Influence of surface diffusion on catalytic reactivity of spatially inhomogeneous surfaces mean field modeling

Kinetics of model catalytic processes proceeding on inhomogeneous surfaces is studied. We employ an extended mean-field model that takes into account surface inhomogeneities. The influence of surface diffusion of adsorbent on the kinetics of the catalytic process is investigated. It is shown that diffusion is responsible for differences in the reaction rate of systems with different arrangements of active sites. The presence of cooperative effects between inactive and active sites is demonstrated and the conditions when these effects are important are discussed. We show that basic catalytic phenomena on nonuniform surfaces can be studied with mean-field modeling methods.Comment: Submitted to Chemical Physics Letters. Includes supporting material in Appendice

Thermodynamics and kinetics of heterogeneous reactions

Thermodynamics and kinetics of sublimation, catalytic, and oxidation reaction

Exact Results for Kinetics of Catalytic Reactions

The kinetics of an irreversible catalytic reaction on substrate of arbitrary dimension is examined. In the limit of infinitesimal reaction rate (reaction-controlled limit), we solve the dimer-dimer surface reaction model (or voter model) exactly in arbitrary dimension $D$. The density of reactive interfaces is found to exhibit a power law decay for $D<2$ and a slow logarithmic decay in two dimensions. We discuss the relevance of these results for the monomer-monomer surface reaction model.Comment: 4 pages, RevTeX, no figure

Mesoscopic Model for Diffusion-Influenced Reaction Dynamics

A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account. Reactive and non-reactive interactions with catalytic solute particles are described by full molecular dynamics. Results are presented for large-scale, three-dimensional simulations to study the influence of diffusion on the rate constants of the A+CB+C reaction. In the limit of a dilute solution of catalytic C particles, the simulation results are compared with diffusion equation approaches for both the irreversible and reversible reaction cases. Simulation results for systems where the volume fraction of catalytic spheres is high are also presented, and collective interactions among reactions on catalytic spheres that introduce volume fraction dependence in the rate constants are studied.Comment: 9 pages, 5 figure

Kinetics and Inhibition Studies of the L205R Mutant of cAMP-Dependent Protein Kinase Involved in Cushing’s Syndrome

Overproduction of cortisol by the hypothalamus–pituitary–adrenal hormone system results in the clinical disorder known as Cushing\u27s syndrome. Genomics studies have identified a key mutation (L205R) in the α‐isoform of the catalytic subunit of cAMP‐dependent protein kinase (PKACα) in adrenal adenomas of patients with adrenocorticotropic hormone‐independent Cushing\u27s syndrome. Here, we conducted kinetics and inhibition studies on the L205R‐PKACα mutant. We have found that the L205R mutation affects the kinetics of both Kemptide and ATP as substrates, decreasing the catalytic efficiency (kcat/KM) for each substrate by 12‐fold and 4.5‐fold, respectively. We have also determined the IC50 and Ki for the peptide substrate‐competitive inhibitor PKI(5–24) and the ATP‐competitive inhibitor H89. The L205R mutation had no effect on the potency of H89, but causes a \u3e 250‐fold loss in potency for PKI(5–24). Collectively, these data provide insights for the development of L205R‐PKACα inhibitors as potential therapeutics

Robustness and modularity properties of a non-covalent DNA catalytic reaction

The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices

Parallel versus off-pathway Michaelis-Menten mechanism for single-enzyme kinetics of a fluctuating enzyme

Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high substrate concentrations, the dimensionless variance of the turnover time distribution shows systematic deviations from the Michaelis-Menten prediction. This difference is attributed to conformational fluctuations in both the enzyme and the enzyme-substrate complex and to the possibility of both parallel and off-pathway kinetics. Here, we use the chemical master equation to model the kinetics of a single fluctuating enzyme that can yield a product through either parallel or off-pathway mechanisms. An exact expression is obtained for the turnover time distribution from which the mean turnover time and randomness parameters are calculated. The parallel and off-pathway mechanisms yield strikingly different dependences of the mean turnover time and the randomness parameter on the substrate concentration. In the parallel mechanism, the distinct contributions of enzyme and enzyme-substrate fluctuations are clearly discerned from the variation of the randomness parameter with substrate concentration. From these general results we conclude that an off-pathway mechanism, with substantial enzyme-substrate fluctuations, is needed to rationalize the experimental findings of single-enzyme turnover kinetics of $\beta$-galactosidase.Comment: 27 pages, 5 figure