Thermal stability of a protein predicted from its three dimensional structure

A native protein in aqueous salt solution usually unfolds reversibly upon h eating at a transition temperature (T-m) with unfolding enthalpy (DeltaH(m) ). The method to predict T-m and DeltaH(m) from the 3D structure assuming s imple two-states transition has been developed using experimental values of T-m, DeltaH(m) and heat capacity change (DeltaC(p,u)) compiled in the data base "ProTherm". In order to account for dependence of thermostability on p H and salt concentration, the difference in electrostatic interactions betw een native and denatured states (DeltaH(u,ele)) was computed applying Debye -Huckel type potential between partial charges located on ionizable side ch ain atoms. Standard unfolding free energy (DeltaG(u)(0)), enthalpy (DeltaH( u)(0)), and DeltaC(p,u) at 25 degreesC after subtracting electrostatic ener gies were obtained using a data set of 63 experimental data on 32 uncharged proteins. Each of these quantities was assumed to be a sum of products of the difference in accessible surface area (Delta ASA) of an i-th constituen t atomic group between the native and unfolded extended structure times a c orresponding adequate constant. Proportional constants for six (aliphatic, aromatic, hydroxyl, amide, carbonyl, and thiol) atomic groups were determin ed using the data set. Thus, DeltaG(u)(0), DeltaH(u)(0), and DeltaC(p,u) fo r a protein at uncharged form of known 3D structure can be computed using i ts Delta ASA value of every group, and DeltaG(u)(T) at T is determined acco rding to thermodynamic relation, adding DeltaH(u,ele)(T). Values of T-m and DeltaH(m) for the protein may, therefore, be evaluated as values at DeltaG (u)(T)=0. The agreement of calculated and experimental values for the data set used for the determination of the constants was practically the same as that for another data set of 33 experimental data on T-m and DeltaH(m) for 19 proteins with standard deviations of about 12 degreesC and 38 kcal/mol, respectively. The stability and instability of correctly and misfolded pro teins (hemerythrin, and Ig-variable domain fragment) were successfully expl ained in terms of DeltaG(u).