Visualitza per autoria "729e867b-61aa-41d8-8449-2910cf17524a"
Ara mostrant els elements 1-16 d 16
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Computational design of biological catalysts
Royal Society of Chemistry (2008)The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze ... -
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, ...
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Diseño computacional de catalizadores biológicos
Real Sociedad Española de Química (2011)Enzymes are a source of inspiration for the design of new and powerful industrial catalysts able to work, in principle, in mild conditions of pressure, temperature and solvents. The Transition State of the reaction is the ...
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Do zwitterionic species exist in the non-enzymatic peptide bond formation?
The Royal Society of Chemistry (2012-09-30)The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different ...
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Mechanism and plasticity of isochorismate pyruvate lyase: a computational study
American Chemical Society (2009)The isochorismate pyruvate lyase (IPL) from Pseudomonas aeruginosa, designated as PchB, catalyzes the transformation of isochorismate into pyruvate and salicylate, but it also catalyzes the rearrangement of chorismate into ... -
Molecular mechanism of chorismate mutase activity of promiscuos MbtI
Springer (2010-06-15)Salicylate synthase from Mycobacterium tuberculosis, MbtI, initiates the biosynthesis of siderophores by converting chorismate to salicylate. Nevertheless, three more distinct activities for wild-type MbtI have been detected ...
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Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
Springer (2017-02)The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution ...
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Predicting an improvement of secondary catalytic activity of promiscuos isochorismate pyruvate pyase by computational design
American Chemical Society (2008)Improvement of the secondary catalytic activity of promiscuous enzymes can be guided by computational protein engineering. This methodology has been applied to isochorismate pyruvate lyase (IPL) that catalyzes isochorismate ...
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Promiscuity in alkaline phosphatase superfamily: unraveling evolution through molecular simulations
American Chemical Society (2011-08)We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents ...
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Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3
Wiley (2017-05)The design of new biocatalysts is a goal in biotechnology to improve the rate, selectivity and environmental impact of industrial chemical processes. In this regard, the use of computational techniques has provided valuable ...
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Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects
American Chemical Society (2013)Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as ...
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Theoretical modeling of the reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase
American Chemical Society (2009)The reaction mechanism of phosphate monoester hydrolysis in alkaline phosphatase is analyzed by means of hybrid QM/MM simulations. A recently developed semiempirical Hamiltonian, AM1/d-PhoT, which takes into account the d ...
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Theoretical QM/MM studies of enzymatic pericyclic reactions
International Association of Scientists in the Interdisciplinary Areas (2010-03)The chorismate to prephenate enzyme catalyzed reaction has been used in this review as the conduit to show different theoretical approaches that have been used over the years in our laboratory to explain its molecular ...
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Theoretical studies of the hydrolysis of antibiotics catalyzed by a metallo-B-lactamase
Elsevier (2015-09-15)In this paper, hybrid QM/MM molecular dynamics (MD) simulations have been performed to explore the mechanisms of hydrolysis of two antibiotics, Imipenen (IMI), an antibiotic belonging to the subgroup of carbapenems, and ...
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Theoretical Study of Phosphodiester Hydrolysis in Nucleotide Pyrophosphatase/Phosphodiesterase. Environmental Effects on the Reaction Mechanism
American Chemical Society (2010)We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP−) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of ...
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Understanding the different activities of highly promiscuous MbtI by computational methods
Royal Society of Chemistry (2012)Salicylate synthase from Mycobacterium tuberculosis, MbtI, is a highly promiscuous Mg2+ dependent enzyme with up to four distinct activities detected in vitro: isochorismate synthase (IS), isochorismate pyruvate lyase ...
