Refining the Structure of cADPR

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Refining the Structure of cADPR

• Rodney Agnant
• and
• Dr. Steven M. Graham
• Harlem Children Society and St. Johns University

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? Introduction ?
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What is cADPR?

• cADPR cyclic Adenosine Diphosphate Ribose
• is an organic molecule comprised of carbon,
  hydrogen, oxygen, nitrogen and phosphorus.
• contains both rings and chains that are able to
  move.
• is important for regulating calcium levels in
  cells calcium regulates many cellular processes.

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? Purpose Hypothesis ?

• Over 100 analogs of cADPR are known.
• Does the precise structure (better conformation
  of cADPR determine its function-its ability to
  cause calcium release?
• cADPR and its analogs have been characterized
  structurally only at a low level of
  sophistication. A thorough structure/function
  study requires a more rigorous approach to
  structure.

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cADPR North and South Conformations
North
South
R-ring
R-ring
A-ring
A-ring
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Two Structure Analysis Programs

• PSEUROT is a program that calculates H-H
  (proton-proton) angles and ribose ring angles.
  The input for Pseurot is H-H coupling data
  obtained from H Nuclear Magnetic Resonance (NMR)
  Spectroscopy.
• HyperChem is a program that allows one to create
  and optimize molecular structures in silico.
  Hyperchem provides H-H and ribose ring angles
  that may not be obtainable from H NMR data.

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? Materials Procedures ?
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HyperChem Procedure

• Twenty different conformations of cADPR were
  built and their structures optimized in
  HyperChem.
• All fCCC/O and fHCCH were extractd from each
  structure. The plots of fCCC/O versus fHCCH were
  constructed

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PSEUROT Procedure
fHCCH A?fCCC/O B
JHCCH
fHCCH A?fCCC/O B
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? Results Conclusion ?
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Pseurot-Hyperchem Comparison

• Pseurot Our Hyperchem
• Default A,B A,B
• 12 1.102, 123.3 1.079 124.4
• 23 1.090, 0.2 1.132-2.0
• 3,4 1.095-124.9 1.102-124.3
• Output Output
• N(60º) S(204º) N(68º) A(210º)
• 31 69 32 68

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Conclusion Future

• When comparing results of Hyperchem derived A, B
  to default and PSEUROT A,B the discrepancy was
  minimal.
• We can conclude that Hyperchem can be used to
  derive the parameters needed for Pseurot
• Our future goals are to obtain and use molecules
  unknown to PSEUROT, for example 2-dA cADPR.

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? Acknowledgments?

• Dr. Steven Graham
• St Johns University Faculty and Staff
• Dr. Sat Baccharaya
• Harlem Children Society Staff