Syed Ausaf Ali, Asimul Islam, Faizan Ahmad
Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
If protein stability is defined as Gibbs free energy change (∆GD°) associated with the denaturation equilibrium, native (N) conformation↔structureless denatured (D) conformation under physiological condition, it then cannot be measured. The reason for saying this is that for proteins, the equilibrium constant for this process is in the range 10-4 to 10-11. However, it is possible to measure Gibbs free energy change (∆GD ) in the presence of chemical denaturant (urea or guanidinium chloride), and from measurements of ∆GD as function of [denaturant], the molar concentration of the denaturant, ∆GD o (value of ∆GD in the absence of the denaturant) of a protein is determined from different extrapolation methods. A problem with these extrapolation procedures is that different extrapolation methods applied on the same set of data (∆GD , [denaturant]) give different values of ∆GD° of a protein. We have developed an empirical method to determine ∆GD° of a protein using information from its atomic coordinates in the PDB, and measured values of Cm (midpoint of the sigmoidal curve of a physical property) and ∆gtr, i (transfer-free energy change of the ith amino acid residue from water to denaturant concentration at Cm). The relation is: ∆GD° = – (Σ fi ∆gtr, i) C m, where fi is the fractional increase in the exposure of the ith amino acid residue (HN-CHR-CO-). fi is defined as fi = (ASAD,i – ASAN,i)/ ASAD,i, where ASA is accessible surface area, and subscript Ni and Di represent the parameter in the N and D states, respectively. For the estimation of ASAN,i we have used different tools, DSSP, CCP4, ProtSA and GETAREA. To calculate ASAD,i we have used the lower bound values of Rose and co-workers as well as the ASC values (ECEPP/2 algorithm) in addition to the ProtSA values. We shall present a comparison of ∆GD° values of proteins obtained from our empirical approach with experimentally observed ones. Read More …