Related papers: ATP concentration regulates enzyme kinetics
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Two simple (rotator and one-particle) mechanistic models are suggested to describe simultaneously at a minimal level of sophistication two basic functions of F$_1$-ATPase: a motor regime driven by ATP hydrolysis and its inverted function as…
Signaling events in eukaryotic cells are often guided by a scaffolding protein. Scaffold proteins assemble multiple proteins in a spatially localized signaling complex and exert numerous physical effects on signaling pathways. To study…
The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
We study the ensemble velocity of non-processive motor proteins, described with multiple chemical states. In particular, we discuss the velocity as a function of ATP concentration. Even a simple model which neglects the strain-dependence of…
Active systems are characterized by a continuous production of entropy at steady state. We study the statistics of entropy production within a lattice-based model of interacting active particles that is capable of motility-induced phase…
Apoptosis is an important area of research because of its role in keeping a mature multicellular organism's number of cells constant hence, ensuring that the organism does not have cell accumulation that may transform into cancer with…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…
The study of active solids offers a window into the mechanics and thermodynamics of dense living matter. A key aspect of the non-equilibrium dynamics of such active systems is a mechanistic description of how the underlying mechano-chemical…
Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various…
Competitive inhibitors can, paradoxically, stimulate an enzymatic reaction at low to moderate doses. Competitive inhibition of an enzyme occurs when an inhibitor binds to the enzyme's binding site and blocks the enzyme's target molecule…
The neuron consumes energy from ATP hydrolysis to maintain a far-from-equilibrium steady state inside the cell, thus all physiological functions inside the cell are modulated by thermodynamics. The neurons that manage information encoding,…
The rational development of specific inhibitors for the ~500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP…
Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…
The synthetic actin network arouses great interest as bio-material due to its soft and wet nature that mimics many biological scaffolding structures. Inside the cell, the actin network is regulated by tens of actin-binding proteins (ABP's),…
The actin cortex of an animal cell is a thin polymeric layer attached to the inner side of the plasma membrane. It plays a key role in shape regulation and pattern formation on the cellular and tissue scale and, in particular, generates the…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…