Solvent Accessible Surface Area Normalized Protein-Water Hydrogen Bonds Defines Protein Folded State Stability and Amyloid Formation

Abstract

Protein stability arises from a delicate balance of protein-water and intra-protein hydrogen bonds. Through molecular dynamics simulations of a large collection of proteins spanning diverse SCOP fold classes and amyloid fibrils, we establish hydrogen bond number density normalized by solvent-accessible surface area (SASA) as a unifying metric of structural integrity. Native folded proteins and fibrillar assemblies consistently maintain ~3–4 protein–water hydrogen bonds per unit SASA and ~0.75–2 intra-protein hydrogen bonds per unit SASA, defining a compactness regime characteristic of stable architectures. Interestingly, for amyloid-forming proteins, both the number of protein–water and intra-protein hydrogen bonds per unit SASA display substantial deviations from these almost conserved per-SASA hydrogen-bond number density ranges. This irregularity persists in both the monomeric β-sheeted state and the helical conformation. Only upon assembly to a protofibrillar organisation, amyloidogenic proteins attain the 3-4 protein-water hydrogen bonds and 0.75–2 intra-protein hydrogen bonds per unit SASA values. During folding/unfolding studies of four different proteins belonging to different SCOP classes, we observed that the partially folded or destabilized states fall below this threshold of 3 protein-water hydrogen bonds per unit SASA. The convergence of distinct fold classes and fibrillar ensembles onto the same per-SASA hydrogen-bond number density range suggests a universal structural constraint underpinning both native state stability and fibril robustness.