相关论文: Temperature dependence of normal mode reconstructi…

We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…

We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…

A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…

Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…

Thermal unfolding of proteins is compared to folding and mechanical stretching in a simple topology-based dynamical model. We define the unfolding time and demonstrate its low-temperature divergence. Below a characteristic temperature,…

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…

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…

We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…

The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…

The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…

For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…

A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…

We introduce a simplified protein model where the solvent (water) degrees of freedom appear explicitly (although in an extremely simplified fashion). Using this model we are able to recover the thermodynamic phenomenology of proteins over a…

Developing microscopic understanding of the thermal properties of liquids is challenging due to their strong dynamic disorder, which prevents characterization of the atomic degrees of freedom. There have been significant research interests…

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…

We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…

We present a general harmonic theory for the temperature dependence of phonon-renormalized properties of solids. Firstly, we formulate a perturbation theory in phonon-phonon interactions to calculate the phonon renormalization of physical…

Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…