Structural Determinants of Folding and Unfolding Kinetics in Two-State and Non-Two-State Proteins: A Comparative Correlation Analysis

Misfolding and abnormal folding kinetics of proteins are involved in many human diseases and are a significant problem in protein engineering. However, the structural factors that define two-state (2S) and non-two-state (N2S) folding processes remain unclear. The current systematic bioinformatics study provides a relationship between structure and kinetics with a curated dataset of experimentally solved proteins with temperature-scaled folding and unfolding rates. A set of contact-based and network-theoretic structural descriptors, including contact order, long-range interaction measures, and clustering coefficients, was assessed across various structural classes. The analysis reveals that contact-order-derived parameters and long-range order are the most critical determinants of folding and unfolding rates, which are kinetic barriers associated with topological complexity. Conversely, the correlation between long-range contact order, clustering coefficient, and kinetic efficiency is positive, and the interplay between the cooperative network of residue interactions is essential. It is interesting to note that non-two-state proteins are susceptible to long-range contact formation, which is consistent with the existence of folding intermediates. These results provide a coherent structural context for the disease mechanisms of folding and can offer a framework for rational protein design and stability optimization.