Related papers: Analysis of Two-State Folding Using Parabolic Appr…
A model which treats the denatured and native conformers of spontaneously-folding fixed two-state systems as being confined to harmonic Gibbs energy-wells has been developed.Within the assumptions of this model the Gibbs energy functions of…
A model which treats the denatured and the native conformers as being confined to harmonic Gibbs energy wells has been used to analyse the non-Arrhenius behaviour of spontaneously folding fixed two-state systems. The results demonstrate…
A model which treats the denatured and the native conformers as being confined to harmonic Gibbs energy wells has been used to rationalize the physical basis for the non-Arrhenius behaviour of spontaneously-folding fixed two-state systems.…
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 thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
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…
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…
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…
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…
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,…
Many protein systems fold in a two-state manner. Random models, however, rarely display two-state kinetics and thus such behavior should not be accepted as a default. To date, many theories for the prevalence of two-state kinetics have been…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
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 fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy. If all chemical problems can be…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
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…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
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 present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…