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Protein Structure and Folding Exercise 2 by 27.2.2002 1. Many proteins in particular small ones are stabilized by disulfide bridges. Lysozyme contains 8 cysteine residues that form 4 four bridges. Derive expression for the number of ways N cysteins can pair with each other. Some proteins like many neutrophic factors contain odd number of cysteins. What kind of pair would you expect in this case? 2. Rearrange equation H - TS = RTln[D]/[N], where [D] is the concentration of the denatured and [N] the native protein, to [D]/([D]+[N]) that is determined by measurement (spectroscopy). Draw the curve [D]/([D]+[N]) vs T and identify the midpoint as Tm. 3. Below are given thermodynamic parameters for folding of few proteins at 25 ºC. Which is the most stable protein? What are the melting temperatures assuming that enthalpy and entropy do not change with temperature? Protein G (kJ/mol) H (kJ/mol) S (kJ/Kmol) Ribonuclease -46 -280 -790 Chymotrypsin -55 -270 -720 Lysozyme -62 -220 -530 Cytochrome C -44 -52 -27 4. Ribonuclease structure is stabilized by G = -7.1 kJ/mol at pH 2.5 and T = 25 ºC. What is the ratio between folded and denatured molecules? The enthalphy for folding is 238.6 kJ/mol at 25 ºC. Assume that enthalpy and entropy do not change when temperature is raised to 37 ºC. What is G at 37 ºC and what is the ratio between folded and denatured molecules? Finally what is the Tm for ribonuclease at pH 2.5? 5. The action of a denaturant such as urea or guanidinium chloride is to solubilize all parts of the polypeptide. To a good approximation the free energy change is proportional to the denaturant concentration G = GH2O – m[denaturant] where m is a constant (gradient of G). Rewrite the equation in 2 for [D]/([D]+[N]) vs [denaturant] and draw the curve.