A rapid‐kinetic study of the class C β‐lactamase of <i>Enterobacter cloacae</i> 908R

Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Because of the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM)-based MD simulations, especially together with density functional theory, predictions of reaction mechanism, and estimation of free-energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed temperature-accelerated sliced sampling method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free-energy estimates in QM/MM MD simulation of enzymatic reactions. Moreover, the method is shown to be efficient in exploring flat and broad free-energy basins that commonly occur in enzymatic reactions. We demonstrate this by studying deacylation and reverse acylation reactions of aztreonam drug catalyzed by a class-C β lactamase (CBL) bacterial enzyme. Mechanistic details and nature of kinetics of aztreonam hydrolysis by CBL are elaborated here. The results of this study point to characteristics of the aztreonam drug that are responsible for its slow hydrolysis.

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“…This is also in agreement with the experimental kinetics results. 50,58 The free energy profile in Fig. 8…”

Section: Conclusion and Discussionmentioning

confidence: 99%

Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study

et al. 2018

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“…The hydrogen bonding interactions between the two residues were maintained throughout the reac- 53 it is known that aztreonam is a slowly hydrolyzing drug and from the measured rate constants for deacylation, we estimate the corresponding free energy barrier as 23 kcal mol −1 (using the transition state theory). This agrees well with our computed free energy barrier of 24.5 kcal mol −1 .…”

Section: Ws-mtdmentioning

confidence: 99%

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

Awasthi

Nair

2017

The Journal of Chemical Physics

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Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

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“…La actividad catalítica y la determinación de los parámetros cinéticos (K M y V max ) de la enzima betalactamasa obtenida en el laboratorio mediante cromatografía de afinidad se determinaron mediante ensayos espectrofotométricos utilizando ampicilina como sustrato en el rango de concentraciones entre 5,5-5.600 μM a una longitud de onda de 235 nm (49,50). Los ensayos se llevaron a cabo en medio de tampón de fosfato de 0,1 M (pH 7,3) a 37 °C y los cambios en la absorbancia se monitorizaron en un tiempo de reacción de cuatro horas con lecturas cada 10 minutos en un espectrofotómetro con lector de platos de 96 pozos (Biotek Powerwave X2 ™ ) y termostato equipado con control de temperatura.…”

Section: Evaluación De La Actividad Inhibitoria Del Compuestounclassified

Actividad inhibitoria de dihidroxifenilpropenona sobre β-lactamasa de Enterobacter cloacae: estudio preliminar en el desarrollo de fármacos para enfrentar la resistencia bacteriana

2013

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A rapid‐kinetic study of the class C β‐lactamase of Enterobacter cloacae 908R

Cited by 21 publications

References 12 publications

Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study

Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

Actividad inhibitoria de dihidroxifenilpropenona sobre β-lactamasa de Enterobacter cloacae: estudio preliminar en el desarrollo de fármacos para enfrentar la resistencia bacteriana

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