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 │Fph│of 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 [Ө] 222 = -29,750 deg.cm 2. decimole -1. Given from reference spectra that 100% helix has a [Ө] 222 = -36,000 deg.cm 2. decimole -1 and 100% coil has a [Ө] 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?