PMC:2724026 / 33862-35256 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/2724026","sourcedb":"PMC","sourceid":"2724026","source_url":"https://www.ncbi.nlm.nih.gov/pmc/2724026","text":"Φ-Value analysis\nThe variation of the logarithm of the observed rate constant with concentration of urea was analysed using Eq. (2); those unfolding rate constants judged to be non-linear were omitted from the fit (see Supplementary Data):(2) lnkobs=ln(kfH2Oexp(−mkf.[urea])+kuH2Oexp(mku.[urea]))where kobs is the observed rate constant, kfH2Oand kuH2O are the folding and unfolding rate constants in 0 M denaturant, respectively, and mkf and mku are the gradients of the folding and unfolding arms, respectively.\nThe variation of the natural logarithm of the observed rate constant with the concentration of urea was also analysed using Eq. (3), which includes a term to account for curvature in the unfolding limb (Hammond fit):(3) lnkobs=ln(kfH2Oexp(−mkf.[urea])+kuH2Oexp(mku.[urea]+mku'.[urea]2))\nAll Φ-values were calculated at 2 M urea using Eq. (4):(4) Φ=ΔΔGD−‡ΔΔGD−Nwhere ΔΔGD-N is the equilibrium constant for unfolding determined from equilibrium denaturation experiments and ΔΔGD-‡ is the change in the free energy difference between the denatured (D) and transition (‡) states for folding upon mutation, calculated as:(5) ΔΔGD−‡=RTln(kfwt/kfmut)kfwt and kfmut are the folding rate constants at 2 M urea for WT and mutant protein, respectively.\nThe β-Tanford (βT) value was calculated using Eq. (6); mkf and mku values were derived from chevrons fit to Eq. (2) only:(6) βT=mkfmkf+mku","divisions":[{"label":"title","span":{"begin":0,"end":16}},{"label":"p","span":{"begin":17,"end":513}},{"label":"label","span":{"begin":239,"end":242}},{"label":"p","span":{"begin":514,"end":800}},{"label":"label","span":{"begin":730,"end":733}},{"label":"p","span":{"begin":801,"end":1255}},{"label":"label","span":{"begin":856,"end":859}},{"label":"label","span":{"begin":1130,"end":1133}},{"label":"label","span":{"begin":1377,"end":1380}}],"tracks":[]}