1. 02.28.2006 02.28.2006Protein Data Bank, SDSC Molecular Biology of Cancer: Content, Data and Tools for Biology Curriculum Development Jeff Milton

2. 02.28.2006 02.28.2006Protein Data Bank, SDSC Protein Data Bank Protein Data Bank Worldwide consortium: EBI, RCSB PDB, PDBj Worldwide consortium: EBI, RCSB PDB, PDBj Protein Data Bank Japan, Osaka University Protein Data Bank Japan, Osaka University Research Collaboratory for Structural Bioinformatics, UCSD & Rutgers Research Collaboratory for Structural Bioinformatics, UCSD & Rutgers European Bioinformatics Institute, Cambridge UK European Bioinformatics Institute, Cambridge UK As of Tuesday Feb 21, 2006 there are 35,246 Structures As of Tuesday Feb 21, 2006 there are 35,246 StructuresTuesday Feb 21, 2006Tuesday Feb 21, 2006 Protein, DNA, RNA, Protein complexes Protein, DNA, RNA, Protein complexes Methods: X-ray Crystallography (29,800), NMR (5254), Electron Microscopy and other methods (192) Methods: X-ray Crystallography (29,800), NMR (5254), Electron Microscopy and other methods (192) Data In: ~200 / week Data In: ~200 / week PDB ID required for structure publication PDB ID required for structure publication Structural Genomics Initiative, NIH Structural Genomics Initiative, NIH Reduce the cost and increase the rate of structure determination Reduce the cost and increase the rate of structure determination Discover protein function Discover protein function Research biomedical problems and better therapeutics Research biomedical problems and better therapeutics

3. 02.28.2006 02.28.2006Protein Data Bank, SDSC Education at the Protein Data Bank, SDSC Molecular Biology of Cancer Molecular Biology of Cancer Compelling Animations by Drew Berry Interviews with field experts, Vega Sciences Productions Dissemination: www.pdb.org. 100,000 unique hits a month from ~150 different countries around the worldwww.pdb.org Software for technology enhanced learning Software for technology enhanced learning Molecular viewers, sequence viewers integrated with data Molecule of the Month Molecule of the Month Web content that highlights functional traits of important molecules. Written by David Goodsell, TSRI CalIT2 Virtual Reality CAVE CalIT2 Virtual Reality CAVE Virtual Cave environment for enhanced visualization of protein structures. Directed by Jurgen Shulze, CalIT2

4. 02.28.2006 02.28.2006Protein Data Bank, SDSC Molecular Biology of Cancer Hanahan DHanahan D, Weinberg RA. Department of Biochemistry, Hormone Research Institute, University of California at San Francisco, 94143, USA.Weinberg RA

5. 02.28.2006 02.28.2006Protein Data Bank, SDSC “The Hallmarks of Cancer” 1. Evading apoptosis 2. Self-sufficiency in growth signals 3. Insensitivity to anti-growth signals 4. Tissue invasion & metastasis 5. Limitless replication potential 6. Sustained angiogenesis Hanahan DHanahan D, Weinberg RA. Department of Biochemistry, Hormone Research Institute, University of California at San Francisco, 94143, USA.Weinberg RA

6. 02.28.2006 02.28.2006Protein Data Bank, SDSC Example: Cell proliferation and self-sustained growth How do cells grow and divide? How do cells learn self-sustained growth? What causes a cell to divide? Start with synthesis of the EGF Receptor protein Start with synthesis of the EGF Receptor protein Central Dogma Central Dogma Localization to the cell membrane Localization to the cell membrane Trans-membrane protein Trans-membrane protein EGF and EGF receptor binding  signal into the cell EGF and EGF receptor binding  signal into the cell EGF-EGFR crystal structure EGF-EGFR crystal structure EGF-EGFR crystal structure EGF-EGFR crystal structure Cascade leads to a protein called RAS Cascade leads to a protein called RAS Molecular Switch Molecular Switch “ON”  cell proliferation “ON”  cell proliferation What is different about cancer cells? e.g. cancer cells require little growth factors e.g. cancer cells require little growth factors

7. 02.28.2006 02.28.2006Protein Data Bank, SDSC A simple view of the pathway 1.EGF binds to EGFR 2.2 EGFRs activate a series of proteins that lead to activation of RAS 3.RAS is activated to the “on” position 4.Cell Division 5.RAS is turned “off” Cell enters irreversibly into “S” phase

8. 02.28.2006 02.28.2006Protein Data Bank, SDSC Mutations lead to self sufficient growth signals Mutations in gene regulation Mutations in gene regulation Over-expression of EGF receptor molecules Over-expression of EGF receptor molecules Cell creates growth factors that it can also bind to. Cell creates growth factors that it can also bind to. Too many receptors cause hypersensitivity to ambient signals Too many receptors cause hypersensitivity to ambient signals Mutations in protein structure Mutations in protein structure EGF receptor may be deployed to the membrane with a mutation that causes it to be stuck in the active state. EGF receptor may be deployed to the membrane with a mutation that causes it to be stuck in the active state. RAS or RasGAP may be mutated, preventing RAS from shutting off RAS or RasGAP may be mutated, preventing RAS from shutting off

9. 02.28.2006 02.28.2006Protein Data Bank, SDSC Rational Drug Design: Iressa Lung Cancer Small molecule that inhibits the auto-stimulatory action of a mutated form of the EGF receptor. Small molecule that inhibits the auto-stimulatory action of a mutated form of the EGF receptor. Doesn’t work on over-expression of the wild type EGF receptor Doesn’t work on over-expression of the wild type EGF receptor

10. 02.28.2006 02.28.2006Protein Data Bank, SDSC Real Structural Data Integration: PDBID: 1WQ1, Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmuller, L., Lautwein, A., Schmitz, F., Wittinghofer, A. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science v277 pp.333-338, 1997 3D structure from the PDB highlights the activation mechanism down to the atomic detail. E.G. How Ras is turned off. This structure shows the molecular switch GTP  GDP What are the consequences of mutations that lead to weak interactions between these protein structures?

11. 02.28.2006 02.28.2006Protein Data Bank, SDSC Connections to related diseases Neurofibromatoses: autosomal dominant Neurofibroma is an enzyme that performs the same function as Ras-GAP. i.e. it turns RAS “off” in certain types of neurons. A known germline mutation in NF1 gene causes failure of this mechanism and an accumulation of RAS in the “on” position. This leads to benign tumors in dermal, brain and spine. This usually leads to series developmental problems, blindness. This debilitating disease affects 1 in 3,000 males and females of all races and ethnic groups. 1NF1, Scheffzek, K., Ahmadian, M.R., Scheffzek, K.Ahmadian, M.R. Wiesmuller, L., Kabsch, W., Stege, P.,Wiesmuller, L.Kabsch, W.Stege, P. Schmitz, F., Wittinghofer, A.Schmitz, F.Wittinghofer, A. Structural analysis of the GAP-related domain from neurofibromin and its implications. EMBO J. v17 pp.4313-4327, 1998

12. 02.28.2006 02.28.2006Protein Data Bank, SDSC ImageMap Query Interface. An ImageMap generator that links schematics to a query at PDB, GenBank, etc. Example: 22 TGF-alpha growth factors and 18 Ras signaling proteins Example Tools for curriculum development Sequence Viewer and Molecular Viewer for highlighting point mutations Virtual Lab from the ChemCollective for Biochemistry activities: Develop experiments to determine the binding constant of RasGAP

13. 02.28.2006 02.28.2006Protein Data Bank, SDSC http://www.pdb.org

14. 02.28.2006 02.28.2006Protein Data Bank, SDSC Integrated software tools for enhanced visualization and data mining. Integrated visualization tools Enhanced searching capabilities: This will be expanded to include searching on structures used in animations.

15. 02.28.2006 02.28.2006Protein Data Bank, SDSC What is the Framework for curriculum development and dissemination Documentary design: Interleave fundamental biological mechanisms with popular science concepts Integrate visual animations and imagery of important biological processes Integrate real experimental data with the biology and highlight directions in discovery and therapeutics. Build tools to help curriculum developers integrate PDB Data with content and publish to the PDB web site according to relevant standards.

16. 02.28.2006 02.28.2006Protein Data Bank, SDSC NSF, Informal Science Education (ISE) Designed to increase interest, engagement and understanding of science, technology, engineering, and mathematics. Designed to increase interest, engagement and understanding of science, technology, engineering, and mathematics. Not curriculum development Not curriculum development Framework for curriculum development Framework for curriculum development Capture important biological processes and provide tools for activity development Capture important biological processes and provide tools for activity development Teachers don’t have time Teachers don’t have time Activities archived and disseminated according to national science standards. Activities archived and disseminated according to national science standards. Assessment? Assessment? http://nsf.gov/pubs/2006/nsf06520/nsf06520.htm http://nsf.gov/pubs/2006/nsf06520/nsf06520.htm http://nsf.gov/pubs/2006/nsf06520/nsf06520.htm