Solvent accessible surface area normalized protein–water hydrogen bonds define protein folded state stability and amyloid formation

Abstract

Protein stability arises from a delicate balance between 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 the 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.