scholarly journals Dependence of enzyme reaction mechanism on protonation state of titratable residues and QM level description: lactate dehydrogenase

2005 ◽  
pp. 5873 ◽  
Author(s):  
Silvia Ferrer ◽  
Estanislao Silla ◽  
Iñaki Tuñón ◽  
Mónica Oliva ◽  
Vicent Moliner ◽  
...  
Keyword(s):  
Reaction Mechanism ◽  
Lactate Dehydrogenase ◽  
Enzyme Reaction ◽  
Protonation State

Kinetics and Reaction Mechanism of the Carbamylphosphate Synthetase of a Multienzyme Aggregate from Yeast

1975 ◽  
Vol 53 (6) ◽  
pp. 721-730 ◽  
Author(s):  
David M. Aitken ◽  
Peter F. Lue ◽  
J. Gordin Kaplan
Keyword(s):  
Reaction Mechanism ◽  
Feedback Inhibition ◽  
Enzyme Reaction ◽  
Competitive Inhibitor ◽  
Potassium Ions ◽  
Ammonium Ions ◽  
Nitrogen Donor ◽  
Sequential Addition ◽  
A Site ◽  
Carbamylphosphate Synthetase

We have studied the kinetics and reaction mechanism of the carbamylphosphate synthetase of an enzyme aggregate functioning in the pyrimidine pathway of yeast. Mg–ATP was found to be one of the substrates of the enzyme reaction which was activated by free Mg2+ and inhibited by free ATP. Feedback inhibition by UTP was non-competitive with respect to both glutamine and bicarbonate. Potassium ions were essential for activity and could not be replaced by sodium. Glutamine could be replaced partially by ammonium ions as nitrogen donor. A bicarbonate-dependent cleavage of ATP was shown to take place in the absence of L-glutamine; L-glutamate was a competitive inhibitor of L-glutamine and the enzyme was shown to synthesize ATP when incubated with ADP and carbamyl phosphate. The reaction mechanism was found to involve sequential addition of the substrates bicarbonate and Mg–ATP and release of ADP, followed by addition of the third substrate glutamine. The purine nucleotide XMP had a pronounced activating effect on the enzyme, acting at a site different from that of UTP. Saturating levels of Mg–ATP eliminated this activation.

scholarly journals Cyclization step of noradrenaline and adrenaline autoxidation: a quantum chemical study

RSC Advances ◽  
2020 ◽  
Vol 10 (28) ◽  
pp. 16650-16658
Author(s):  
Nejc Umek
Keyword(s):  
Reaction Mechanism ◽  
Quantum Chemical ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Protonation State ◽  
Noradrenaline And Adrenaline

The quinone group protonation state determines the reaction mechanism of noradrenaline and adrenaline o-quinone cyclization.

scholarly journals The kinetics of the reversible inhibition of heart lactate dehydrogenase through the formation of the enzyme–oxidized nicotinamide–adenine dinucleotide–pyruvate compound

1968 ◽  
Vol 106 (3) ◽  
pp. 683-687 ◽  
Author(s):  
H. Gutfreund ◽  
R. Cantwell ◽  
C. H. McMurray ◽  
R. S. Criddle ◽  
G. Hathaway
Keyword(s):  
Lactate Dehydrogenase ◽  
Kinetic Analysis ◽  
Nicotinamide Adenine Dinucleotide ◽  
Enzyme Reaction ◽  
Rapid Decrease ◽  
Protein Fluorescence ◽  
Different Temperatures ◽  
Pertinent Information ◽  
Reversible Formation ◽  
Kinetics Of

The inhibition of lactate dehydrogenase at high pyruvate concentration was studied in three ways. First, a rapid decrease in the rate of the enzyme reaction was observed; secondly, the rate of formation of a pyruvate–NAD+ compound was followed by the change in E325; thirdly, the rate of quenching of the protein fluorescence was measured. The data obtained at pH6·0 at different temperatures and ionic strengths as functions of pyruvate, NAD+ and enzyme concentrations show that the extent of inhibition can be correlated with the reversible formation of a compound between pyruvate and enzyme-bound NAD+. It is suggested that the detailed kinetic analysis of the formation of this abortive ternary compound will give pertinent information about properties of the enzyme–NAD+ compound involved in the normal catalytic process.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase

2018 ◽  
Vol 20 (23) ◽  
pp. 15784-15794 ◽  
Author(s):  
Wen-Juan Wang ◽  
Wen-Jie Wei ◽  
Rong-Zhen Liao
Keyword(s):  
Reaction Mechanism ◽  
Protonation State

QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.

scholarly journals With or without light: comparing the reaction mechanism of dark-operative protochlorophyllide oxidoreductase with the energetic requirements of the light-dependent protochlorophyllide oxidoreductase

2014 ◽  
Author(s):  
Pedro J Silva
Keyword(s):  
Reaction Mechanism ◽  
Electron Donor ◽  
Ph Dependence ◽  
Single Point ◽  
Enzyme Reaction ◽  
Single Electron ◽  
Simple Explanation ◽  
Dependent Manner ◽  
Protochlorophyllide Oxidoreductase ◽  
Sequence Of Events

The addition of two electrons and two protons to the C17=C18 bond in protochlorophyllide is catalyzed by a light-dependent enzyme relying on NADPH as electron donor, and by a light-independent enzyme bearing a (Cys)3Asp-ligated [4Fe-4S] cluster which is reduced by cytoplasmic electron donors in an ATP-dependent manner and then functions as electron donor to protochlorophyllide. The precise sequence of events occurring at the C17=C18 bond has not, however, been determined experimentally in the dark-operating enzyme. In this paper, we present the computational investigation of the reaction mechanism of this enzyme at the B3LYP/6-311+G(d,p)// B3LYP/6-31G(d) level of theory. The reaction mechanism begins with single-electron reduction of the substrate by the (Cys)3Asp-ligated [4Fe-4S], yielding a negatively-charged intermediate. Depending on the rate of Fe-S cluster re-reduction, the reaction either proceeds through double protonation of the single-electron-reduced substrate, or by alternating proton/electron transfer. The computed reaction barriers suggest that Fe-S cluster re-reduction should be the rate-limiting stage of the process. Poisson-Boltzmann computations on the full enzyme-substrate complex, followed by Monte Carlo simulations of redox and protonation titrations revealed a hitherto unsuspected pH-dependence of the reaction potential of the Fe-S cluster. Furthermore, the computed distributions of protonation states of the His, Asp and Glu residues were used in conjunction with single-point ONIOM computations to obtain, for the first time, the influence of all protonation states of an enzyme on the reaction it catalyzes. Despite exaggerating the ease of reduction of the substrate, these computations confirmed the broad features of the reaction mechanism obtained with the medium-sized models, and afforded valuable insights on the influence of the titratable amino acids on each reaction step. Additional comparisons of the energetic features of the reaction intermediates with those of common biochemical redox intermediates suggest a surprisingly simple explanation for the mechanistic differences between the dark-catalyzed and light-dependent enzyme reaction mechanisms.

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