Related papers: Conformations of Proteins in Equilibrium

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…

In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…

We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…

Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…

Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…

There are several simple criteria of folding to a native state in model proteins. One of them involves crossing of a threshold value of the RMSD distance away from the native state. Another checks whether all native contacts are…

We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…

The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…

We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…

We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…

We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…

Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…

We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…

Protein-protein and protein nucleic acid interactions are vitally important for a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have…