ListarQFA_Articles por tema "molecular dynamics"
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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 ... -
Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease
American Chemical Society (2018)Cruzain, a cysteine protease of the papain family, is essential in the development of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas disease, making it an attractive target for developing new drugs. The ... -
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 ... -
Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase
Wiley-VCH (2010)A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD+), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The ... -
Evidence for the formation of metallic In after laser irradiation of InP
AIP Publishing (2019-07-12)Structural and electronic changes induced by laser irradiation are currently of interest owing to the possibility to tune the mechanical, optical, and transport properties of the irradiated materials. In this work, we ... -
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 ... -
Heavy Enzymes and the Rational Redesign of Protein Catalysts
Wiley (2019-11-18)An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled “heavy” dihydrofolate reductases and their natural‐abundance counterparts has suggested ... -
Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations
Wiley (2013-11-20)In Nature, the family of copper monooxygenases comprised of peptidylglycine α-hydroxylating monooxygenase (PHM), dopamine β-monooxygenase (DβM), and tyramine β-monooxygenase (TβM) is known to perform dioxygen-dependent ... -
Molecular Insights into the Substrate-Assisted Mechanism of Viral DNA 3′-End Processing in Intasome of Prototype Foamy Virus Integrase from Molecular Dynamic and QM/MM Studies
American Chemical Society (2019-05)Integrases participate in two important steps for virus replication such as 3′-end processing of viral DNA (vDNA) and nuclear entry of host DNA (hDNA). In this work, insight into the structural changes in intasome of ... -
QM/MM Theoretical Studies of a de Novo Retro-Aldolase Design
American Chemical Society (2019)The design of innovative enzymes is a standing goal to obtain original specific catalysts to work under mild conditions of temperature and pressure. Attempts to get artificial enzymes become particularly difficult when the ... -
Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host
Wiley (2018-09-17)There has been growing interest in performing organocatalysis within a supramolecular system as a means of controlling reaction reactivity and stereoselectivity. Here, a protein is used as a host for iminium catalysis. A ... -
Special issue in computational modeling on biological systems
Elsevier (2015-09-15) -
The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach
Royal Society of Chemistry (2013)Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation ... -
Theoretical Estimation of Redox Potential of Biological Quinone Cofactors
Wiley (2017-05)Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to ...