Benchmarking fold recovery: implicit-solvent atomistic & coarse grained simulations of two vs non two state proteins

Abstract

Protein folding is a fundamental biological process through which a polypeptide adopts its functional three-dimensional structure. In this study, we systematically investigated the structural response of proteins to thermal denaturation using both atomistic and coarse-grained (CG) molecular dynamics simulations. A curated set of 138 proteins from the PFDB (89 two-state and 49 non-two-state folders) was subjected to a heat–quench protocol (300 K → 1000 K → 300 K) in implicit solvent. Structural recovery was assessed through RMSD and radius of gyration (Rg) calculations after Kabsch superimposition, alongside MM/PBSA energy evaluations. Post-quench alignment revealed distinct behaviors: two-state proteins consistently showed lower RMSD, greater compaction (ΔRg < 0), and higher native contact retention than non-two-state proteins. Furthermore, a significant inverse correlation was observed between log10(kf) and final RMSD in the two-state subset, linking folding rate to structural resilience. Results from CG simulations mirrored these trends, validating their utility for rapid, cost-effective screening. These findings underscore the importance of structural alignment in post-simulation analysis and highlight heat–quench recovery as a powerful proxy for foldability. The combined pipeline offers a scalable framework for evaluating folding kinetics and native-state robustness across protein families.