Biological Chemistry LaboratoryBiology 3515/Chemistry 3515
Spring 2020
Lecture 10
More on Crystallography and Protein Structures
6 February 2020c©David P. Goldenberg
University of [email protected]
Clicker Question #1: How Big is an Enzyme?
A) 10−10m
B) 10−9m
C) 10−8m
D) 10−7m
E) 10−6m?
Why Not an X-Ray Microscope?
Scattering from individual atoms is very weak, especially from elementswith low atomic numbers.
Very difficult to make lenses for X-rays.
In crystallography:
• Use crystals to increase the total scattering intensity.
• Use a mathematical technique, the Fourier transform, to do the job of a lens.
Diffraction from a Duck
Film
A Real Diffraction Pattern From a Pretend Duck
Taylor, C. & Lipson, H. (1964). Optical Transforms: Their preparation and application to X-ray diffractionproblems. Cornell Univ. Press, Ithaca, NY.
Steps in Protein Crystallography
1. Grow Crystals
Entirely empirical andidiosyncratic.
Protein crystals are about 50%water and are kept suspended ina salt solution; close tophysiological conditions.
Resolution of final structure ishighly dependent on how wellordered the crystals are.
Crystal pictures from: http://biophysics.uoguelph.ca/central/facilities.htm
Steps in Protein Crystallography
2. Collect Diffraction Data
Pictures from:
http://www.nsrrc.org.tw/english/research8_1_circle_Diffractometer.aspx
http://www.bnl.gov/nufo/facilities.asp
Steps in Protein Crystallography
3. Determine PhasesDiffraction data contain intensities of scattered X-ray waves, but not theirphases. Both are needed to reconstruct structure.
One way: Comparing diffraction intensities of crystals containing differentheavy-atom derivatives.
4. Calculate electron density map
Molecular model is built into the electron density map.
Figure from Berg, Tymoczko and Stryer Biochemistry, 5thed. (2002) W.H. Freeman, New York.
Atomic Coordinates are Deposited
in the Protein Data Bank (PDB)
http://www.rcsb.org
The Protein Data Bank Since 1976
PD
P S
tru
ctu
re e
ntr
ies (
tho
usa
nd
s)
0
20
40
60
80
100
120
140
Year
1980 1985 1990 1995 2000 2005 2010 2015
Annual increase
Total
1976
(13)
1981
(85)
What happened in the1990s?
Genetic engineering:Ability to make largeamounts of manyproteins.
Synchrotron X-raysources:Much faster datacollection.
Bigger and fastercomputers.
