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1.
Tatiana Vasilevskaya Maria G. Khrenova Alexander V. Nemukhin Walter Thiel 《Journal of computational chemistry》2015,36(21):1621-1630
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. 相似文献
2.
A. V. Nemukhin A. M. Kulakova S. V. Lushchekina A. Yu. Ermilov S. D. Varfolomeev 《Moscow University Chemistry Bulletin》2015,70(6):274-277
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. 相似文献
3.
4.
B. L. Grigorenko A. V. Nemukhin M. G. Khrenova D. A. Novichkova 《Moscow University Chemistry Bulletin》2014,69(1):1-4
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. 相似文献
5.
B. L. Grigorenko A. V. Nemukhin J. P. Zhang P. Wang 《Moscow University Chemistry Bulletin》2011,66(2):80-82
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. 相似文献
6.
I. V. Polyakov A. A. Moskovskii M. G. Khrenova A. V. Nemukhin 《Moscow University Chemistry Bulletin》2013,68(2):77-79
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. 相似文献
7.
S. D. Varfolomeev E. D. Kots M. G. Khrenova S. V. Lushchekina A. V. Nemukhin 《Doklady Physical Chemistry》2017,474(2):89-92
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. 相似文献
8.
A. V.?Nemukhin B. L.?Grigorenko A. V.?Rogov I. A.?TopolEmail author S. K.?Burt 《Theoretical chemistry accounts》2004,111(1):36-48
A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH3(NHCO-CH2)2 – HN–CO–(CH2–NHCO)CH3 the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor. 相似文献
9.
The structures, spectra, and electron density distributions of the alumophenylsiloxane (APS) complex and its fragments have
been calculated using semiempirical (AM1) and ab initio (SCF/3-21G and SCF/6-31G*) quantum chemical approximations. It has been shown that the local properties of the central fragment of alumophenylsiloxane,
which is a slightly distorted tetrahedron AlO4, are described with the (LiO)2AlOBe(OH) cluster.
M. V. Lomonosov Moscow State University. I. M. Gubkin State Academy of Oil and Gas. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 3, pp. 410–417, May–June, 1995.
Translated by I. Izvekova 相似文献
10.
IR spectra of 24 structural isomers of (HF)
n
(n=4–8) clusters were calculated in the framework of semiempirical theory of polyatomic molecule vibrations. Based on the results
obtained and available experimental data it is proposed that (HF)
n
associates comprising 3–5-membered cycles with attached monomeric HF units are present in molecular beams and gas phase.Ab initio calculations performed by the SCF method show the existence of local minima corresponding to such structures on the potential
energy surface of (HF)
n
clusters (n=4–6).
Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 435–443, March, 1997. 相似文献