Related papers: Allostery and Kinetic Proofreading
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
We model and simulate the stepping dynamics of the kinesin motor including electric and mechanical forces, environmental noise, and the complicated potentials produced by tracking and neighboring protofilaments. Our dynamical model supports…
In this paper we study the relation between the property of detailed balance and the ability of discriminating between different ligands for a class of stochastic models of kinetic proofreading. We prove the existence of a critical amount…
Protein assembly plays an important role in the regulation of biological systems. The cytoskeleton assembly activity is provided by the binding cofactors GTP (guanidine triphosphate) or ATP(adenosine triphosphate) to monomeric protein, and…
Kinesins are processive motor proteins that move along microtubules in a stepwise manner, and their motion is powered by the hydrolysis of ATP. Recent experiments have investigated the coupling between the individual steps of single kinesin…
Mismatch repair is a critical step in DNA replication that occurs after base selection and proofreading, significantly increasing fidelity. However, the mechanism of mismatch recognition has not been established for any repair enzyme.…
Polymerases select nucleotides before incorporating them for chemical synthesis during gene replication or transcription. How the selection proceeds stepwise efficiently to achieve sufficiently high fidelity and speed is essential for…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
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,…
Molecular motors belonging to the kinesin and myosin super family hydrolyze ATP by cycling through a sequence of chemical states. These cytoplasmic motors are dimers made up of two linked identical monomeric globular proteins. Fueled by the…
Conventional kinesin is a homodimeric motor protein that is capable of walking unidirectionally along a cytoskeletal filament. While previous experiments indicated unyielding unidirectionality against an opposing load up to the so-called…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
The cytoskeleton is an active composite of filamentous proteins that dictates diverse mechanical properties and processes in eukaryotic cells by generating forces and autonomously restructuring itself. Enzymatic motors that act on the…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
F1-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F1-ATPase does not follow the widely believed Michaelis-Menten mechanism. Instead, the hydrolysis mechanism…