Related papers: Proofreading through spatial gradients
Electron cryomicroscopy (cryo-EM) is an imaging technique widely used in structural biology to determine the three-dimensional structure of biological molecules from noisy two-dimensional projections with unknown orientations. As the…
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,…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here, we study a general model…
One of the causes of high fidelity of copying in biological systems is kinetic discrimination. In this mechanism larger dissipation and copying velocity result in improved copying accuracy. We consider a model of a polymerase which…
We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…
An important issue for the origins of life is ensuring the accurate maintenance of information in replicating polymers in the face of inevitable errors. Here, we investigated how this maintenance depends on reaction kinetics by…
Self-assembly processes in biological and synthetic biomolecular systems are often governed by the spatial separation of biochemical processes. While previous work has focused on optimizing self-assembly through fine-tuned reaction…
Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…
Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. Performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal…
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…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
We study the impact of different discretization choices on the accuracy of SPH and we explore them in a large number of Newtonian and special-relativistic benchmark tests. As a first improvement, we explore a gradient prescription that…
Recent observations of the growth of protein crystals have identified two different growth regimes. At low supersaturation, the surface of the crystal is smooth and increasing in size due to the nucleation of steps at defects and the…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Chemotaxis of enzymes in response to gradients in the concentration of their substrate has been widely reported in recent experiments, but a basic understanding of the process is still lacking. Here, we develop a microscopic theory for…
This paper proposes a sign gradient descent (SGD) algorithm for predicting the three-dimensional folded protein molecule structures under the kinetostatic compliance method (KCM). In the KCM framework, which can be used to simulate the…