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How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study
2020
<div>In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.</div>
Low temperature optical spectroscopy of cobalt-substituted hemocyanin from Carcinus maenas
1993
In this work we report the optical absorption spectra of three cobalt-substituted derivatives of hemocyanin (He) from Carcinus maenas, in the temperature range 300–20 K. The derivatives studied are the mononuclear (Co2+)-He with a single cobalt ion in the “CuA” site, the binuclear (Co2+)2-He and the binuclear mixed metal (Co2+-Cu1+)-He. At low temperature three main bands are clearly resolved; the temperature dependence of their zeroth, first and second moments sheds light on the stereodynamic properties in the surroundings of the chromophore. Within the limits of the reported analysis, in the binuclear derivatives the motions coupled to the chromophore appear to be “essentially harmonic” i…
Selektivit�tsstudien: OH-, NH- und SH-gruppenspezifische Reagentien - ihre Anwendung in der organischen Analytik und als Schutzgruppen in der Synthese
1992
Selectivity: OH-, NH- and SH-Groupspecific Reagents. The Application in Organic Analysis and as Protective Groups Phosphylhalides and -pseudohalides R1R2P(O)X (X = Cl, F, CN, N3, OC6H4NO2(p)) reactdepending on X- with a different selectivity with OHNH- and SH-groups. Vinylsulfones ArSO2CH = CH2 are SH-selective. Silanes R3SiH are OH-selective. By exchange of one ligand bound on P, SO2 or Si by the 5-dimethylamino resp. the 5-methoxynaphthalinogroup reagents are formed, which combine group selectivity with fluorescence. The fluorescence is quenched if a ligand or the leaving group is substituted by a NO2-group. The fluorescence appears again if after the group selective fixation the ligand w…
Theoretical studies of HIV-1 reverse transcriptase inhibition
2012
Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design. We herein present a theoretical study of the binding of five different ligands to one of the proteins responsible for the human immunodeficiency virus type 1 (HIV-1) cycle replication; the HIV-1 reverse transcriptase (RT). Two types of approaches are used based on molecular dynamics (MD) simulations within hybrid QM/MM potentials: the alchemical free energy perturbation method, FEP, and the pathway method, in which the ligand is physically pulled away from the binding site, thus rendering a potential of mean force (PMF) for the binding process. Our com…
Computational Modeling of Biological Systems: The LDH Story
2010
Lactate dehydrogenases, LDH, catalyzed reaction has been used in this chapter as a conductor wire to present the evolution and difficulties on computing methods to model chemical reactions in enzymes, since the early calculations based at semiempirical level carried out in gas phase to the recent sophisticated simulations based on hybrid Quantum Mechanical/Molecular Mechanics Dynamics (QM/MM MD) schemes. LDH catalyzes the reversible transformation of pyruvate into lactate. The chemical step consists in a hydride and a proton transfer from the cofactor (NADH) and a protonated histidine (His195), respectively. This fact has generated a lot of controversy about the timing of both transfers in …
Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study
2015
The elucidation of the catalytic role of LinA dehydrohalogenase in the degradation processes of hexachlorocyclohexane (HCH) isomers is extremely important to further studies on the bioremediation of HCH polluted areas. Herein, QM/MM free energy simulations are employed to provide the details of the dehydrochlorination reaction of two HCH isomers (γ and β). In particular, the role of the protonation state of one of the catalytic residues-His73-is explored. Based on our calculations, two distinct minimum free energy pathways (concerted and stepwise) were found for γ-HCH and β-HCH. The choice of the reaction channel for the dehydrochlorination reactions of γ- and β-HCH was shown to depend on t…
Cu/P(4-PVP) stereochemistry in tetralin liquid-phase oxidation
2007
Abstract Cu/P(4-PVP) catalyst was used as catalyst for oxidation of tetralin in liquid phase. The catalyst was prepared by reaction of a Cu(II) salt with a 4-vinylpyridine-co-divinylbenzene polymer receptor and characterized by solid 1 H and 13 C NMR, XPS, FTIR, ESR spectroscopies, and by chemical reaction with pure tetralin. That information was used to gain insight into the stereochemistry of the active site needed to orient the reaction toward tetralone production. It was found that the Cu coordination with the pyridine was critical in influencing the peroxy-radical catalytic reaction, and that polyvinylpyridine was able to limit the autothermal oxidation. The active center is postulated…
An ab initio conformational study on captopril
2003
Abstract Captopril can interact regio- and stereo-specifically with various functional groups present at the active site of angiotensin converting enzyme (ACE). Since no X-ray structure of ACE is available, Captopril, as an ACE inhibitor may be used as a ‘molecular caliper’, to estimate upper and lower bound values for separation d, where the mercaptidic terminal group of the molecule is linked to the enzyme Zn2+ cofactor, while the carboxylate links via an hydrogen bond to the guanidine moiety of an arginine side chain. As the results of this Ab Initio study, the conformations of the dianionic form of the full captopril molecule are reported here.
Chemoselektive Fluoreszenzstudien am Subtilisin und “Thiosubtilisin”
1985
Chemoselective Fluorescence Studies with Subtilisin and “Thiosubtilisin” The serine hydroxy group in the active site of subtilisin is selectively “phosphylated”3). This is demonstrated using the fluorescent phosphinic fluoride 1. “Thiosubtilisin” does not react with 1 but with the SH-selective and fluorescent vinyl sulfone 2.
Proteolytic cleavage of soybean Bowman-Birk inhibitor monitored by means of high-performance capillary electrophoresis. Implications for the mechanis…
1996
The hydrolysis of the soybean Bowman-Birk inhibitor in the presence of catalytic amounts of bovine trypsin and the formation of the non-covalent enzyme-inhibitor complex with an equimolar amount of enzyme are monitored by means of high-performance capillary electrophoresis (HPCE). The inhibitor is cleaved in the trypsin-reactive and more slowly in the chymotrypsin-reactive subdomain. HPCE proves itself as the only reliable analytical tool to monitor these reactions in clear contrast to classical electrophoretic, chromatographic and enzymatic methods. The most efficient separation of the intact and the two active site cleaved forms of the inhibitor was achieved in borate buffer at pH 10.0. T…