Related papers: Chetaev Instability Framework for Kinetostatic Com…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
We introduce a machine learning approach for extracting fine-grained representations of protein evolution from molecular dynamics datasets. Metastable switching linear dynamical systems extend standard switching models with a…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
Cooperativity is a hallmark of proteins, many of which show a modular architecture comprising discrete structural domains. Detecting and describing dynamic couplings between structural regions is difficult in view of the many-body nature of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
Knots in proteins have been proposed to resist proteasomal degradation. Ample evidence associates proteasomal degradation with neurodegeneration. One interesting possibility is that indeed knotted conformers stall this machinery leading to…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
The derivation of the equations of motion for nonholonomic systems remains a central issue in analytical mechanics, primarily due to the tension between the d'Alembert-Lagrange differential principle and integral variational approaches.…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
The cytoskeleton, consisting of biopolymer filaments, molecular motors, and passive crosslinking proteins, provides the internal structure of cells that facilitate movement, growth, and cell division. Understanding the microscopic…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…