimates of the reaction energetics.

The nature of the hydrolysis of phosphate monoester dianions in solutions and in proteins is explored by systematic calculations of the potential surfaces of the reactions of a series of phosphate monoesters with different leaving groups. The results have indicated that the nature of the potential surfaces for the phosphoryl transfer reactions in solution and proteins is complicated and cannot be determined in a conclusive way without the use of theoretical studies.

The nature of enzyme catalysis is examined in terms of a solute solvent coordinate, focusing on the S(sub N)2 reaction of dehalogenase (DhIA). It is demonstrated that almost the entire catalytic effect is associated with the preorganization of the protein-solvent coordinate.

According to the study conducted the catalytic reaction of lipoxygenase that is characterized as an extremely large kinetic isotope effect is presented. The study also presents the nature of the reorganization energy in the enzyme and solutions reactions.

A systematic quantitative analysis is presented to study the origin of catalytic power of chorismate mutase. It is found that this enzyme works by providing electrostatic transition state stabilization.

The very rapid rate of OH(super -) attack on the neutral phosphate monoester casts doubt on one of the most widely accepted basic assumptions in phosphate hydrolysis. This rate was previously underestimated since it was assumed that the rate constant of the reaction is similar to the rate constant of trimethyl phosphate hydrolysis at high pH. Such very fast rate of OH(super -) attack indicates that the hydrolysis of phosphate monoesters in aqueous solution is consistent with a mechanism involving proton transfer to the phosphate oxygen, followed by nucleophilic attack on the phosphorus.

The potential surface for general base-catalyzed methanolysis of formamide was evaluated, in the study of serine proteases.

One of the most useful ways of describing and analyzing enzyme catalysis is the description of the enzyme as an effective solvent for the reacting substrate. Here, we illustrate this concept by considering the SN2 reaction of haloalkan dehalogenase (DhIA), analyze the energetics and dynamics of the solvent coordinate, and evaluate their relative catalytic effect. It is demonstrated that almost the entire catalytic effect is associated with the preorganization of the protein-solvent coordinate. It is clarified that this effect is associated with the fact that the transition state is "solvated" by the protein more than in the reference solution reaction. This effect is fundamentally different than the frequently proposed desolvation mechanism. The possible catalytic role of dynamical effects is analyzed by considering several reasonable ways of defining "dynamical contributions to catalysis". It is found that these contributions are small regardless of the definition used. It is also shown that the effect of the difference in the relaxation time of the solvent coordinate in the enzyme and solution reaction is rather trivial relative to the effect of the corresponding changes in reorganization free energy. [ABSTRACT FROM AUTHOR]

Examines the microscopic validity of linear free energy relationships for adiabatic reactions in solutions. Computer simulation methods and realistic potential surfaces; Quantum mechanical corrections of the activation energies; Effectiveness of the empirical valence bond approach for studies of chemical processes in solutions.