Related papers: Dynamics of allosteric action in multisite protein…

In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…

The protein NLRP3 and its complexes are associated with an array of inflammatory pathologies, among which neurodegenerative, autoimmune, and metabolic diseases. Targeting the NLRP3 inflammasome represents a promising strategy for easing the…

Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…

Nonlinear effects in protein dynamics are expected to play role in function, particularly of allosteric nature, by facilitating energy transfer between vibrational modes. A recently proposed method focusing on the non-Gaussian shape of the…

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…

The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…

We apply tools from real algebraic geometry to the problem of multistationarity of chemical reaction networks. A particular focus is on the case of reaction networks whose steady states admit a monomial parametrization. For such systems we…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two…

Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action…

During the lifecycle of a virus, viral proteins and other components self-assemble to form a symmetric protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a…

Multisite covalent modification of proteins is omnipresent in eukaryotic cells. A well-known example is the mitogen-activated protein kinase (MAPK) cascade, where in each layer of the cascade a protein is phosphorylated at two sites. It has…

Allostery is an intrinsic spatiotemporal property of all proteins, resulting from long range correlations in the order of several nanometers and time scales of nanoseconds. Information is carried asymmetrically from one part to another by…

Disordered elastic networks are a model material system in which it is possible to achieve tunable and trainable functions. This work investigates the modification of local mechanical properties in disordered networks inspired by allosteric…

The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…

Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…

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…

Allosteric effects are often underlying the activity of proteins and elucidating generic design aspects and functional principles which are unique to allosteric phenomena represents a major challenge. Here an approach which consists in the…

The cytoskeletal component actomyosin is a canonical example of active matter since the powerstroke cycle locally converts chemical energy in the form of adenoside triphosphate (ATP) into mechanical work for remodelling. Observing myosin II…