Related papers: How flexibility can enhance catalysis
Spatial organization in metabolic pathways can arise from the interplay between enzymatic reaction kinetics and diffusion-driven instabilities. In this work we investigate how reversible enzyme--substrate binding influences pattern…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
A comparison is made between conventional Michaelis-Menten kinetics and two models that take into account the duration of the conformational changes that take place at the molecular level during the catalytic cycle of a monomer. The models…
Chemical reactions are usually studied under the assumption that both substrates and catalysts are well mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
The key to understanding a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility and function of…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
Recent experiments have revealed that cytoplasms become glassy when their metabolism is suppressed, while they maintain fluidity in a living state. The mechanism of this active fluidization is not clear, especially for bacterial cytoplasms,…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis,…
The ability of cells to sense and respond to the mechanical properties of their environments is fundamental to a range of cellular behaviours, with substrate stiffness increasingly being found to be a key signalling factor. Although active…
At stationary environmental conditions, a catalyst's reaction rates may be restricted by thermodynamic laws, and certain performances can never be achieved (e.g., catalysts can not change the free energy difference between reactants and…
This article describes our hypothesis on how transmutations may be induced by solid state effects in a crystalline lattice. We discuss the chemical reaction case, our extension to the nuclear binding case, and a tri-body model of a heavy…
This is a comment on a recently published paper in Langmuir: Mandal, N. S.; Sen, A. Relative Diffusivities of Bound and Unbound Protein Can Control Chemotactic Directionality. Langmuir 2021, PMID: 34647749 [arXiv:2103.13469]. In this study,…
Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity couples to molecular motion…
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
Entangled knots form spontaneously in flexible filaments, yet the influence of the surrounding environment on this process is poorly understood. Here we demonstrate that free-moving particles act as kinetic catalysts for spontaneous…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
Many loads have flexibility in demand that can be used to provide ancillary services to power grids. A large body of literature exists on designing algorithms to coordinate actions of many loads to provide such a service. The topic of…