Related papers: Allostery and Kinetic Proofreading
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation…
A numerical model is built, simulating the principles of kinetic gas theory, to predict pressures of molecules in a spherical pressure vessel; the model tracks a single particle and multiplies the force on the spherical walls by a mole of…
Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…
Double phosphorylation of protein kinases is a common feature of signalling cascades. This motif may reduce cross-talk between signalling pathways, as the second phosphorylation site allows for proofreading, especially when phosphorylation…
The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modelling meticulously executed. Furthermore, to enable the…
We study microscopic engines that use a single active particle as their "working medium". Part of the energy required to drive the directed motion of the particle can be recovered as work, even at constant temperature. A wide class of…
A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It…
The enzyme FoF1-ATP synthase provides the 'chemical energy currency' adenosine triphosphate (ATP) for living cells. Catalysis is driven by mechanochemical coupling of subunit rotation within the enzyme with conformational changes in the…
The peristaltic motion of the stomach walls combines with the secretion of enzymes to initiate the process that breaks down food. Computational modelling of this phenomenon can help reveal the details that would be hard to capture via…
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…
F1F0 ATP synthase (ATPase) either facilitates the synthesis of ATP in the mitochondrial membranes and bacterial inner membranes in a process driven by the proton moving force (pmf), or uses the energy from ATP hydrolysis to pump protons…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
HIPSTER (Heavily Ionising Particle Standard Toolkit for Event Recognition) is an open source Python package designed to facilitate the use of TensorFlow in a high energy physics analysis context. The core functionality of the software is…
Understanding the mechanisms responsible for the formation and growth of FtsZ polymers and their subsequent formation of the $Z$-ring is important for gaining insight into the cell division in prokaryotic cells. In this work, we present a…
Kinesin-1 is an ATP-driven, two-headed motor protein that transports intracellular cargoes along microtubule. Based on recent experimental observations, we formulate a mechanochemical model for it, in which forward/backward/futile cycle of…
How molecular motors like Kinesin regulates the affinity to the rail protein in the process of ATP hydrolysis remains to be uncovered. To understand the regulation mechanism, we investigate the structural fluctuation of KIF1A in different…