Statics, metastable states and barriers in protein folding: A replica variational approach

Abstract

Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used to describe the coil-globule transition (characterized by T_CG), glass transitions (by T_A and T_K) and folding transition (by T_F). Trapping on the free energy landscape is characterized by two characteristic temperatures, one dynamic, T_A the other static, T_K (T_A> T_K), which are similar to those found in mean field theories of the Potts glass. 1)Above T_A, the free energy landscape is monotonous and polymer is melted both dynamically and statically. 2)Between T_A and T_K, the melted phase is still dominant thermodynamically, but frozen metastable states, exponentially large in number, appear. 3)A few lowest minima become thermodynamically dominant below T_K, where the polymer is totally frozen. In the temperature range between T_A and T_K, barriers between metastable states are shown to grow with decreasing temperature suggesting super-Arrhenius behavior in a sufficiently large system. Due to evolutionary constraints on fast folding, the folding temperature T_F is expected to be higher than T_K, but may or may not be higher than T_A. Diverse scenarios of the folding kinetics are discussed based on phase diagrams that take into account the dynamical transition, as well as the static ones.

41 pages, LaTeX, 9 EPS figures

References in corpus (3)

• Diffusive Dynamics of the Reaction Coordinate for Protein Folding Funnels
• Folding Kinetics of Protein Like Heteropolymers
• Kinetic and thermodynamic analysis of proteinlike heteropolymers: Monte Carlo histogram technique

Cited by in corpus (11)

• Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics
• Barrier Softening near the onset of Non-Activated Transport in Supercooled Liquids: Implications for Establishing Detailed Connection between Thermodynamic and Kinetic Anomalies in Supercooled Liquids
• Variational theory for site resolved protein folding free energy surfaces
• Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach
• Competitive nucleation in reversible Probabilistic Cellular Automata
• Competitive nucleation and the Ostwald rule in a generalized Potts model with multiple metastable phases
• Techniques of replica symmetry breaking and the storage problem of the McCulloch-Pitts neuron
• Random Heteropolymer Dynamics
• Universal energy distribution for interfaces in a random field environment
• Localization and freezing of a Gaussian chain in a quenched random potential
• Embedding a Native State into a Random Heteropolymer Model: The Dynamic Approach