Modeling of the glycine tripeptide cyclization in the Ser65Gly/Tyr66Gly mutant of green fluorescent protein

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Modeling chemical transformations at the active sites of cholinesterases by quantum-based simulations

The significance of the quantum-mechanical–molecular-mechanical (QM/MM) method in modeling chemical transformations at the active sites of cholinesterases is discussed. Diverse versions of the QM/MM approach are applied to understand the molecular mechanisms of the reactivation reaction of butyrylcholinesterase phosphorylated by the catalytic serine residue.     

Mechanism of proteolysis in matrix metalloproteinase‐2 revealed by QM/MM modeling

The mechanism of enzymatic peptide hydrolysis in matrix metalloproteinase‐2 (MMP‐2) was studied at atomic resolution through quantum mechanics/molecular mechanics (QM/MM) simulations. An all‐atom three‐dimensional molecular model was constructed on the basis of a crystal structure from the Protein Data Bank (ID: 1QIB), and the oligopeptide Ace‐Gln‐Gly～Ile‐Ala‐Gly‐Nme was considered as the substrate. Two QM/MM software packages and several computational protocols were employed to calculate QM/MM energy profiles for a four‐step mechanism involving an initial nucleophilic attack followed by hydrogen bond rearrangement, proton transfer, and C? N bond cleavage. These QM/MM calculations consistently yield rather low overall barriers for the chemical steps, in the range of 5–10 kcal/mol, for diverse QM treatments (PBE0, B3LYP, and BB1K density functionals as well as local coupled cluster treatments) and two MM force fields (CHARMM and AMBER). It, thus, seems likely that product release is the rate‐limiting step in MMP‐2 catalysis. This is supported by an exploration of various release channels through QM/MM reaction path calculations and steered molecular dynamics simulations. © 2015 Wiley Periodicals, Inc.     

Supercomputer technologies for structural-kinetic study of mechanisms of enzyme catalysis: A quantum-chemical description of aspartoacylase catalysis

The results of modeling of the complete catalytic cycle of aspartoacylase-catalyzed N-acetylaspartate hydrolysis by the combined quantum mechanics/molecular mechanics method and with the use of umbrella sampling replica-exchange molecular dynamics simulations are reported. It has been shown that the decrease in the high-energy barriers of rate-limiting stages is achieved through the preceding equilibrium stages, such as proton transfer and conformational changes. General features of the catalytic behavior of enzymes have been formulated.     

Quantum chemical modeling of components of dye-sensitized solar cells

Ab initio approaches of quantum chemistry, including the fragment molecular orbital (FMO) method, as well as the multiconfigurational quasidegenerate perturbation theory (XMCQDPT2) and time-dependent density functional theory (TD DFT) were applied to compute optical spectra of a polyene dye molecule on the surface of titanium dioxide.     

The structure of the enzyme-substrate complex of the phosphodiesterase catalytic domain with cyclic diguanosine monophosphate

A three-dimensional, all-atom structure of the enzyme-substrate complex of the phosphodiesterase catalytic domain with diguanosine monophosphate was constructed based on the results of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations.     

Modeling of calcium binding in the light-harvesting complex of photosynthetic reaction center of the <Emphasis Type="Italic">Thermochromatium tepidum</Emphasis> bacterium

A three-dimensional model of subunit structure for the LH1 light-harvesting complex of the photosynthetic reaction center of Thermochromatium tepidum bacterium is constructed on the basis of the primary sequence of amino acid residues of the α-and β-polypeptide helixes; the specific binding site of the calcium ion is suggested.     

Structure and dynamics of photoactivatable adenylyl cyclase

Russian Chemical Bulletin - The full-atom 3D model of the dimer of the photoregulated adenylyl cyclase is constructed. It contains a molecule of flavin mononucleotide chromophore in the...     

Effect of solvation water shells on enzyme active sites in zinc-dependent hydrolases

Structural Chemistry - In this work, we focus on some structural aspects of enzyme catalysis by modeling effects of the electrostatic potential created by the solvation water shells on properties...