Search results for "Active site"

Comparative computational analysis of different active site conformations and substrates in a chalcone isomerase catalyzed reaction.

2006

Chalcone isomerase catalyzes the transformation of chalcones to flavanones. We present a computational study of the rate-limiting chemical step, an intramolecular Michael addition of a 2'-oxyanion to the alpha,beta-double bound. By using quantum mechanical/molecular mechanical hybrid methods we traced the free-energy profiles associated with the reaction of two different substrates (chalcone and 6'-deoxychalcone) in two different conformations of the active site that are described in the different crystallographic structures available. We have obtained significant differences (about 4 kcal/mol) in the free-energy barriers calculated for the two active sites. According to our results, the ac…

Enzymatic effects on reactant and transition states. The case of chalcone isomerase.

2007

Chalcone isomerase catalyzes the transformation of chalcone to naringerin as a part of flavonoid biosynthetic pathways. The global reaction takes place through a conformational change of the substrate followed by chemical reaction, being thus an excellent example to analyze current theories about enzyme catalysis. We here present a detailed theoretical study of the enzymatic action on the conformational pre-equilibria and on the chemical steps for two different substrates of this enzyme. Free-energy profiles are obtained in terms of potentials of mean force using hybrid quantum mechanics/molecular mechanics potentials. The role of the enzyme becomes clear when compared to the counterpart eq…

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomer…

2015

The electrostatic behavior of active site residues in enzyme catalysis is quite different from that of water molecules in solution. To highlight the electrostatic differences between both environments, we propose a QM/MM strategy to study the role of the environment in chemical reactions. The novelty of the present communication is that free energy surfaces are generated by means of two distinguished reaction coordinates: a solute coordinate and the electrostatic potential created by the environment. This is applied to analyze the origin of catalysis in the transformation of a chalcone into a flavanone, a Michael addition that requires the desolvation of the nucleophile.

Insights on the origin of catalysis on glycine N-methyltransferase from computational modeling.

2018

The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three mutants to test whether recent experimental observations of rate-constant reductions and variations in inverse secondary α-3H kinetic isotope effects (KIEs) should be attributed to changes in the methyl donor−acceptor distance (DAD): is catalysis due to a compression effect? Semiempirical (AM1) and DFT (M06-2X) methods were used to describe the QM subset of atoms, while OPLS-AA and TIP3P classical force fields were used for the protein and water molecules, respectively. The …

ZrO2 Acting as a Redox Catalyst

2016

Surface defects are discussed and reviewed with regards to the use of ZrO2 in applications involving interactions with CO, H2, CH4, CO2, water and hydrocarbons. Studies of catalytic partial oxidation of methane reveal that part of the surface lattice oxygen in terraces can be removed by methane at high temperatures (e.g. 900 °C). The reaction proceeds via a surface confined redox mechanism. The studies presented here also highlight that defects play a decisive role in the water–gas-shift reaction, since the reaction is likely carried out via OH groups present at defect sites, which are regenerated by dissociating water. Hydroxyl chemistry on ZrO2 is briefly reviewed related to the studies p…

Multidentate Tetrahydrofurfuryloxide Ligand in a Ziegler−Natta Catalyst Studied by Molecular Modeling

2008

The transition from a generation III Ziegler-Natta catalyst with a monodentate Lewis base to a more modem generation 1V/V system, containing a tetrahydrofuran derivative, the tetrahydrofurturyloxide C 4 H 7 O-CH 2 O - bidentate ligand (THFFO), was studied by means of molecular modeling and DFT calculations. This particular ligand was carefully chosen so that it remained in the titanium coordination sphere in the model active site. With such a constraint, the dual role of tetrahydrofurfuryloxide was identified: it was demonstrated how the presence of this ligand limits the number of isomeric active sites as well as enhances the selectivity of the species that can still exist. The results ind…

Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism

2021

AbstractRibozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, apparently, they existed in cells of primitive biological systems. Unveiling the details of these “fossils” enzymes can contribute not only to the understanding of the origins of life but also to the development of new simplified artificial enzymes. A computational study of the reactivity of the pistol ribozyme carried out by means of classical MD simulations and QM/MM hybrid calculations is herein presented to clarify its catalytic mechanism. Analysis of the geometries…

ChemInform Abstract: Analysis of Active Site Distribution in ZSM-5 Crystals by IR Microscopy.

2010

Engineering of a bacterial tyrosinase for improved catalytic efficiency towards D-tyrosine using random and site directed mutagenesis approaches

2013

The tyrosinase gene from Ralstonia solanacearum (GenBank NP518458) was subjected to random mutagenesis resulting in tyrosinase variants (RVC10 and RV145) with up to 3.2-fold improvement in kcat, 5.2-fold lower Km and 16-fold improvement in catalytic efficiency for D-tyrosine. Based on RVC10 and RV145 mutated sequences, single mutation variants were generated with all variants showing increased kcat for D-tyrosine compared to the wild type (WT). All single mutation variants based on RV145 had a higher kcat and Km value compared to the RV145 and thus the combination of four mutations in RV145 was antagonistic for turnover, but synergistic for affinity of the enzyme for D-tyrosine. Single muta…

Crystal structure of human gamma-butyrobetaine hydroxylase.

2010

Gamma-butyrobetaine hydroxylase (GBBH) is a 2-ketoglutarate-dependent dioxygenase that catalyzes the biosynthesis of l-carnitine by hydroxylation of gamma-butyrobetaine (GBB). l-carnitine is required for the transport of long-chain fatty acids into mitochondria for generating metabolic energy. The only known synthetic inhibitor of GBBH is mildronate (3-(2,2,2-trimethylhydrazinium) propionate dihydrate), which is a non-hydroxylatable analog of GBB. To aid in the discovery of novel GBBH inhibitors by rational drug design, we have solved the three-dimensional structure of recombinant human GBBH at 2.0A resolution. The GBBH monomer consists of a catalytic double-stranded beta-helix (DBSH) domai…