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Protein Modeling (Coaches Clinic)
Shuchismita Dutta October 27, 2007
2007 State Champions: Ola Hadaya, Sarah Goodman, and Yong Kim from Princeton High School
Protein Modeling (Coaches Clinic) Shuchismita Dutta October 27, - - PowerPoint PPT Presentation
Protein Modeling (Coaches Clinic) Shuchismita Dutta October 27, - - PowerPoint PPT Presentation
Protein Modeling (Coaches Clinic) Shuchismita Dutta October 27, 2007 2007 State Champions: Ola Hadaya, Sarah Goodman, and Yong Kim from Princeton High School General Introduction Water Amino Acids Protein folding Water: love it or leave it
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Water: love it or leave it
l Hydrogen bonds l Hydrophobic and Hydrophilic structures
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Amino Acids
Hydrophobic Hydrophilic Acidic Basic
From www.bachem.com
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Proteins
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Primary Secondary Tertiary Quaternary …LWGK…
L W G K
Alpha-helix Beta chain of Hemoglobin Hemoglobin
Protein Structure
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Some Rules to ‘Fold’ a Protein
l Covalent interactions
l Protein Sequence l Di-sulfide bridges
l Non-covalent interactions
l Hydrophobic interactions l Hydrogen bonds l Salt bridges (positive negative interactions) l Metal coordination
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Protein Modeling: Toober and Thumb Tacks model
l 1Toober l 10 thumb tacks
l 1 Blue (Basic) l 1 Red (Acidic) l 4 Yellow (Hydrophobic) l 2 White (Hydrophilic) l 2 Green (Cysteine) http://www.3dmoleculardesigns.com/15_Tacks.pdf
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Interaction rules
l Hydrophobic (yellows should be away from
water, and whites should be near water)
l Charge based (red and blue should pair up) l Disulphide (the greens should pair up to form
a bond)
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PDB & Protein Models
Protein Structures Protein Data Bank Protein Modeling
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Why Structure?
l Allows you to “visualize” the shape and
details of the protein
l Offers clues about the role in the body l May hold key to developing new medicines
and diagnostic procedures for diseases like avian flu, HIV, West Nile Virus, parts of the protein associated with Alzheimer’s disease, Cancers, etc.
shown: the ribosome
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Understanding Protein Structures
X-ray
(X-ray crystallography)
NMR
(Nuclear Magnetic Resonance)
EM
(Electron Microscopy)
Protein Data Bank Free download for use
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The Protein Data Bank
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The Structure Explorer Page
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The PDB file
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The PDB file – con’t.
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Visualization (RasMol or Jmol)
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Structure Representation
Spacefill Wireframe Ribbons
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WebMol
Graphics
KiNG Jmol Default image Protein Explorer
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Zinc Finger Toober Model
l Download the 1ZAA pdb file (www.pdb.org) l Create image in Jmol, identify key features l Fold a Mini-Toober model
l Material modifications
l Blue thumb tack (N-terminus) l Red thumb tack (C-terminus) l Colored Pipe-cleaners to represent Cys, His, Arg18,
Phe16 and Leu22
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NJSO 2008
Basic information
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Information
l Regional and State level contests
l Protein Calmodulin (PDB ID 1CLL)
l Rules
l Pre-build: Bring in toober model and short abstract l On-site build: Build a designated part of 1CLL
using a mini-Toober and Jmol
l On-site exam: Answer questions about structure,
function, importance and history of modeled
- protein. Materials will be provided.
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Molecule of the Month
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Structure Explorer Page
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Jmol
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How we judge
Rubrics available from education.pdb.org/olympiad
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Help
l Details and links at
http://education.rcsb.org/olympiad/
l If you have questions or to borrow the