Simplified lattice model for polypeptide fibrillar transitions

The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics

Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.

Physical mechanism for biopolymers to aggregate and maintain in non-equilibrium states

Many human or animal diseases are related to aggregation of proteins. A viable biological organism should maintain in non-equilibrium states. How protein aggregate and why biological organisms can maintain in non-equilibrium states are not well understood. As a first step to understand such complex systems problems, we consider simple model systems containing polymer chains and solvent particles. The strength of the spring to connect two neighboring monomers in a polymer chain is controlled by a parameter s with s → ∞ for rigid-bond. The strengths of bending and torsion angle dependent interactions are controlled by a parameter s A with s A  → -∞ corresponding to no bending and torsion angle dependent interactions. We find that for very small s A , polymer chains tend to aggregate spontaneously and the trend is independent of the strength of spring. For strong springs, the speed distribution of monomers in the parallel (along the direction of the spring to connect two neighboring monomers) and perpendicular directions have different effective temperatures and such systems are in non-equilibrium states.

Finite-size corrections and scaling for the dimer model on the checkerboard lattice

Lattice models are useful for understanding behaviors of interacting complex many-body systems. The lattice dimer model has been proposed to study the adsorption of diatomic molecules on a substrate. Here we analyze the partition function of the dimer model on a 2M×2N checkerboard lattice wrapped on a torus and derive the exact asymptotic expansion of the logarithm of the partition function. We find that the internal energy at the critical point is equal to zero. We also derive the exact finite-size corrections for the free energy, the internal energy, and the specific heat. Using the exact partition function and finite-size corrections for the dimer model on a finite checkerboard lattice, we obtain finite-size scaling functions for the free energy, the internal energy, and the specific heat of the dimer model. We investigate the properties of the specific heat near the critical point and find that the specific-heat pseudocritical point coincides with the critical point of the thermodynamic limit, which means that the specific-heat shift exponent λ is equal to ∞. We have also considered the limit N→∞ for which we obtain the expansion of the free energy for the dimer model on the infinitely long cylinder. From a finite-size analysis we have found that two conformal field theories with the central charges c=1 for the height function description and c=-2 for the construction using a mapping of spanning trees can be used to describe the dimer model on the checkerboard lattice.