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Introduction to Structural Bioinformatics

Introduction to Structural Bioinformatics. A glimpse into the course material. Topic 1. Course Information. Curricula materials: Structural Bioinformatics , 2nd edition Editors : Gu and Bourne Publisher: Wiley - Blackwell Year: 2009 ISBN -10: 0470181052 Course website:

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Introduction to Structural Bioinformatics

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  1. Introduction to Structural Bioinformatics A glimpse into the course material Topic 1

  2. Course Information Curricula materials: Structural Bioinformatics, 2nd edition Editors: Gu and Bourne Publisher: Wiley-Blackwell Year: 2009 ISBN-10: 0470181052 Course website: http://coitweb.uncc.edu/~drlivesa/BINF6202.html Syllabus: http://coitweb.uncc.edu/~drlivesa/BINF6202/BINF6202_syllabus.pdf Acknowledgement: Many of the slides used in this class were originally created by Dr. Jun-taoGuo. Thanks for sharing Jun-tao!

  3. The Central Dogma of Molecular Biology Protein-DNA 2I1C 4TRA Protein-RNA RNA Crick, F.H.C. (1958): On Protein Synthesis. Symp. Soc. Exp. Biol. XII, 139-163. Crick, F. (1970): Central Dogma of Molecular Biology. Nature 227, 561-563.

  4. Protein Functions Catalysis: Enzymes Structural proteins: keratin, actin, tubulin… Signalling proteins: insulin, growth hormone… Immunity: antibodies Transport proteins: ion transport, O2 transport… …

  5. Protein and Protein Structure Proteinname Protein sequence >1MBN:_ MYOGLOBIN (154 AA) MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHL KTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKI PIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKEL GYQG Protein structure Protein function Oxygen storage

  6. Molecular modeling with kindergarten supplies Linus Pauling won the Nobel Prize in Chemistry in 1954 "for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances". Pauling summarized his work on the chemical bond in The Nature of the Chemical Bond, one of the most influential chemistry books ever published. See: http://www.youtube.com/watch?v=yh9Cr5n21EE

  7. The 1962 Nobel Prize in Chemistry Goes to… Max Perutz and John Kendrew "for their studies of the structures of globular proteins”. “As a result of Kendrew's and Perutz' contributions it is thus becoming possible to see the principles behind the construction of globular proteins. The goal has been reached after twenty-five years' labour, and initially with only modest results” --Professor Hagg

  8. The 1962 Nobel Prize in Physiology or Medicine… The Nobel Prize in Physiology or Medicine 1962 was awarded jointly to Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material".

  9. Experimental Methods for Structure Determination X-ray crystallography Nuclear magnetic resonance (NMR) Protein purification “Protein Structure and Function”, Petsko GA and Ringe D

  10. Protein Data Bank (PDB) http://www.rcsb.org/pdb/

  11. Yearly Growth of Total Protein Structures • The first reported structure is myoglobin • PDB was set up in 1971 • As of Jan. 5, 2010, there are 57,769 protein structures Year

  12. Timeline of Structural Determination of Some Key Bio-molecules Laskowski, RA. Thornton, JM. Nature Review Genetics, 9:141-151

  13. Molecular Machinery: A Tour of the Protein Data Bank

  14. Structure Visualization Pymol image Gallery: http://www.pymol.org

  15. Protein Structure Classification “Evolutionary relationship?” Class (C), Architecture (A), Topology (T) Homologous superfamily (H). Hou et al. PNAS 2005 102:3651-3656

  16. Protein Structure Prediction and CASP MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHL KTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKI PIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKEL GYQG CASP: Critical Assessment of techniques for protein Structure Prediction http://predictioncenter.org/ **Modified image from Yang Zhang’s lab at University of Michigan

  17. Sub-problems of Protein Structure Prediction • Disordered region prediction • Transmembranesegment prediction • Solvent accessibility prediction • Residue-residue contact prediction • Side-chain packing prediction • Secondary structure prediction • Loop modeling **Images from Pondr and Rost, 1998

  18. Prediction of Protein Function From Structure Number of new functions Hypothetical SCOP domains Pazos and Sternberg, PNAS, 2004, 101:14754-14759

  19. Prediction of Protein Function From Structure Breakdown of prior information for the 282 MCSG structures Watson et al. J Mol Biol. 2007 Apr 13;367(5):1511-22

  20. Dynamic Personalities of Proteins Richard Feynman said,“Everything that the living things do can be understood in terms of the jigglings and wigglings of atoms.”

  21. Dynamic Personalities of Proteins nitrogen regulatory protein C

  22. My lab = Biophysics + Bioinformatics

  23. Protein Design Problems Annu. Rev. Biochem. 2008, 77:363 & Nature, 2009, 462:182

  24. Protein-protein Docking and CAPRI **Image from San Diego Supercomputer Center at UC San Diego http://www.sdsc.edu/Gallery/vs_protein_docking.html CAPRI: Critical Assessment of PRediction of Interactions

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