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Rational design of biomimetics with QM/MM Car-Parrinello simulations

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Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase

Matteo Dal Peraro, Marco Stenta, Thomas Lemmin, Matteo Thomas Degiacomi, Christophe Bovigny

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-all ...

Amer Chemical Soc2014

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

Ursula Röthlisberger, Pablo Campomanes Ramos

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals a ...

2014

A Mechanochemical Switch to Control Radical Intermediates

Ursula Röthlisberger, Elizabeth Claire Brunk

B-12-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiri ...

2014

Ligand-Controlled Regiodivergent Pathways of Rhodium(III)-Catalyzed Dihydroisoquinolone Synthesis: Experimental and Computational Studies of Different Cyclopentadienyl Ligands

Nicolai Cramer, Matthew Wodrich, Jérôme Florian Gonthier, Baihua Ye

Rh-III-catalyzed directed C-H functionalizations of arylhydroxamates have become a valuable synthetic tool. To date, the regioselectivity of the insertion of the unsaturated acceptor into the common cyclometalated intermediate was dependent solely on intri ...

Wiley-V C H Verlag Gmbh2014

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Recent analysis of a set of reductive dehalogenases revealed that sequence similarity and substrate specificity are not correlated, making functional prediction from sequences difficult (1). To this respect, several enrichment cultures were investigated fo ...

2014

Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis

Ursula Röthlisberger, Andrea Cavalli, Pablo Campomanes Ramos, Giulia Palermo, Marilisa Neri

The serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. T ...

Amer Chemical Soc2013

Geometry as a Catalyst: How Vapor Cavities Nucleate from Defects

Simone Meloni

The onset of cavitation is strongly enhanced by the presence of rough surfaces or impurities in the liquid. Despite decades of research, the way the geometry of these defects promote the nucleation of bubbles and its effect on the kinetics of the process r ...

Amer Chemical Soc2013

delta-Hexachlorocyclohexane (delta-HCH), one of the prevalent isomers of technical HCH, was enantioselectively dehydrochlorinated by the dehydrochlorinases LinA1 and LinA2 from Sphingobium indicum B90A to the very same delta-pentachlorocyclohexene enantiom ...

American Society for Microbiology2013

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Control of the N-glycosylase reaction by the DNA repair enzyme, MutY, entails the organization of solvent molecules. Classical molecular dynamics and QM/MM simulations were used to investigate the solvent and environment effects contributing to catalysis. ...

2012

Metallo-beta-lactamases (M beta Ls) are Zn(II)-based bacterial enzymes that hydrolyze beta-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from point to either two zinc ...

2012