ListarUJI: Investigación por tema "QM/MM"
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A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH
Elsevier (2011-11)Serumtransferrin (sTf) transports iron in serum and internalizes in cells via receptor mediated endocytosis. Additionally, sTf has been identified as the predominant aluminum carrier in serum. Some questions remain unclear ... -
Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase
American Chemical Society (2020-09-03)The design of biocatalysts is a goal to improve the rate, selectivity and environmental friendship of chemical processes in biotechnology. In this regard, the use of computational techniques has provided valuable assistance ... -
Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer
American Chemical Society (2017-02)Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these ... -
Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase
Springer Nature (2018-03)In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics ... -
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes
American Chemical Society (2021-07-16)Convergent evolution has resulted in nonhomologous enzymes that contain similar active sites that catalyze the same primary and secondary reactions. Comparing how these enzymes achieve their reaction promiscuity can yield ... -
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformatión for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases
Royal Society of Chemistry (2009)Molecular dynamics simulations have been performed for non-covalent complexes of phenyl b-xylobioside with the retaining endo-b-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. ... -
Computational strategies for the design of new enzymatic functions
Elsevier (2015-09-15)In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels–Alder and Retro-Aldolase, ... -
Computational Studies of Candida Antarctica Lipase B to Test Its Capability as a Starting Point to Redesing New Diels-Alderases
American Chemical Society (2016-03)The design of new biocatalysts is a target that is receiving increasing attention. One of the most popular reactions in this regard is the Diels-Alder cycloaddition due to its applications in organic synthesis and the ... -
Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease
American Chemical Society (2017)Cysteine proteases of the papain family are involved in many diseases, making them attractive targets for developing drugs. In this paper, different catalytic mechanisms of cruzain cysteine protease have been studied on ... -
Convergence of Theory and Experiment on the Role of Preorganization, Quantum Tunneling, and Enzyme Motions into Flavoenzyme-Catalyzed Hydride Transfer
American Chemical Society (2017)Hydride transfer is one of the most common reactions catalyzed by enzymatic systems, and it has become an object of study because of possible significant quantum tunneling effects. In the present work, we provide a combination ... -
Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies
MDPI (2022)20S proteasome is a main player in the protein degradation pathway in the cytosol, thus intervening in multiple pivotal cellular processes. Over the years the proteasome has emerged as a crucial target for the treatment ... -
Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases
Wiley (2021-04-14)A computational study of the two possible inhibition mechanisms of rhodesain cysteine protease by the dipeptidyl enoate Cbz-Phe-Leu-CH=CH−CO2C2H5 has been carried out by means of molecular dynamics simulations with hybrid ... -
Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism
American Chemical Society (2021-07-02)Δ1-Dehydrogenation of 3-ketosteroids catalyzed by flavin adenine dinucleotide (FAD)-dependent 3-ketosteroid dehydrogenases (Δ1-KSTD) is a crucial step in steroid degradation and synthesis of several steroid drugs. The ... -
Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′
Springer Berlin Heidelberg (2019)Quantum mechanical (QM) semiempirical methods (SMs), combined with molecular mechanics (MM) force fields, are extensively used in theoretical studies of enzymatic reactions. Despite being several orders of magnitude faster ... -
Exploring the Catalytic Mechanism of the RNA Cap Modification by nsp16-nsp10 Complex of SARS-CoV-2 through a QM/MM Approach
MDPI (2021-12-28)The inhibition of key enzymes that may contain the viral replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have assumed central importance in drug discovery projects. Nonstructural proteins (nsps) ... -
Exploring the Origin of Amidase Substrate Promiscuity in CALB by a Computational Approach
American Chemical Society (2020)Enzyme promiscuity attracts the interest of the industrial and academic sectors because of its application in the design of biocatalysts. The amidase activity of Candida antarctica lipase B (CALB) on two different substrates ... -
First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones
ACS Publications (2015-05-12)Cruzain is a primary cysteine protease expressed by the protozoan parasite Trypanosoma cruzi during Chagas disease infection, and thus, the development of inhibitors of this protein is a promising target for designing ... -
Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L
American Chemical Society (2023-05-05)Cysteine proteases (CPs) are an important class of enzymes, many of which are responsible for several human diseases. For instance, cruzain of protozoan parasite Trypanosoma cruzi is responsible for the Chagas disease, ... -
Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L
American Chemical Society (2023-10-03)Cathepsin L (CatL) is a lysosomal cysteine protease whose activity has been related to several human pathologies. However, although preclinical trials using CatL inhibitors were promising, clinical trials have been ... -
Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV2 Mpro Explored by QM\/MM Simulations
American Chemical Society (2021-12-26)The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 ...