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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.

Although computational enzyme design is of great importance, the advances utilizing physics-based approaches have been slow, and further progress is urgently needed. One promising direction is using machine learning, but such strategies have not been established as effective tools for predicting the catalytic power of enzymes. Here, we show that the statistical energy inferred from homologous sequences with the maximum entropy (MaxEnt) principle significantly correlates with enzyme catalysis and stability at the active site region and the more distant region, respectively. This finding decodes enzyme architecture and offers a connection between enzyme evolution and the physical chemistry of enzyme catalysis, and it deepens our understanding of the stability-activity trade-off hypothesis for enzymes. Overall, the strong correlations found here provide a powerful way of guiding enzyme design. [ABSTRACT FROM AUTHOR]

A variety of signals, including inflammasome activation, trigger the formation of large transmembrane pores by gasdermin D (GSDMD). There are primarily two functions of the GSDMD pore, to drive lytic cell death, known as pyroptosis, and to permit the release of leaderless interleukin-1 (IL-1) family cytokines, a process that does not require pyroptosis. We are interested in the mechanism by which the GSDMD pore channels IL-1 release from living cells. Recent studies revealed that electrostatic interaction, in addition to cargo size, plays a critical role in GSDMD-dependent protein release. Here, we determined computationally that to enable electrostatic filtering against pro-IL-1β, acidic lipids in the membrane need to effectively neutralize positive charges in the membrane-facing patches of the GSDMD pore. In addition, we predicted that salt has an attenuating effect on electrostatic filtering and then validated this prediction using a liposome leakage assay. A calibrated electrostatic screening factor is necessary to account for the experimental observations, suggesting that ion distribution within the pore may be different from the bulk solution. Our findings corroborate the electrostatic influence of IL-1 transport exerted by the GSDMD pore and reveal extrinsic factors, including lipid and salt, that affect the electrostatic environment. [ABSTRACT FROM AUTHOR]

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.

Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme's conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions. [ABSTRACT FROM AUTHOR]

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.