Download Protein Structure and Folding

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 - TS = 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.