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Protein structures

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  1. Protein structures Haixu Tang School of Inforamtics

  2. A covalent peptide bond

  3. Protein conformation is specified by tts Amino Acid sequence • Steric interactions • Weak non-covalent bonds • hydrogen bonds • ionic bonds • van der Waals attractions • Hydrophobic interaction • distribution of its polar and nonpolar amino acids

  4. Protein folding: lowest energy conformation

  5. Protein denaturalization

  6. Visualizing protein conformations • Protein structures in atomic level • Protein Data Bank (PDB) http://www.rcsb.org • Pymol: http://pymol.sourceforge.net/ • Rasmol: http://www.umass.edu/microbio/rasmol/

  7. Protein secondary structure

  8. Secondary structure prediction • Prefer a-helix: Ala, Leu, Met, Phe, Glu, Gln, His, Lys, Arg (sidechains cover and protect the backbone H-bonds) • Prefer b-sheet: Tyr, Trp, Phe, Ile, Val, Thr, Cys (large bulky sidechains) • Disrupt secondary structure: Gly, Pro, Ser, Asp, Asn (small, restrained, or sidechain hydrogen bonds)

  9. Coiled coil

  10. Protein Domains • Independent structural unit • Independent function • Independent folding • Independent evolve

  11. Protein families

  12. Protein structural classification(SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/) • Class • Folds • Super-families • Families

  13. Sulfur-sulfur (disulfur) bonds

  14. Assembly of Large Structures

  15. Experimental determination of protein structures • X-ray crystallography • NMR (Nuclear Magnetic Resonance) Spectroscopy

  16. X-ray crystallography

  17. NMR spectrum