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Protein structures Haixu Tang School of Inforamtics A covalent peptide bond 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 Protein folding: lowest energy conformation Protein denaturalization 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/ Protein secondary structure 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) Coiled coil Protein Domains • Independent structural unit • Independent function • Independent folding • Independent evolve Protein families Protein structural classification (SCOP: http://scop.mrc-lmb.cam.ac.uk/scop/) • Class • Folds • Super-families • Families Sulfur-sulfur (disulfur) bonds Assembly of Large Structures Experimental determination of protein structures • X-ray crystallography • NMR (Nuclear Magnetic Resonance) Spectroscopy X-ray crystallography NMR spectrum