相关论文: Mechanistic rules for de novo design of enzymes

Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…

A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…

Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…

Under temperature oscillation, cyclic molecular machines such as catalysts and enzymes could harness energy from the oscillatory bath and use it to drive other processes. Using a novel geometrical approach, under fast temperature…

In this paper we present a new method for determining optimal designs for enzyme inhibition kinetic models, which are used to model the influence of the concentration of a substrate and an inhibition on the velocity of a reaction. The…

We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…

In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…

Designing enzymes with substrate-binding pockets is a critical challenge in protein engineering, as catalytic activity depends on the precise interaction between pockets and substrates. Currently, generative models dominate functional…

Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…

The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…

Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…

There are many exotic thermodynamic processes that are hard to study in nature. Here, we synthesize a structured environment to explore the extremes of thermodynamics. We present an engine running at extreme temperatures of above ten…

Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…

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,…

Systems containing active components are intrinsically out of equilibrium, while binary mixtures reach their equilibrium configuration when complete phase separation is achieved. Active particles are found to stabilise non-equilibrium…

Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…

Enzymes are essential to maintain organisms alive. Some of the reactions they catalyze are associated with a change in reagents chirality, hence their activity can be tracked by using optical means. However, illumination affects enzyme…

We present a simple mechanism for intra-molecular refrigeration, where parts of a molecule are actively cooled below the environmental temperature. We discuss the potential role and applications of such a mechanism in biology, in particular…

The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…