The probable conformation of substrates recognized by dipeptidyl-peptidase IV and some aspects of the catalytic mechanism derived from theoretical investigations

Summary By theoretical conformational investigations of substrates and nonsubstrates of the enzyme dipeptidyl-peptidase IV (DP IV) as well as dipeptide-esters using the ECEPP83 method we determined the structure of peptides recognized and cleaved by the enzyme. From a comparison of all possible structures for the substrates with conformations not possible in nonsubstrates we concluded that a single conformation explains substrate specificities of DP IV. This conformation is characterized by the following dihedral angles: {ie159-1}, {ie159-2}, {ie159-3}, {ie159-4}, and {ie159-5}. The conclusions were supported by comparisons of molecular electrostatic potentials calculated with the molecular graphics program HAMOG.     

The catalytic power of pyruvate decarboxylase. A stochastic model for the molecular evolution of enzymes.

Pyruvate decarboxylase (PDC) catalyzes the decarboxylation of pyruvate anion by a factor of around 10(12), compared with the non-enzymic decarboxylation by thiamine, under standard state conditions of 1 mM pyruvate and thiamine diphosphate (TDP), pH 6.2. Free-energy diagrams constructed on the basis of earlier measurements for the enzymic and non-enzymic reactions give some information on catalysis by PDC. PDC stabilizes the reactant state preceding TDP addition to pyruvate by 76 kJ mol-1 and the transition state for the addition by 83 kJ mol-1. PDC stabilizes the reactant state preceding decarboxylation (presumably alpha-lactyl-TDP) by 27 kJ mol-1 and the transition state for decarboxylation by 68 kJ mol-1. In addition, the free-energy diagrams reveal a leveling of reactant-state free energies in the enzymic reaction compared with the non-enzymic reaction, in that the former are nearly equal to each other. The enzyme-bound transition-state energies are similarly leveled. The energetic leveling of reactant states has been noted by Albery, Knowles and their coworkers in many enzymic reactions and termed 'matched internal thermodynamics.' They showed that the result would arise naturally (and inevitably) in the 'evolution to perfection' of enzymes, when the evolutionary process was treated by a deterministic model. The critical assumption of this model was the validity of a Marcus-type or Br?nsted-type linear free-energy relationship between rate and equilibrium constants for reactions occurring wholly within enzyme complexes. Here a completely stochastic simulation of molecular evolution, with no deterministic assumptions, is shown to reproduce both 'matched internal thermodynamics' and the 'matched internal kinetics' or leveling of transition-state energies noted here. The Albery-Knowles result is thus more general than might have been supposed.     

Chaotic Expansion of Elements of the Universal Enveloping Algebra of a Lie Algebra Associated with a Quantum Stochastic Calculus

The functional Ito formula, in the form df() = f( + d ) –f(),is formulated and proved in the context of a Lie algebra L associatedwith a quantum (non-commutative) stochastic calculus. Here fis an element of the universal enveloping algebra U of L, andf() + d() – f() is given a meaning using the coproductstructure of U even though the individual terms of this expressionhave no meaning. The Ito formula is equivalent to a chaoticexpansion formula for f() which is found explicitly. 1991 MathematicsSubject Classification: primary 81S25; secondary 60H05; tertiary18B25.     

Oxalate/hydrogen peroxide chemiluminescence reaction. A 19F NMR probe of the reaction mechanism

The mechanism of the oxalate/hydrogen peroxide chemiluminescence reaction has been examined by magnetic resonance techniques. Investigation of the reactive intermediates involved in chemiluminescence was carried out with bis(2,6-difluorophenyl)oxalate (DFPO) using 19F NMR to probe its reactions with aqueous hydrogen peroxide. Formation and reactions of the intermediate hydroperoxy oxalate ester B along with the formation of the half ester product C and difluorophenol D were monitored by 19F NMR. When the reaction of DFPO and aqueous hydrogen peroxide was carried out in the presence of dansylphenylalanine, a typical fluorescent analyte, the intensity of the resonance due to the intermediate B was diminished in direct proportion to the concentration of the analyte. Comparison of the time/intensity profile of the chemiluminescence emission with that of the 19F NMR transient suggests that the hydroperoxy oxalate ester B is the likely 'reactive' intermediate, capable of participating in a chemically initiated electron exchange luminescence mechanism.