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Important thermodynamic parameters including denaturant equilibrium m values (m(eq)) and heat capacity changes (ΔCp) can be predicted based on changes in Solvent Accessible Surface Area (SASA) upon unfolding. Crosslinks such as disulfide bonds influence the stability of the proteins by decreasing the entropy gain as well as reduction of SASA of unfolded state. The aim of the study was to develop mathematical models to predict the effect of crosslinks on ΔSASA and ultimately on m(eq) and ΔCp based on in silico methods. Changes of SASA upon computationally simulated unfolding were calculated for a set of 45 proteins with known m(eq) and ΔCp values and the effect of crosslinks on ΔSASA of unfolding was investigated. The results were used to predict the m(eq) of denaturation for guanidine hydrochloride and urea, as well as ΔCp for the studied proteins with overall error of 20%, 31% and 17%, respectively. The results of the current study were in close agreement with those obtained from the previous studies.
Dependence of A) meq value for GdnHCI denaturation, B) meq value for urea denaturation, and C) heat capacity changes upon unfolding on ∆SASA after correction for the effect of crosslinks by taking out 918.5 Å2 per crosslink for the 45 proteins in our data set (see text for further explanation)
Presentation
This figure shows the snapshots of conform-ational changes during unfolding simulation of IgG binding domain of protein G (IBPG) which has 56 residues with no crosslink. As time evolves, both tertiary and secondary structures of IBPG are lost and at the same time its SASA increases. The maximum SASA achieved during 10 ns is 5772 Å2 which is less than that estimated for fully extended con-formation (8143 Å2).
Molecular dynamics simulation of IgG binding domain of protein G (PDB code 1PGB) solvated in 4.4 M urea in water at 500 ºK for 10 ns using GROMOS-96 force field parameters. The non-protein molecules (i.e. water and urea) are not shown for the sake of clarity.
The figure above shows the molecular dynamics simulation of lysozyme (hen egg white) (PDB code 1AKI) solvated in 4.4 M urea in water at 500 ºK for 10 ns using GROMOS-96 force field parameters The unfolded conformation of lysozyme (hen egg white), a 129-residue protein with four disulfide bonds, retained more globular shape at the end of MD simulation, although it loses the elements of secondary structures.