Related papers: How flexibility can enhance catalysis
We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies…
We have a general knowledge of the principles by which catalysts accelerate the rate of chemical reactions but no precise understanding of the geometrical and physical constraints to which their design is subject. To analyze these…
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor…
Understanding the fundamental limits of state convertibility is crucial for establishing the boundaries of quantum information processing and thermodynamic efficiency. While auxiliary systems, catalysts, can facilitate otherwise impossible…
Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
Catalysis, the acceleration of chemical reactions by molecules that are not consumed in the process, is essential to living organisms but currently absent in physical systems that aspire to emulate biological functionalities with artificial…
Catalysts speed up chemical reactions with no energy input and without being transformed in the process, therefore leaving equilibrium constants unchanged. Some catalysts, however, are much more efficient at accelerating one direction of a…
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the other removing a…
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the…
Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…
We explore how inherent flexibility of a protein molecule influences the mechanism controlling the kinetics of allosteric transitions using a variational model inspired from work in protein folding. The striking differences in the predicted…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
The use of ancillary quantum systems known as catalysts is known to be able to enhance the capabilities of entanglement transformations under local operations and classical communication. However, the limits of these advantages have not…
Recent experiments have revealed that the diffusivity of exothermic and fast enzymes is enhanced when they are catalytically active, and different physical mechanisms have been explored and quantified to account for this observation. We…
We analyze the standard model of enzyme-catalyzed reactions at various substrate-enzyme ratios to identify the regions of validity of the quasi-steady-state approximation. Certain prevalent conditions are checked and compared against the…