Calculations enzymatic mechanisms

Hadzi, D., M. Hodoscek, D. Turk, and V. Harb. 1988. Theoretical Investigations of Structure and Enzymatic Mechanisms of Aspartyl Protcinascs Part 2. Ab initio calculations on some possible initial steps of proteolysis. J. Mol. Struct. (Theochem) 181, 71-80. 

Stein, M., van Lenthe, E., Baerends, E. J. and Luhitz, W. (2001b) Relativistic DFT calculations of the paramagnetic intermediates of [NiFe] hydrogenase. Implications for the enzymatic mechanism./. Am. Chem. Soc. (in press). 

Stein M, Lubitz W (2004) Relativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase a contribution to understanding the enzymatic mechanism. J. Inorg. Biochem. 

The application of NullSpace yields the correct stoichiometric number matrix. Thus the calculation from the standpoint of the further transformed Gibbs energy G yields the expected number of constraints introduced by the enzyme mechanism. This reaction is a dramatic example of the difference between chemical reactions and some enzyme-catalyzed reactions. It is the enzymatic mechanism that introduces the three constraints in addition to atom balances. 

Electronic Properties Effects of the Surrounding. The proton affinity of the zinc-bound water molecule is a key property for the enzymatic mechanism. The acidity of the zinc bound water is the result of a subtle fine tuning via hydrogen-bonded networks and electrostatic environment effects. This quantity can thus serve as a sensitive indicator of differences in the electronic structure that will have a critical influence on the enzymatic reaction. As a first attempt to quantify the effect of the electrostatic environment and the varying size of the cluster model we have therefore calculated the proton affinities for the different models. 

Although the last step in the reaction sequence, abstraction of a proton from C4, followed by aromatization of the a, 6-unsaturated ketone, will occur spontaneously without assistance by a protein, it seems reasonable to assume that product formation is accelerated considerably by an enzymatic mechanism. Again, DFT calculations suggest that deprotonated HisllO could accept a proton from the previously generated water molecule, which in turn accepts the C4 proton. Protonation of the ketone could occur by the catalytic water bound by the two tyrosines. 

A final important area is the calculation of free energies with quantum mechanical models [72] or hybrid quanmm mechanics/molecular mechanics models (QM/MM) [9]. Such models are being used to simulate enzymatic reactions and calculate activation free energies, providing unique insights into the catalytic efficiency of enzymes. They are reviewed elsewhere in this volume (see Chapter 11). 

The values determined from Figure 5.23 agree well with the values calculated from the equations (Table 5.5), with an error of 3.81% for the slope and 4.65% for the intersect, respectively. The obtained experimental data were consistent with the proposed enzymatic reaction and the reaction mechanisms with uncompetitive substrate inhibition and the noncompetitive product inhibition model. 

Theoretical calculations have been carried out on a number of zinc-containing enzymatic systems. For example, calculations on the mechanism of the Cu/Zn enzyme show the importance of the full protein environment to get an accurate description of the copper redox process, i.e., including the electronic effects of the zinc ion.989 Transition structures at the active site of carbonic anhydrase have been the subject of ab initio calculations, in particular [ZnOHC02]+, [ZnHC03H20]+, and [Zn(NH3)3HC03]+.990... 

Oxidation by direct H transfer from the a-carbon of alcohols to the pyrroloquinoline quinone (PQQ) cofactor of alcohol dehydrogenases was studied using ab initio quantum mechanical methods <2001JCC1732>. Energies and geometries were calculated at the 6-31G(d,p) level of theory, results were compared to available structural and spectroscopic data, and the role of calcium in the enzymatic reaction was explored. Transition state searches at the semi-empirical and STO-3G(d) level of theory provided evidence that direct transfer from the alcohol to C-5 of PQQ is energetically feasible. 

The mechanism of an enzymatic reaction is ultimately defined when all the intermediates, complexes, and conformational states of the enzyme are characterized and the rate constants for their interconversion are determined. The task of the kineticist in this elucidation is to detect the number and sequence of these intermediates and processes, define their approximate nature (that is, whether covalent intermediates are formed or conformational changes occur), measure the rate constants, and, from studying pH dependence, search for the participation of acidic and basic groups. The chemist seeks to identify the chemical nature of the intermediates, by what chemical paths they form and decay, and the types of catalysis that are involved. These results can then be combined with those from x-ray diffraction and NMR studies and calculations by theoretical chemists to give a complete description of the mechanism. 

Enzyme kinetics deals with the rate of enzyme reaction and how it is affected by various chemical and physical conditions. Kinetic studies of enzymatic reactions provide information about the basic mechanism of the enzyme reaction and other parameters that characterize the properties of the enzyme. The rate equations developed from the kinetic studies can be applied in calculating reaction time, yields, and optimum economic condition, which are important in the design of an effective bioreactor. 

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