相关论文: Thresholds, long delays and stability from general…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Post-translational modification (PTM) of proteins plays a key role in signal transduction, and hence significant effort has gone toward understanding how PTM networks process information. This involves, on the theory side, analyzing the…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
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…
Post-translational modifications (PTMs) have vital roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a…
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital…
Allostery is a fundamental mechanism of protein regulation and is commonly interpreted as modulating enzymatic activity or product abundance. Here we show that this view is incomplete. Using a stochastic model of allosteric regulation…
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into intracellular organelles for the regulation of the activity…
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Allostery, the phenomenon by which the perturbation of a molecule at one site alters its behavior at a remote functional site, enables control over biomolecular function. Allosteric modulation is a promising avenue for drug discovery and is…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF…