Presentation on theme: "A glimpse into the course material Topic 1. Course Information Curricula materials: Structural Bioinformatics, 2nd edition Editors: Gu and Bourne Publisher:"— Presentation transcript:
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: Course website: Syllabus: 02_syllabus.pdf Acknowledgement: Many of the slides used in this class were originally created by Dr. Jun-tao Guo. Thanks for sharing Jun-tao!
Crick, F.H.C. (1958): On Protein Synthesis. Symp. Soc. Exp. Biol. XII, Crick, F. (1970): Central Dogma of Molecular Biology. Nature 227, The Central Dogma of Molecular Biology Protein-DNA 2I1C 4TRA RNA Protein-RNA
Protein Functions Catalysis : Enzymes Structural proteins : keratin, actin, tubulin… Signalling proteins : insulin, growth hormone… Immunity : antibodies Transport proteins : ion transport, O 2 transport… …
>1MBN:_ MYOGLOBIN (154 AA) MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHL KTEAEMKASEDLKKAGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKI PIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAAKYKEL GYQG Protein name Protein sequence Protein structure Oxygen storage Protein function Protein and Protein Structure
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:
“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 The 1962 Nobel Prize in Chemistry Goes to… Max Perutz and John Kendrew "for their studies of the structures of globular proteins”.
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".
Experimental Methods for Structure Determination “Protein Structure and Function”, Petsko GA and Ringe D X-ray crystallography Nuclear magnetic resonance (NMR) Protein purification
Protein Data Bank (PDB)
Yearly Growth of Total Protein Structures Year The first reported structure is myoglobin PDB was set up in 1971 As of Jan. 5, 2010, there are 57,769 protein structures
Laskowski, RA. Thornton, JM. Nature Review Genetics, 9: Timeline of Structural Determination of Some Key Bio-molecules
Molecular Machinery: A Tour of the Protein Data Bank
Structure Visualization Pymol image Gallery:
Protein Structure Classification Hou et al. PNAS : Class (C), Architecture (A), Topology (T) Homologous superfamily (H). “Evolutionary relationship?”
MVLSEGEWQLVLHVWAKVEADVAGHG QDILIRLFKSHPETLEKFDRFKHL KTEAEMKASEDLKKAGVTVLTALGAI LKKKGHHEAELKPLAQSHATKHKI PIKYLEFISEAIIHVLHSRHPGNFGA DAQGAMNKALELFRKDIAAKYKEL GYQG Protein Structure Prediction and CASP CASP: Critical Assessment of techniques for protein Structure Prediction **Modified image from Yang Zhang’s lab at University of Michigan
Disordered region prediction Transmembrane segment prediction Solvent accessibility prediction Residue-residue contact prediction Side-chain packing prediction Secondary structure prediction Loop modeling Sub-problems of Protein Structure Prediction **Images from Pondr and Rost, 1998
Pazos and Sternberg, PNAS, 2004, 101: Prediction of Protein Function From Structure Number of new functions Hypothetical SCOP domains
Prediction of Protein Function From Structure Watson et al. J Mol Biol Apr 13;367(5): Breakdown of prior information for the 282 MCSG structures
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. ”
Dynamic Personalities of Proteins nitrogen regulatory protein C