Related papers: Cooperativity in Protein Folding: From Lattice Mod…
A statistical mechanical distance constraint model (DCM) is presented that explicitly accounts for network rigidity among constraints present within a system. Constraints are characterized by local microscopic free energy functions.…
We present a new lattice model for proteins that incorporates a tube-like anisotropy by introducing a preference for mutually parallel alignments in the conformations. The model is demonstrated to capture many aspects of real proteins.
The change in the lattice parameters or the lattice disorder is claimed as a cause of the slight reduction in the transition temperature by carbon doping in MgB2. In this work, an extensive investigation on the effects of carbohydrate…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
We study correlations in fermionic lattice systems with long-range interactions in thermal equilibrium. We prove a bound on the correlation decay between anti-commuting operators and generalize a long-range Lieb-Robinson type bound. Our…
What are the molecular mechanisms that dictate protein-protein binding stability and whether those are related to the ones behind protein fold stability are still largely open questions. Indeed, despite many past efforts, we still lack…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
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…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We introduce a lattice gas implementation that is based on coarse-graining a Molecular Dynamics (MD) simulation. Such a lattice gas is similar to standard lattice gases, but its collision operator is informed by an underlying MD simulation.…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
We study the collapse transition of a polymer on a square lattice with both nearest-neighbor and next nearest-neighbor interactions, by calculating the exact partition function zeros up to chain length 36. The transition behavior is much…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…