Related papers: Allostery and Kinetic Proofreading
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Kinesin motors have been studied extensively both experimentally and theoretically. However, the microscopic mechanism of the processive movement of kinesin is still an open question. In this paper, we propose a hand-over-hand model for the…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Conformational changes are observed in many enzymes, but their role in catalysis is highly controversial. Here we present a theoretical model that illustrates how rigid catalysts can be fundamentally limited and how a conformational change…
A new steady-state kinetic model of ammonia decomposition is presented and analyzed regarding the electronic properties of metal catalysts. The model is based on the classical Temkin-Ertl mechanism and modified in accordance with…
Signalling pathways are conserved across different species, therefore making yeast a model organism to study these via disruption of kinase activity. Yeast has 159 genes that encode protein kinases and phosphatases, and 136 of these have…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich…
The pump process of the ratchet model inspired by the $F_o$ rotatory motor of ATP synthase is investigated. In this model there are two kinds of characteristic time. One is dynamical, the relaxation time of the system. Others are chemical,…
Cytoskeletal active nematics exhibit striking non-equilibrium dynamics that are powered by energy-consuming molecular motors. To gain insight into the structure and mechanics of these materials, we design programmable clusters in which…
ATP-driven proton pumps, which are critical to the operation of a cell, maintain cytosolic and organellar pH levels within a narrow functional range. These pumps employ two very different mechanisms: an elaborate rotary mechanism used by…
An active learning (AL) algorithm seeks to construct an effective classifier with a minimal number of labeled examples in a bootstrapping manner. While standard AL heuristics, such as selecting those points for annotation for which a…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…
We introduce a method of exploring potential energy contours in complex dynamical systems based on potentiostatic kinematics wherein the systems are evolved with minimal changes to their potential energy. We construct a simple iterative…
In the presence of ATP, kinesin proceeds along the protofilament of microtubule by alternated binding of two motor domains on the tubulin binding sites. Since the processivity of kinesin is much higher than other motor proteins, it has been…
Path integral Monte Carlo (PIMC) simulations are a cornerstone for studying quantum many-body systems. The analytic continuation (AC) needed to estimate dynamic quantities from these simulations is an inverse Laplace transform, which is…
Kinetic Monte-Carlo simulation is applied to study the partial oxidation of methane over a nickel catalyst. Based on the Langmuir-Hinshelwood mechanism, the kinetic behavior of this reaction is analyzed and the results are compared with…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
We have used numerical simulations to investigate how the properties of motor proteins control the dynamical behavior of a driven flexible filament. The filament is pinned at one end and positioned on top of a patch of anchored motor…
Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…