MECHANISMS OF ENZYMATIC REACTIONS - New Trends in Enzyme Catalysis and Biomimetic Chemical Reactions - page 71

the lessened bond energy of C(4)-axial-H as compared to C(4)-equatorial-H can provide a
kinetic advantage to hydride transfer.
According to (Bruice and Benkovic, 2000 and references therin) multiple electrostatic
interactions between the formate and nicotinamide of in the formate degydrogenase
pretransition state (PTS) persist in the TS. These two states differ only by a lengthening of
the hydrogen bond between the positively charged guanidine group of Arg284 and the
negative formate oxygen by 0.4 Å, and a shortening of the hydrogen bond between the
nicotinamide amide carbonyl oxygen and the imidazole of His332 by 0.5 in TS as

compared to PTS. The MD simulations showed a similarity between TS and PTS in
catecholate O-methyltransferase, haloalkane dehydrogenase and other enzymes (Bruice
and Benkovic, 2000; and references therein).
Recently the investigation of the structure, molecular dynamics and action mechanism
of enzymes revealed that protein globules of many enzymes consist of two tightly packed
knots (matrix, domains, blocks) tethered with a relatively flexible spacer. (Lumry, 1995a,b,
2002; and references herein) (See also Section 4.1). The enzyme active sites are most
commonly located in a cleft between these domains. Binding of substrates and inhibitors
depends on the extend of matrix contraction (Fersht, 1999).
For example, the absolute value of negative entropy of parent substrate N-acetyl-L-
tryptophan binding to chymotrypsin (-25 cal/moleK) was found to be markedly less than
that for inhibitors indole and N-acetyl-D-tryptophan (-60 and -135 cal/moleK,
respectively) It was proposed that the excess free energy (10 -12 kcal/mole) in the
enzyme-subsrate complex is converted to energy of the substrate compression from the
protein matrix contraction. An artificial substrate siltone, having a five-membered ring
with strain energy 23 kcal/mole, forms acetyl derivative with opening of the ring in the
chymotrypsin active site. Because an equilibrium-binding constant is close to unity, the
ring energy compensates presumably the matrix contraction at binding of “regular”
substrates and inhibitors. The several methods for measuring matrix contraction, including
analysis of B-factors and protein dynamics data, indicate a correlation between
aforementioned thermodynamic estimations and the enzyme matrix state.
During last decades the domains C-2 symmetry (the dyad rotation symmetry) of low-B
palindrome was established in many enzymes (chymotrypsin, trypsin, aspartyl proteinases,
HIV-1 protease, carboxypeptidase A, phospholipase A-2 ribonuclease, etc.) (Lumry, 2002;
and references therein). It is proposed that the pair domain closure causes constrain of
pretransition state complex that activates cleavage or formation of chemical bonds. Thus
control of strong bonds by the cooperation of many matrix or knots bonds takes place. As
an example, in the active site of carboxypeptidase A the zinc ion is attached to one of the
catalytic domains by histidine 69 and glutamine 72 and connected by hystidine 196 to the
second domain. Similar structures were found in the chymotrypsin and pepsin active sites
where protons are driven under compression of the domains closure.

Å

2.9. Principle of “optimum motion” and mechanisms of enzymes reactions

From point of view of considerations, which led to the formulation of POM, the formation
of pretransition states have to be preceded by a number elementary steps optimally