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.
15.13 X-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 8N, CH 3 6N7NH, and H 2 N7NH 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 nitrogenase molybdenum-iron protein from Azotobacter
9inelandii. Nature 360, 553–9.
Ostermann, A., Waschiphy, R., Parak, F.G., and
Nienhaus, G.U. (2000) Ligand binding and conformational 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 antibioticus. 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.
9781405124362_4_015.qxd 4/29/08 9:13 Page 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.
15.13 X-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 8N, CH 3 6N7NH, and H 2 N7NH 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 nitrogenase molybdenum-iron protein from Azotobacter
9inelandii. Nature 360, 553–9.
Ostermann, A., Waschiphy, R., Parak, F.G., and
Nienhaus, G.U. (2000) Ligand binding and conformational 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 antibioticus. 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.
9781405124362_4_015.qxd 4/29/08 9:13 Page 342