Representations of 3D Structures

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A real example. The rat fatty acid acyl
carrier protein. Involved in fatty
acid biosynthesis and part of a larger subunit,
the synthase, Is it structured by itself??
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Summary of the Sequential and Secondary NOEs
observed for rat FAS ACP - most definitely
structured
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What next? STRUCTURE CALCULATIONS

• From NOE I know close atom-atom distances, but
  that doesnt give a structure
• The information you have up to this stage is a
  list of distance constraints
• The structure can be determined by inputting this
  information to computer minimization software.
• The computer program also contains information
  about amino acids, bond lengths/angles and
  standard information about atom-atom interactions
  such as minimum distance (i.e. Van der Waals
  radii)
• With all this information you can generate a
  model of the structure.
• Important NMR gives you a number of possible
  solutions
• (all almost identical, rmsd lt1Å), This can range
  from 5-20 models
• X-ray crystallography give one average structure
• NMR structures can be averaged to give one
  average structure as well

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A simulated annealing trajectory over the first
few picoseconds
4 helices begin to condense
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Unfolded
Correctly folded
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Representations of 3D Structures
Precision is not Accuracy
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These 2D methods work for proteins up to about
100 amino acids, and even here, anything from
50-100 amino acids is difficult. We need to
reduce the complexity of these 2D spectra.
We can start by replacing 14N with 15N, a spin
1/2 nucleus.
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1H-15N HSQC of rat FAS ACP
15N shift of nitrogen of amide bond
X 89!
1H Chemical Shift
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