Related papers: Information Transmission and Processing in G-Prote…
Biological information processing often arises from mesoscopic molecular systems operating far from equilibrium, yet their complexity can make the underlying principles difficult to visualize. In this study, we introduce a macroscopic…
We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…
Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…
G protein-coupled receptors (GPCRs) govern diverse physiological processes and are central to modern pharmacology. Yet discovering GPCR modulators remains challenging because receptor activation often arises from complex allosteric effects…
G-protein coupled receptors (GPCRs), a major gatekeeper of extracellular signals on plasma membrane, are unarguably one of the most important therapeutic targets. Given the recent discoveries of allosteric modulations, an allosteric wiring…
Dynamics and functions of G-protein coupled receptors (GPCRs) are accurately regulated by the type of ligands that bind to the orthosteric or allosteric binding sites. To glean the structural and dynamical origin of ligand-dependent…
GTPases regulate a wide range of cellular processes, such as intracellular vesicular transport, signal transduction, and protein translation. These hydrolase enzymes operate as biochemical switches by toggling between an active guanosine…
GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, and signal transduction. These enzymes operate by toggling between an active ("ON") guanosine triphosphate…
Phase-transition phenomena in deep learning (grokking, emergent capabilities, and ontological reorganization under context shift) have been studied through several lenses, including representational compression, singular learning theory,…
Eukaryotic cells transmit extracellular signal information to cellular interiors through the formation of a ternary complex made up of a ligand (or agonist), G-protein, and G-protein coupled receptor (GPCR). Previously formalized theories…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
This paper investigates the nonlinear dynamics and phase transitions in power packet network connected with routers, conceptualized as macroscopic information-ratchets. In the emerging paradigm of cyber-physical energy systems, the…
G-protein-coupled receptors (GPCRs), primary targets for over one-third of approved therapeutics, rely on intricate conformational transitions to transduce signals. While Molecular Dynamics (MD) is essential for elucidating this…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
The aim of this paper is to study the qualitative behaviour predicted by a mathematical model for the initial stage of T cell activation. The state variables in the model are the concentrations of phosphorylation states of the T cell…
Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the…
We quantify the influence of the topology of a transcriptional regulatory network on its ability to process environmental signals. By posing the problem in terms of information theory, we may do this without specifying the function…
G-Protein Coupled Receptors (GPCRs) are integral to numerous physiological processes and are the target of approximately one-third of FDA-approved therapeutics. Despite their significance, only a limited subset of GPCRs has been…