How do I access the

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How do I access the 3D structure of a protein?
Tristan J. Fiedler Computational Postdoctoral
Fellow Laboratory of Professor Lincoln
Stein 24-25 Apr 07 Woodbury Genome Center Cold
Spring Harbor Laboratory
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Asked What are proteins? the public are
perplexed
Antibodies Receptors Enzymes Neurotransmitters Cha
nnels pores
http//www.rothamsted.ac.uk/notebook/courses/guide
/prot.htm
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Research Areas
wwPDB Visualization Secondary Structure
Classification Structure Determination Structure
Analysis (Geometry) Alignment Prediction of
Structure Protein - Ligand Docking Molecular
Dynamics
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Fundamentals of Structural Biology
C-C 1.54 Å (0.154 nm) CC 1.34 Å C-N 1.47 Å
wps.prenhall.com/wps/media/objects/602/616516/Medi
a_Assets/Chapter07/Text_Images/FG07_02.JPG
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Fundamentals of Structural Biology
www.elmhurst.edu/chm/vchembook/582dnadoublehelix.
html
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Fundamentals of Structural Biology
Peptide bond is single, double or partial
double?
www.codefun.com
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Fundamentals of Structural Biology
What protein is this? (latest ab)
http//www.rothamsted.ac.uk/notebook/courses/guide
/images/secst2.gif
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Fundamentals of Structural Biology
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Structural Biology - general stats

• Central Dogma (Protein nucleotide)
• How many aa? Single letter abbrev.
• 20 aa, not BJOUXZ
• How large are most prok proteins?
• 300 aa/protein prok
• How large are most euk domains?
• 200 aa/domain euk
• Ca to Ca distance ?
• 3.8 Å
• average residue Leucine
• non-H backbone atoms?
• 4
• non-H side chain atoms?
• 4
• Volume
• 150 Å3
• Many xyz triplets/protein !

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PDB Searches PDB tutorial www.rcsb.org/pdbstati
c/tutorials/tutorial.html

• enable java
• http//pdbbeta.rcsb.org - (click help anytime)
• Click PDB statistics - Growth of Released
  Structures, Summary Table, Unreleased,
  Redundancy
• enter PDB ID 1AEW
• On Result Page - click on Structure Summary tab
• Image, Exp Details, Functional Classif, Chemical
  Components
• Images Visualization Asymm Unit vs Biological
  Molecule
• Who solved the structure (not paper citation)?
• Hempstead, P.D., Yewdall, S.J., Lawson, D.M.,
  Harrison, P.M., Artymiuk, P.J.
• How big is the protein (hint abstract)?
• 24 mer (each is 174 aas). Any other 24-mers in
  the PDB?
• Yes, ferritins and glycerol phosphate dehydratase
  (click keyword in abstract)

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PDB SearchesPDB tutorial www.rcsb.org/pdbstati
c/tutorials/tutorial.html

• Type of structure ? NMR, Computational Model,
  X-ray diffraction
• X-ray diffraction
• Electron density (EDS)
• Browser dependent, select residue graph gt Rama
• Protein function
• iron storage
• Crystallized from what source?
• Horse
• How many Equus protein in PDB?
• 28 (Results per page gt 100 Show Query
  Details)
• What are the horse proteins?
• Alcohol dehydrogenase, Ferritin, Allergen Equ C,
  Myoglobin,

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PDB Searches

• Back to 1AEW Structure Summary Page
• What other iron storage protein structures are
  known and how many total?
• Apoferritin, bacterioferritin,ferritin - 19 total
• Back to 1AEW Structure Summary Page
• Were any heteroatoms determined in the structure?
• Cd2 (Ligand Interaction - view!)
• Why is Cadmium in the structure?
• http//www.pubmedcentral.gov/articlerender.fcgi?ar
  tid1186421
• What is the biologically active protein size?
• Display Files gt PDB file -- 24 mer of 174 aas
• Are all cadmium ions tightly bound?
• No, 50 and 33 occupancy are observed
• What is the predominant secondary structure?
• alpha helices in an up/down arrangement
• Geometry Tab gives bond length angle stats

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PDB Searches

• Blue - determined by experiment
• Red - interpretation of primary data
• Viewing
• Various viewers - webmol
• left mouse - Rotate, right mouse - Zoom, center
  mouse - translate
• alter molecular surface (SASA, vdw, cavity)
• Coordinates
• Display Files gt PDB file (or click icon by
  Structure ID)
• More searches
• Blue - text is a new query term (eg SCOP
  classification)
• if single hit, opens structure page, if not,
  opens a query results page

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Finding Information

• Two ways to search abstract
• Pubmed icon
• PDB searchable abstract
• What is the formula weight of the protein?
• 19859.6 on Biology Chemistry tab (down on both
  sites currently)
• To find all ferritin structures enter Ferritin
  in main search box
• Author Search
• autocomplete feature
• Davey, CA - 6 structures (myeloperoxidase,
  nucleosome core, SsuD)
• Related structures
• Structure summary gt SCOP classification
• How many (all alpha) proteins?
• 62 structures in Ferritin family
• Medical Relevance

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Quick viewing
http//www.rcsb.org/pdb/explore/images.do?struct
ureId1A2V rotate, etc in IMAGE gt Interactive
view Copper Amine Oxidase Hansenula
polymorpha PDB ID 1A2V Slow browsers - use
1p6v
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Resources
Structural Bioinformatics (Methods of Biochemical
Analysis v 44) Philip E. Bourne, Helge
Wessig Protein Structure Prediction A Practical
Approach Michael J. E. Sternberg Introduction to
Protein Structure Carl Branden Foundations of
Structural Biology Leonard J. Banaszak Crystallog
raphy Made Crystal Clear Gail Rhodes Bioinformat
ics Sequence and Genome Analysis David W.
Mount Acta Crystallographica Section F
Introduction to Structural Bioinformatics www.bio
informaticscourses.com/ISB/ Wessig, 2004