Search results for "enzyme catalysis"
showing 10 items of 60 documents
Theoretical insights in enzyme catalysis
2004
In this tutorial review we show how the methods and techniques of computational chemistry have been applied to the understanding of the physical basis of the rate enhancement of chemical reactions by enzymes. This is to answer the question: Why is the activation free energy in enzyme catalysed reactions smaller than the activation free energy observed in solution? Two important points of view are presented: Transition State (TS) theories and Michaelis Complex (MC) theories. After reviewing some of the most popular computational methods employed, we analyse two particular enzymatic reactions: the conversion of chorismate to prephenate catalysed by Bacillus subtilis chorismate mutase, and a m…
Lipase-catalysed preparation of acyl derivatives of the germacranolide cnicin
2009
Several acyl derivatives of cnicin were obtained through lipase-catalysed acylation and alcoholysis reactions. In most reactions lipases showed a regioselective behaviour affording only one product. Longer chain acyl derivatives were prepared at lower temperature than the used in lipase-catalysed reactions, to preclude side products formation. The enzymatic approach let to prepare a family of novel acetyl and fatty acid derivatives of cnicin which are not obtainable following traditional organic synthetic procedures. Fil: Monsalve, Leandro Nicolas. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad de Microanálisis…
Minimization of dynamic effects in the evolution of dihydrofolate reductase
2015
Protein isotope labeling is a powerful technique to probe functionally important motions in enzyme catalysis and can be applied to investigate the conformational dynamics of proteins.
Elucidating the catalytic reaction mechanism of orotate phosphoribosyltransferase by means of X-ray crystallography and computational simulations
2020
15 p.-8 fig.-2 tab.1 graph. abst.+ 8 fig. supl.-1 tab. supl.
Quantifying the limits of transition state theory in enzymatic catalysis
2017
Significance Transition state theory (TST) is the most popular theory to calculate the rates of enzymatic reactions. However, in some cases TST could fail due to the violation of the nonrecrossing hypothesis at the transition state. In the present work we show that even for one of the most controversial enzymatic reactions—the hydride transfer catalyzed by dihydrofolate reductase—the error associated to TST represents only a minor correction to the reaction rate. Moreover, this error is actually larger for the reaction in solution than in the enzymatic active site. Based on this finding and on previous studies we propose an “enzymatic shielding” hypothesis which encompasses various aspects …
Enzymatically catalyzed synthesis of photocrosslinkable oligophenols
2000
The HRP-catalyzed oligomerization of cinnamoyl-hydroquinone-ester and cinnamoyl-4-hydroxyanilide led to the formation of soluble polyphenols. The oligomers were synthexized in water/1,4-dioxane and in water/acetone mixtures and characterized by NMR, FTIR and SEC. Upon UV treatment of the homogenoes films the polyphenols were crosslinked due to [2+2]-cycloadditions of the cinnamoyl functions.
Lipase-catalysed preparation of acyl derivatives of the germacranolide sesquiterpenoid cnicin
2009
Several acyl derivatives of cnicin were obtained through lipase-catalysed acylation and alcoholysis reactions. In most reactions lipases showed a regioselective behaviour affording only one product. Longer chain acyl derivatives were prepared at lower temperature than the used in lipase-catalysed reactions, to preclude side products formation. The enzymatic approach let to prepare a family of novel acetyl and fatty acid derivatives of cnicin which are not obtainable following traditional organic synthetic procedures.
Preorganization and reorganization as related factors in enzyme catalysis: the chorismate mutase case.
2003
In this paper a deeper insight into the chorismate-to prephenate-rearrangement, catalyzed by Bacillus subtilis chorismate mutase, is provided by means of a combination of statistical quantum mechanics/molecular mechanics simulation methods and hybrid potential energy surface exploration techniques. The main aim of this work is to present an estimation of the preorganization and reorganization terms of the enzyme catalytic rate enhancement. To analyze the first of these, we have studied different conformational equilibria of chorismate in aqueous solution and in the enzyme active site. Our conclusion is that chorismate mutase preferentially binds the reactive conformer of the substrate--that…
1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, through 1,3-Dipolar Cycloadditions
2014
1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…
Do dynamic effects play a significant role in enzymatic catalysis? A theoretical analysis of formate dehydrogenase.
2010
A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD + ), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The analysis of free downhill molecular dynamic trajectories, performed in the enzyme and compared with the reaction in aqueous solution, has allowed the study of the dynamic coupling between the reacting fragments and the protein or the solvent water molecules, as well as an estimation of the dynamic effect contribution to the catalytic effect from calculation of the transmission coefficient in the enzyme and in solution. The obtained transmission coefficients for the enzyme…