What Gives an Insulin Hexamer Its Unique Shape and Stability? Role of Ten Confined Water Molecules

Abstract

Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn, Ca, etc., in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations, and X-ray analyses to discover that a team of approximately 10 water molecules confined inside a barrel-shaped nanocavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly. These cavity water molecules exhibit interesting dynamical features like intermittent escape and reentrance. We find that these water molecules are dynamically slower than the bulk and weave an intricate hydrogen bond network among themselves and with neighboring protein residues to generate a robust backbone at the center of the hexamer that holds the association strongly from inside and maintains the barrel shape.

Calculating the absolute binding free energy of the insulin dimer in an explicit solvent

“…44 . The role of the confined water molecules to the stability of the insulin hexamer is studied in ref. 52 .…”

“…42 These studies suggest that both of the insulin dimerization and dissociation are enthalpy control. As to the simulations, the dynamic properties of the insulin monomer, 43,44 dimer 45-50 and hexamer 51,52 in water are also investigated by some groups. For instance, two distinct surfaces (the dimer forming surface and the hexamer forming surface) on an insulin monomer are characterized in ref.…”

Insulins for the long term management of diabetes mellitus in dogs: a review

“…While the monomer is the biologically active form of insulin, hexamers act as a store of pre-formed hormone that is resistant to formation of higher-order aggregates of decreased bioavailability [ 7 ]. The classical 2-Zn insulin hexamer is known as T 6 , in which each of the six protomers is in the T state, with a structure similar to that of monomeric insulin [ 8 ].…”

Investigations of Albumin–Insulin Detemir Complexes Using Molecular Dynamics Simulations and Free Energy Calculations

“…Computational studies on insulin and insulin analogues have for instance investigated the dimerization pathway of the peptides, 23,24 the effect of mutations on protein stability and potency, 25,26,27 interactions with excipients at different physicochemical conditions, 28,29 and the effect of water molecules and hydrogen bond network on peptide stability. 30,31 The main focus of albumin studies has been albumin's capability to bind potential therapeutic, small organic molecules, 32,33,34 chemical additives, 35 and natural products such as monosaccharides 36 and flavonoids 37 to determine binding poses of the ligands, binding free energy of the ligands and key interactions between albumin and the ligands. Albumin-ligand and albumin-ion interactions have also been studied in different physicochemical conditions.…”