Related papers: Conformation changes and protein folding induced b…
Different models such as diffusion-collision and nucleation-condensation have been used to unravel how secondary and tertiary structures form during protein folding. However, a simple mechanism based on physical principles that provide an…
Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta \Delta G$ data,…
Molecular dynamics studies of Go models of proteins with the 10-12 contact potential and the bond and dihedral angle terms indicate statistical similarities to other Go models, e.g. with the Lennard-Jones contact potentials. The folding…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…