342 PART 2 QUANTUM MECHANICS AND SPECTROSCOPY
Problems
15.1 Why are X-rays needed to determine the structure of proteins in diffraction?
15.2 Why are protein structures not directly observable in an X-ray microscope?
15.3 How is the X-ray scattering factor dependent on atomic number and angle?
15.4 Using Bragg’s law, calculate the angle at which the n=1 diffraction peak is observed,
λ=1 Å and (a) d=5 nm and (b) d=0.5 nm.
15.5 What is a protein crystal?
15.6 Explain how the composition of a protein crystal differs from that of a simple salt crystal.
15.7 Explain what the ‘phase problem’ is for solving protein structures.
15.8 Explain how Figure 15.14 is used in protein crystallography, including a description of
the symbols in the figure.
15.9 Explain the difference between isomorphous replacement and anomalous dispersion.
15.10 Explain how a Ramachandran plot is used in model building.
15.11 Why are mirror symmetries excluded for protein crystals but not inorganic crystals?
15.12 X-rays can be generated using copper targets. Calculate the wavelength of a photon that
is emitted when an electron makes a transition from the n=3 level to the n=1 level in
copper.
15.13X-rays can be generated using molybdenum targets. Calculate the wavelength of a photon
that is emitted when an electron makes a transition from the n=3 level to the n=1 level
in molybdenum.
15.14 Explain why synchrotrons are useful for solving structures of proteins.
References
Barney, B.M., Lee, H.I., Dos Santos, P.C. et al.
(2006) Breaking the N 2 triple bond: insights into
the nitrogenase mechanism. Dalton Transactions
2006 , 2277– 84.
Barney, B.M., Yang, T.C., Igarashi, I. et al. (2005)
Intermediates trapped during nitrogenase reduction
of N 8 N, CH 36 N 7 NH, and H 2 N 7 NH 2. Journal of the
American Chemical Society 127 , 14960 –1.
Einsle, O., Tezcan, F.A., Andrade, S.L.A. et al. (2002)
Nitrogenase MoFe-protein at 1.16 Å resolution: a
central ligand in the FeMo-cofactor. Science 297 ,
1696 –1700.
Kim, J. and Rees, D.C. (1992) Crystallographic
structure and functional implications of the nitro-
genase molybdenum-iron protein from Azotobacter
9 inelandii. Nature 360 , 553 – 9.
Ostermann, A., Waschiphy, R., Parak, F.G., and
Nienhaus, G.U. (2000) Ligand binding and con-
formational motions in myoglobin. Nature 404 ,
205 – 8.
Peters, J.W. and Szilagyi, R.K. (2006) Exploring new
frontiers of nitrogenase structure and mechanism.
Current Opinion in Chemical Biology 10 , 101– 8.
Smith, A.W., Camara-Artigas, A., Olea, C., et al.
(2004) Crystallization and initial X-ray analysis
of phenoxazinone synthase from Streptomyces anti-
bioticus. Acta Crystallographica D 60 , 1453 –5.
Smith, A.W., Camara-Artigas, A., Wang, M., et al.
(2006) Structure of phenoxazinone synthase from
Streptomyces antibioticus reveals a new type 2 copper
center.Biochemistry 45 , 4328–87
Tezcan, F.A., Kaiser, J.T., Mustafi, D. et al. (2005)
Nitrogenase complexes: multiple docking sites for
a nucleotide switch protein. Science 309 , 1377– 80.
Yachandra, V.K. (1995) X-ray absorption spectroscopy
and applications in structural biology. Methods in
Enzymology 246 , 638 – 75.