Related papers: Coupled folding-binding versus docking: A lattice …
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…
Molecular docking plays a crucial role in predicting the binding mode of ligands to target proteins, and covalent interactions, which involve the formation of a covalent bond between the ligand and the target, are particularly valuable due…
We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
The one-dimensional Kondo lattice model with attractive interaction among the conduction electrons is analyzed in the case of half-filling. It is shown that there are three distinct phases depending on the coupling constants of the model.…
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 simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Through Monte Carlo simulations and the Associating Lattice Gas Model, the phases of a two-dimensional fluid under hydrophilic confinement are evaluated. The model, in its unconfined version, reproduces the anomalous behavior of water…
Cells exhibit qualitatively different behaviors on substrates with different rigidities. The fact that cells are more polarized on the stiffer substrate motivates us to construct a two-dimensional cell with the distribution of focal…
The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off--lattice model featuring spherocylinders with continuous…
Protein structures in nature often exhibit a high degree of regularity (secondary structures, tertiary symmetries, etc.) absent in random compact conformations. We demonstrate in a simple lattice model of protein folding that structural…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
Applying a force to certain supramolecular bonds may initially stabilize them, manifested by a lower dissociation rate. We show that this behavior, known as catch bonding and by now broadly reported in numerous biophysics bonds, is…