Related papers: ATP concentration regulates enzyme kinetics
ATPases cyclically convert chemical energy in the form of ATP gradients into directed motion inside cells. To function, ATPases rely on allosteric communication between at least two binding sites, an internal signaling mechanism that is not…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
We present a model for the actin contractile ring of adherent animal cells. The model suggests that the actin concentration within the ring and consequently the power that the ring exerts both increase during contraction. We demonstrate the…
We mathematically modeled the receptor-activated MAP kinase signaling by incorporating the regulation through cellular phosphatases. Activation induced the alignment of a phosphatase cascade in parallel with the MAP kinase pathway. A novel…
We study the dynamics of a tunable 2D active nematic liquid crystal composed of microtubules and kinesin motors confined to an oil-water interface. Kinesin motors continuously inject mechanical energy into the system through ATP hydrolysis,…
Site-specific information on how adenosine triphosphate in the aqueous phase (ATP$_{(aq)}$) interacts with magnesium (Mg$^{2+}_{(aq)}$) is a prerequisite to understanding its complex biochemistry. To gather such information, we apply…
Active fluids have applications in micromixing, but little is known about the mixing kinematics of systems with spatiotemporally-varying activity. To investigate, UV-activated caged ATP was used to activate controlled regions of…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…
We present a thermodynamically consistent model describing the dynamics of a multi-component mixture where one enzyme component catalyzes a reaction between other components. We find that the catalytic activity alone can induce phase…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This papers…
We propose a new attention mechanism with linear complexity, ATP, that fixates \textbf{A}ttention on \textbf{T}op \textbf{P}rincipal keys, rather than on each individual token. Particularly, ATP is driven by an important observation that…
Actin is one of the most studied cytoskeleton proteins showing a very rich span of structures. It can self-assemble actively into dynamical structures that govern the mechanical properties of the cell, its motility and its division.…
In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of…
In cell proliferation, stem cell differentiation, chemoresistance and tissue organization, the ubiquitous role of YAP/TAZ continues to impact our fundamental understanding in numerous physiological and disease systems. YAP/TAZ is an…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…
The pump process of the ratchet model inspired by the $F_o$ rotatory motor of ATP synthase is investigated. In this model there are two kinds of characteristic time. One is dynamical, the relaxation time of the system. Others are chemical,…
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…