Project Prion: Evolution and Structural Connections

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Project Prion Evolution and Structural
Connections
MDG5101 Group 2
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Historical Background

• The earliest record dates from several centuries
  ago, when scrapie was first observed in sheep
• In 1972, Tikvah Alper was the first to suggest
  the agent of scrapie might replicate without
  nucleic acid
• And in 1982, Stanley Prusiner coined the term
  prion (pree-on)

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What is prion?

• A prion has been defined as "small proteinaceous
  infectious particles which resist inactivation by
  procedures that modify nucleic acids".
• ------ Prion Diseases Just as nucleic acids can
  carry out enzymatic reactions, proteins
  can be genes.   Reed Wickner.
  Microbiology _at_
  Leicester Virology Prions

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Prion conformations

• http//users.rcn.com/jkimball.ma.ultranet/BiologyP
  ages/P/Prions.html

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Classification
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Spongiform Encephalopathies
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Usefulness of Bioinformatics

• Prion diseases, e.g. CJD, can take on different
  forms
• due to specific mutations in the primary amino
  acid sequence

• Protein functions dependent on Tertiary or
  Quaternary Structure
• Mutations can lead to a change in 3D structure
• ? could change protein function

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Usefulness of Bioinformatics

• Various 3D protein visualization tools available
  
• RasMol, CHIME, MAGE, DeepView, etc
• Used to predict 3D structures of proteins
• Enable us to compare structures of various
  mutated forms of human PrP
• Allows us to visualize the change in protein
  structures caused by different mutations

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Our Bioinformatics Approach

• Searching
• Visualising
• Validating
• Predicting

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Searching
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Searching
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Searching for Structures

• Most commonly used protein databases
• RCSB PDB
• NCBI Entrez Structure
• Search query human prion

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Visualizing

• RasMol
• DeepView
• CN3D
• Features Vs Learning Curve

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Visualizing Human PrPc
RasMol
DeepView
CN3D
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Validating

• Make point mutations, using DeepView, on the
  human PrPc
• But how accurate will our model be in simulating
  mutation and predicting its effects?

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Validating
Variants of PrP found in Creutzfeldt-Jakob
Disease (CJD)
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Validating
Solution Structure of the E200K Variant of Human
PrP (NMR spectroscopy)

• The only major consequence of the mutation is the
  change of surface electrostatic potential. (red
  -, blue )

Backbone tertiary structure is nearly identical.

• This change may disturb the interaction of PrP
  with auxiliary proteins/chaperones or cellular
  membranes.

• This may cause a spontaneous PrPc to PrPsc
  conversion in the E200K form of hereditary prion
  disease.

Zhang Y, et al.J. Biol. Chem. 27533650-33654(2000
).
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Validating Backbone Structure
E200K
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Validating Electrostatic Potential
red - blue
E200K
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Exception

• Variant V203I created
• No difference in electrostatic potential
  distribution after mutation
• Mutation may cause change in H-bond distribution

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Exception (Electrostatic Potential)
red - blue
V203I
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Exception (H-bonds)
E200K
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Predicting

• Does point mutation(s) really affect conformation
  of the prion?
• Key factors for protein folding
• H-bonds
• Surface Electrostatic Potential

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Predicting backbone structure and H-bond
distribution
E200K E196K V203I E211Q
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Predicting surface electrostatic potential
distribution
red - blue
E200K E196K V203I E211Q
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Predicting CJD PrPc Model

• How will the CJD PrPc protein structure look like
  after mutations?

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CJD PrPc Model (Backbone structure and H-bonds)
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CJD PrPc Model(Electrostatic Potential)
red - blue
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Conclusion

• Mutations can lead to changes in distributions in
  H-bonds and electrostatic potential
• Changes may increase the PrPcs susceptibility to
  conformational change towards PrPsc

• Bioinformatics is definitely a useful and
  essential tool for visualising, predicting and
  understanding protein structures

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Thanks For Your Attention!