Related papers: Proofreading through spatial gradients
Proofreading/editing in protein synthesis is essential for accurate translation of information from the genetic code. In this article we present a theoretical investigation of efficiency of a kinetic proofreading mechanism that employs…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
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…
Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction is required to improve assembly yield beyond equilibrium limits,…
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a…
In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this…
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…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here we propose that inter-molecular frustration…
In this paper we study the relation between the property of detailed balance and the ability of discriminating between different ligands for a class of stochastic models of kinetic proofreading. We prove the existence of a critical amount…
To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation site allows for proofreading, especially when phosphorylation…
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…
Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding…
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…
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…
Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical…
Environment specific substitution tables have been used effectively for distinguishing structural and functional constraints on proteins and thereby identify their active sites (Chelliah et al. (2004)). This work explores whether a similar…
Position determination in biological systems is often achieved through protein concentration gradients. Measuring the local concentration of such a protein with a spatially-varying distribution allows the measurement of position within the…