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A generalized reaction scheme for the kinetic interaction of two reactants in a metabolic pathway has been examined in order to establish what minimal mechanistic patterns are required to support a damped oscillatory transient‐state kinetic behaviour of such a two‐component system when operating near a steady state. All potentially oscillating sub‐systems inherent in this scheme are listed and bri
The extent to which different stromal metabolites affecting ADPglucose pyrophosphorylase control the rate of photosynthetic starch production in the chloroplast of C3 plants has been examined by kinetic model studies. The results indicate that ATP, glucose 1‐phosphate, 3‐phosphoglycerate, fructose 6‐phosphate, and orthophosphate may provide significant contributions to the starch synthesis rate ch
The regulatory implications of the interaction of ribulosebisphosphate carboxylase with metabolites participating in the Calvin photosynthesis cycle has been examined by control analysis based on our recently described kinetic model for photosynthetic carbohydrate formation in the chloroplast of C3 plants. The results provide clear evidence that the Calvin cycle activity under conditions of light
A mathematical model is presented for photosynthetic carbohydrate formation in C3 plants under conditions of light and carbon dioxide saturation. The model considers reactions of the Calvin cycle with triose phosphate export and starch production as main output processes, and treats concentrations of NADPH, NAD+, CO2, and H+ as fixed parameters of the system. Using equilibrium approximations for a
A simple model based on rapid‐equilibrium assumptions is derived which relates the steady‐state activity of the Calvin cycle for photosynthetic carbohydrate formation in C3 plants to the kinetic properties of a single cycle enzyme (fructose bisphosphatase) and of the phosphate translocator which accounts for the export of photosynthate from the chloroplast. Depending on the kinetic interplay of th
The catalytic interaction of glyceraldehyde‐3‐phosphate dehydrogenase with glyceraldehydes‐3‐phosphate has been examined by transient‐state kinetic methods. The results confirm previous reports that the apparent Km for oxidative phosphorylation of glyceraldehydes‐3‐phosphate decreases at least 50‐fold when the substrate is generated in a coupled reaction system through the action of aldolase on fr
The coordination chemistry of the zinc ion in the active site of alcohol dehydrogenase has been studied by the ab initio Hartree–Fock method. Geometry optimizations were performed using analytical gradients and basis sets of double‐zeta quality. Correlation effects were included at the MP2 level. The active site was modeled by Zn(HS)2XL(H2O)0–2, where X denotes ammonia or imidazole and L denotes w
A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force‐field reproduces excellently the geometry of quantum chemically op
The geometry of several realistic models of the metal coordination sphere in the blue copper proteins has been optimised using high-level quantum chemical methods. The results show that the optimal vacuum structure of the Cu(II) models is virtually identical to the crystal structure of oxidised blue copper proteins. For the reduced forms, the optimised structure seems to be more tetrahedral than t
Theoretical computations (molecular dynamics and combined quantum chemical and molecular mechanical geometry optimizations) have been performed on horse liver alcohol dehydrogenase. The results provide evidence that Glu‐68, a highly conserved residue located 0.47 nm from the catalytic zinc ion, may intermittently coordinate to the zinc ion. Structures with Glu‐68 coordinated to the zinc ion are al
The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in t
The coordination number of the catalytic zinc ion in alcohol dehydrogenase has been studied by integrated ab initio quantum-chemical and molecular mechanics geometry optimisations involving the whole enzyme. A four-coordinate active-site zinc ion is 100-200 kJ/mol more stable than a five-coordinate one, depending on the ligands. The only stable binding site for a fifth ligand at the zinc ion is op
Calculations of the electric field gradient (EFG) at the cadmium nucleus have been carried out on Cd2+ in the field of two point charges, CdF2, CdCl2, and CdF2Cl2 2- at the RHF, MPn (n = 2, 3, 4), and CCSD(T) levels of theory, in order to evaluate the effects of electron correlation, relativity, and basis set truncation. The EFG has furthermore been calculated in two large molecules (approximately
The electronic spectrum of the blue copper protein plastocyanin has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method). The six lowest electronic transitions have been calculated and assigned with an error of less than 2000 cm-1. The singly occupied orbital in the ground state is Cu 3d-S(Cys) 3pπ antibonding with some N(His) 2pσ character. The brigh
The significance of the so-called trigger reaction in the reaction mechanism of the calicheamicin γI 1 anti-cancer drug has been studied with ab initio quantum chemical methods. The structures of four fragments of calicheamicin γI 1, consisting of either 39 or 41 atoms, have been fully optimized using the Becke-Perdew86 density functional method and the 6-31G* basis sets. The four structures const
The structure of eleven complexes of cadmium-substituted alcohol dehydrogenase with or without coenzyme and with different non-protein cadmium ligands has been estimated by combined quantum chemical and molecular mechanical geometry optimisations. The geometry of the optimised complexes is similar to the crystal structure of cadmium-substituted alcohol dehydrogenase, indicating that the method beh
Four methods for deriving partial atomic charges from the quantum chemical electrostatic potential (CHELP, CHELPG, Merz-Kollman, and RESP) have been compared and critically evaluated. It is shown the charges strongly depend on how and where the potential points are selected. Two alternative methods are suggested to avoid the arbitrariness in the point-selection schemes and van der Waals exclusion
The electronic spectrum of the azurin Met121Gln mutant, a model of the blue copper protein stellacyanin, has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method), including the effect of the protein and solvent by point charges. The six lowest electronic transitions have been calculated and assigned with an error of less than 2400 cm-1. The ground-sta
The role of the cysteine thiolate ligand for the unusual copper coordination geometry in the blue copper proteins has been studied by comparing the electronic structure, geometry, and energetics of a number of small Cu(II) complexes. The geometries have been optimised with the density functional B3LYP method, and energies have been calculated by multi- configurational second-order perturbation the
The inner-sphere reorganization energy for several copper complexes related to the active site in blue-copper protein has been calculated with the density functional B3LYP method. The best model of the blue-copper proteins, Cu(Im)2(SCH3)(S(CH'3)2)(0/+), has a self-exchange inner-sphere reorganization energy of 62 kJ/mol, which is at least 120 kJ/mol lower than for Cu(H2O)(+/2+)/4 This lowering of
