1. What is a Patterson Map and how can it contribute to protein structure determination by X-ray analysis?
2. a) How does an Argand diagram help to understand structure factors in X-ray analysis.
b) After X-ray data collection and processing of a heavy atom derivative of a protein crystal you obtain a structure factor magnitude Fphof 6 for a particular X-ray reflection hkl. The position of the bound heavy atom determined from a difference Patterson map gives a calculated Fh of 2 and a phase of 45o for the same reflection. The native protein crystal gave Fp of 5. Use a Harker diagram to estimate the phase of this hkl. If you repeated this process for all the measured reflections, would this enable the production of a useful electron density map? If not, what should be done next?
3. For a protein containing no -sheet secondary structure the CD spectrum gives [Ó¨] 222 = -29,750 deg.cm 2. decimole -1. Given from reference spectra that 100% helix has a [Ó¨] 222 = -36,000 deg.cm 2. decimole -1 and 100% coil has a [Ó¨] 222 = +3,000 deg.cm 2. decimole -1.
a) What is the percentage alpha helical content of the protein? Show your working.
b) The protein and a short duplex oligonucleotide are added at equimolar concentration in a buffer containing 100 mM NaCl and then in a buffer containing 1 M NaCl, the two samples are analysed by CD. The spectra in the 250 to 280 nm region differs considerably between the samples but the spectrums in the 200 230 nm range are similar. What hypothesis can you form concerning the protein?
