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The ABC (ATP Binding Cassette) transporter protein superfamily comprises a large number of ubiquitous and functionally versatile proteins conserved from archaea to humans. ABC transporters have a key role in many human diseases and also in…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
The anisotropic Kondo necklace model in 2D and 3D is treated as a genuine model for magnetic to Kondo singlet quantum phase transitions in the heavy fermion (HF) compounds. The variation of the quantum critical point (QCP) with anisotropy…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Control of transcription presides over a vast array of biological processes, including those mediated by gene regulatory circuits that exhibit multistability. Within these circuits, two- and three-gene network motifs are particularly…
Experimental evidence suggests that the computational state of cortical systems change according to behavioral and stimulus context. However, it is still unknown what mechanisms underlie this adaptive processing in cortical circuitry. In…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
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…
Proteins are translated from the N- to the C-terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the protein data bank (PDB). We find…
The mutation-selection mechanism of Darwinian evolution gives rise not only to adaptation to environmental conditions but also to the enhancement of robustness against mutations. When two or more phenotypes have the same fitness value, the…
Recent experimental breakthroughs have finally allowed to implement in-vitro reaction kinetics (the so called {\em enzyme based logic}) which code for two-inputs logic gates and mimic the stochastic AND (and NAND) as well as the stochastic…
Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins,…
AMP activated protein kinase (AMPK) is a critical energy sensor, regulating signaling networks involved in pathology including metabolic diseases and cancer. This increasingly recognized role of AMPK has prompted tremendous research efforts…
Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in…
Identifying actionable driver mutations in non-small cell lung cancer (NSCLC) can impact treatment decisions and significantly improve patient outcomes. Despite guideline recommendations, broader adoption of genetic testing remains…
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…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…