Protein Classification and Structure Prediction Amino acid ...

Experimentation to grow
protein crystals
X-Ray Crystallography
Trial-and-error
Experimentation
Observables
Partial Success
~0.5mm
Trial 1
Control
Parameters
Failure
Success
Trial 3
Trial 2
• The crystal is a mosaic of millions of copies
of the protein.
• As much as 70% is solvent (water)!
• May take months (and a “green” thumb) to
grow.
Krane & Raymer
Krane & Raymer
X-Ray diffraction
• Image is averaged over:
• Space (many copies)
• Time (of the diffraction experiment)
Protein Crystal Growth in Space
• Protein crystal growth experiments on over 20 shuttle
missions since 1984
• Larger Crystals in 45.4% of the cases
• New Crystal Structures in 18% of the cases
• ≥ 10% increase in X-Ray X
Crystallography Brightness in 58%
of the cases
• Less thermal motion in 27.2% of the cases
• An X-Ray X
Crystallography resolution improvement of ~0.3 Å
in 42.4% of the cases
• An X-Ray X
Crystallography resolution improvement of 0.3 to
0.5 Å in 9.9% of the cases
• An X-Ray X
Crystallography resolution improvement of 0.5 to
1.0 Å in 9.9% of the cases
Krane & Raymer
The Protein Folding Problem
• Proteins self-assemble in solution. Almost all of the
information necessary to determine the complex 3-D 3
structure is in the amino acid sequences
• Central dogma:
Sequence specifies structure
• Central question:
“Given a particular sequence of
amino acid residues (primary structure), what will the
tertiary/quaternary structure of the resulting protein be?”
Levinthal’s paradox
• Consider a 100 residue protein. If each residue
can take only 3 positions, there are 3 100 = 5 ×
10 47 possible conformations.
• If it takes 10 -13
s to convert from 1 structure to
another, exhaustive search would take 1.6 × 10 27
years!
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