scholarly journals Bioengineering of Cytochrome P450 OleTJE: How Does Substrate Positioning Affect the Product Distributions?

Molecules ◽  
2020 ◽  
Vol 25 (11) ◽  
pp. 2675 ◽  
Author(s):  
Fabián G. Cantú Reinhard ◽  
Yen-Ting Lin ◽  
Agnieszka Stańczak ◽  
Sam P. de Visser
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Active Site ◽  
Density Functional ◽  
Computational Study ◽  
Cation Radical ◽  
Wild Type ◽  
Compound I ◽  
Substrate Activation ◽  
Product Distributions

The cytochromes P450 are versatile enzymes found in all forms of life. Most P450s use dioxygen on a heme center to activate substrates, but one class of P450s utilizes hydrogen peroxide instead. Within the class of P450 peroxygenases, the P450 OleTJE isozyme binds fatty acid substrates and converts them into a range of products through the α-hydroxylation, β-hydroxylation and decarboxylation of the substrate. The latter produces hydrocarbon products and hence can be used as biofuels. The origin of these product distributions is unclear, and, as such, we decided to investigate substrate positioning in the active site and find out what the effect is on the chemoselectivity of the reaction. In this work we present a detailed computational study on the wild-type and engineered structures of P450 OleTJE using a combination of density functional theory and quantum mechanics/molecular mechanics methods. We initially explore the wild-type structure with a variety of methods and models and show that various substrate activation transition states are close in energy and hence small perturbations as through the protein may affect product distributions. We then engineered the protein by generating an in silico model of the double mutant Asn242Arg/Arg245Asn that moves the position of an active site Arg residue in the substrate-binding pocket that is known to form a salt-bridge with the substrate. The substrate activation by the iron(IV)-oxo heme cation radical species (Compound I) was again studied using quantum mechanics/molecular mechanics (QM/MM) methods. Dramatic differences in reactivity patterns, barrier heights and structure are seen, which shows the importance of correct substrate positioning in the protein and the effect of the second-coordination sphere on the selectivity and activity of enzymes.

scholarly journals On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study

2020 ◽  
Vol 21 (12) ◽  
pp. 4551
Author(s):  
Mario Prejanò ◽  
Isabella Romeo ◽  
Nino Russo ◽  
Tiziana Marino
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Catalytic Activity ◽  
Molecular Mechanics ◽  
Active Site ◽  
Esterase Activity ◽  
De Novo ◽  
Computational Study ◽  
Catalytic Triad ◽  
Molecular Mechanics Calculations

Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme–substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.

scholarly journals High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement withPHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure

2018 ◽  
Vol 74 (11) ◽  
pp. 1063-1077 ◽  
Author(s):  
Oleg Borbulevych ◽  
Roger I. Martin ◽  
Lance M. Westerhoff
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
High Throughput ◽  
Active Site ◽  
Binding Modes ◽  
Acta Cryst ◽  
Structure Based Drug Design ◽  
Energy Functionals ◽  
Conventional Methods ◽  
The Impact

Conventional macromolecular crystallographic refinement relies on often dubious stereochemical restraints, the preparation of which often requires human validation for unusual species, and on rudimentary energy functionals that are devoid of nonbonding effects owing to electrostatics, polarization, charge transfer or even hydrogen bonding. While this approach has served the crystallographic community for decades, as structure-based drug design/discovery (SBDD) has grown in prominence it has become clear that these conventional methods are less rigorous than they need to be in order to produce properly predictive protein–ligand models, and that the human intervention that is required to successfully treat ligands and other unusual chemistries found in SBDD often precludes high-throughput, automated refinement. Recently, plugins to thePython-based Hierarchical ENvironment for Integrated Xtallography(PHENIX) crystallographic platform have been developed to augment conventional methods with thein situuse of quantum mechanics (QM) applied to ligand(s) along with the surrounding active site(s) at each step of refinement [Borbulevychet al.(2014),Acta CrystD70, 1233–1247]. This method (Region-QM) significantly increases the accuracy of the X-ray refinement process, and this approach is now used, coupled with experimental density, to accurately determine protonation states, binding modes, ring-flip states, water positions and so on. In the present work, this approach is expanded to include a more rigorous treatment of the entire structure, including the ligand(s), the associated active site(s) and the entire protein, using a fully automated, mixed quantum-mechanics/molecular-mechanics (QM/MM) Hamiltonian recently implemented in theDivConpackage. This approach was validated through the automatic treatment of a population of 80 protein–ligand structures chosen from the Astex Diverse Set. Across the entire population, this method results in an average 3.5-fold reduction in ligand strain and a 4.5-fold improvement inMolProbityclashscore, as well as improvements in Ramachandran and rotamer outlier analyses. Overall, these results demonstrate that the use of a structure-wide QM/MM Hamiltonian exhibits improvements in the local structural chemistry of the ligand similar to Region-QM refinement but with significant improvements in the overall structure beyond the active site.

scholarly journals Computational Study of Methane C–H Activation by Main Group and Mixed Main Group–Transition Metal Complexes

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2794
Author(s):  
Carly C. Carter ◽  
Thomas R. Cundari
Keyword(s):  
Transition Metal Complexes ◽  
Active Site ◽  
Density Functional ◽  
Computational Study ◽  
Divalent Metal ◽  
Main Group ◽  
Free Energies ◽  
Functional Theory ◽  
Activation Barriers ◽  
Experimental Values

In the present density functional theory (DFT) research, nine different molecules, each with different combinations of A (triel) and E (divalent metal) elements, were reacted to effect methane C–H activation. The compounds modeled herein incorporated the triels A = B, Al, or Ga and the divalent metals E = Be, Mg, or Zn. The results show that changes in the divalent metal have a much bigger impact on the thermodynamics and methane activation barriers than changes in the triels. The activating molecules that contained beryllium were most likely to have the potential for activating methane, as their free energies of reaction and free energy barriers were close to reasonable experimental values (i.e., ΔG close to thermoneutral, ΔG‡ ~30 kcal/mol). In contrast, the molecules that contained larger elements such as Zn and Ga had much higher ΔG‡. The addition of various substituents to the A–E complexes did not seem to affect thermodynamics but had some effect on the kinetics when substituted closer to the active site.

The reaction mechanism of retaining glycosyltransferases

2016 ◽  
Vol 44 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Albert Ardèvol ◽  
Javier Iglesias-Fernández ◽  
Víctor Rojas-Cervellera ◽  
Carme Rovira
Keyword(s):  
Quantum Mechanics ◽  
Reaction Mechanism ◽  
Molecular Mechanics ◽  
Active Site ◽  
Molecular Mechanisms ◽  
Catalytic Mechanism ◽  
Strong Support ◽  
Front Face ◽  
Displacement Reaction ◽  
Displacement Mechanism

The catalytic mechanism of retaining glycosyltransferases (ret-GTs) remains a controversial issue in glycobiology. By analogy to the well-established mechanism of retaining glycosidases, it was first suggested that ret-GTs follow a double-displacement mechanism. However, only family 6 GTs exhibit a putative nucleophile protein residue properly located in the active site to participate in catalysis, prompting some authors to suggest an unusual single-displacement mechanism [named as front-face or SNi (substitution nucleophilic internal)-like]. This mechanism has now received strong support, from both experiment and theory, for several GT families except family 6, for which a double-displacement reaction is predicted. In the last few years, we have uncovered the molecular mechanisms of several retaining GTs by means of quantum mechanics/molecular mechanics (QM/MM) metadynamics simulations, which we overview in the present work.

scholarly journals Molecular mechanism of lytic polysaccharide monooxygenases

2018 ◽  
Vol 9 (15) ◽  
pp. 3866-3880 ◽  
Author(s):  
Erik Donovan Hedegård ◽  
Ulf Ryde
Keyword(s):  
Density Functional Theory ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Molecular Mechanism ◽  
Density Functional ◽  
Functional Theory ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

The lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism and hence boost generation of biofuel from e.g. cellulose. By employing density functional theory in a combination of quantum mechanics and molecular mechanics (QM/MM), we report a complete description of the molecular mechanism of LPMOs.

New Chalcone Derivative: Synthesis, Characterization, Computational Studies and Antioxidant Activity

2019 ◽  
Vol 17 (1) ◽  
pp. 46-53
Author(s):  
Reşat Ustabaş ◽  
Nevin Süleymanoğlu ◽  
Namık Özdemir ◽  
Nuran Kahriman ◽  
Ersan Bektaş ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Density Functional ◽  
Computational Study ◽  
Dft Method ◽  
Basis Set ◽  
Basis Sets ◽  
Isomeric Form ◽  
Compound I ◽  
Chalcone Derivative ◽  
Reducing Ability

A new chalcone derivative, called as 1-(4-(benzylideneamino)phenyl)-3-(furan-2-yl)prop-2- en-1-one (I), was synthezised and characterized by spectral methods (infrared (IR) and proton and carbon- 13 nuclear magnetic resonance (1H- and 13C-NMR) spectroscopy). A computational study was performed by the density functional theory (DFT) method. Spectral data of compound I optimized by using 6-311G(d,p) and 6-311++G(d,p) basis sets were obtained by 6-311++G(d,p) basis set. The E-Z isomerism for newly synthesized chalcone derivative was investigated by considering four isomeric form, E/E, E/Z, Z/E and Z/Z. The results show that, as assumed and thus named, the chalcone derivative is in the E/E form. In addition, quantum chemical parameters were calculated by using DFT method with 6-311++G(d,p) basis set. Antioxidant activity of compound I was determined by the ferric reducing ability of plasma (FRAP) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay methods. Compound I has low antioxidant activity.

Sign in / Sign up

Export Citation Format

Share Document