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The relationship between the reduced catalytic power of thermophilic enzymes (Tm) and mesophilic enzymes (Ms) and their thermal stability is examined on the bases of dihydrofolate reductase (DHFR). The Tm enzyme showed larger displacement coordinates than the Ms enzyme which suggest that optimized catalysts are less stable.

The effect of the protein residues, taking human DNA polymerase [beta] as a model system, is studied for understanding of catalytic control, specifically on the transition state (TS) binding energy. It is seen that the protein reorganization between the open, unbound form and the closed from does not change the magnitude of the calculated mutational effects and the success of the PDLD/SLRA approach in computing that energy of the TS can help in rapid mutational screening of TS analogues.

Many investigators have asked whether 'dynamical effects' play a significant role in enzyme catalysis. Combined quantum mechanical/molecular mechanics (QM/MM) methods provide a generic way of obtaining potential surfaces and activation free energies of chemical processes in enzymes.

The evaluation of ab inito QM/MM free-energy surfaces and activation free energies of reactions in enzymes and in solutions is carried out by using the empirical valence bond (EVB) method as a reference potential and then using linear response approximation (LRA). This new method evaluates the free energy associated with both the substrate and the solvent and helps in obtaining a free-energy barrier that reflects the solute entropy properly.

Microscopic calculations of free energy profiles for ion transport through biological ion channels present a very serious challenge to modern simulation approaches. The main problem is due to the major convergence problems associated with the heterogeneous landscape of the electrostatic environment in ion channels and with the need to evaluate the profile associated with the transfer of the ion from bulk water to the channel environment.

The molecular basis of proton conductance the gA channel is examined by using a full empirical valence bond (EVB) model to obtain the free energy profile and then using a simplified EVB model to obtain the time dependence of the proton transduction (PTR) process. It concludes that the barrier associated with the electrostatic energy of the transferred proton determines the rate of the PTR process.

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.

Several strategies that allow one to perform practical ab initio QM/MM calculations of free energy profiles in solutions and proteins are presented. The performance of both approaches is examined by calculating by calculating the potential of mean force for the autodissociation reaction of water in solution.

The relative stability of Watson-Crick and mismatched dNTP template base pairs in the active site of T7 DNA polymerase (pol T7) was examined using linear-response molecular dynamics simulations. It was found that pol T7 provides a larger binding contribution to the replication fidelity than pol beta by discriminating more effectively against mismatches that are most probable to occur in the neutral anti-anti configurations.

A theoretical study of the selection of right/wrong deoxy-ribonucleotide triphosphates substrates by DNA polymerases at the initial binding step, a major component of the DNA replication fidelity is presented. Calculations are performed to predict the effects of amino acid substitutions on the fidelity for mutant forms of pol beta, thus providing a deeper understanding of the role of the polymerase active site in ensuring replication accuracy.

Research has been conducted on the biological processes' molecular dynamics simulations. The study of the photobiological reactions carried out via the use of these simulations is presented.

Results show that the ground-state destabilization does not play a role in enzyme catalysis as shown by the rate enhancement measurements of orotidine 5'-phosphate decarboxylase (ODCase). Data reveal that electrostatic effects are involved in the catalysis reactions which, in turn are associated with transition state stabilization.

The way in which GTPase reaction of Ras is catalyzed by GAP is discussed based on a computer simulation study. Feasibility of the associative and dissociative mechanism in the GTPase reaction of Ras was explored. One conclusion is that the reaction is mostly likely to involve an associative mechanism. The effect of Arg 789 was seen to be associated with its direct interaction with the transition state charge distribution. The oncogenic effect of mutating Gln61 was explored.

Research is presented using a computational approach within a Langevin dipoles solution model to determine the entropies of transfer of molecules from the gas phase to aqueous solution.

A kinetic study of the catalytic hydrolysis of adenosine 2',3'-cyclic monophosphate (cAMP) by Cu(II) terpyridine (Cutrpy) was conducted. Results indicate that a single Cutrpy interacts with one cAMP substrate in the rate-determining step of hydrolysis at biological hydrogen-ion concentration. It was later determined that a Cutrpy-bound hydroxide serves as the reactive catalyst. Furthermore, this hydroxide was found to function as a nucleophile but not as a general base.

Research was conducted to examine the potentials of mean force for the association of adenine, guanine, uracil, purine, thymine and cytosine in aqueous solution using Langevin dipoles solvation model and ab initio MP2/6-31G measurements. Using the linear relationship between entropies and binding enthalpies, the entropy contributions to the free energies for hydrogen bonding and stacking were calculated. Results indicate that pure bases are more stable than their pyrimidine-containing counterparts.

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.

Empirical valence bond (EVB) method facilitates the simulation of enzyme interactions, and is applicable to charge separation and translocation reactions, in addition to reactions incorporating resonance structure. EVB method's forte is its potential simulation of diabatic free-energy surfaces of the essential resonance structures, which enables the substantial microscopic validation of linear free-energy relationships (LFERs). LFERs are applicable to the enzyme-active sets, subject to the condition that they correspond to the intrinsic resonance structural energetics addition to the energetics of 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 general base (GB61) hydrolysis mechanism proposes that Gln61 is the general base that facilitates the nucleophilic attack on the gamma-phosphate by activating a water molecule. The role of Gln 61 in ras p21 was examined by the empirical valence bond (EVB) approach which simulates the correlations of structure and energetics of the system by a computer. Free energy perturbation calculations and well-defined electrostatic considerations were used to verify EVB results. The findings indicate that Gln 61 is not likely the general base in the hydrolysis reaction. Alternatively, gamma-phosphate might act as a general base while Gln 61 only stabilizes the OH- nucleophile.