791_ak_lecture1

791_ak_lecture1 - Protein Structure Outline of the next...

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Unformatted text preview: Protein Structure Outline of the next part of the course 4/1 Protein Structure Comparison & Classification 4/6 Principles of Molecular Mechanics 4/8 X-ray crystallography and NMR 4/13 Modeling Mutants and Homologs 4/15 Threading and Ab Initio Structure Prediction 4/22 Computational Protein Design 7.91 April 1, 2004 Amy Keating 7.91 April 1, 2004 Amy Keating Introduction to Protein Structure & Classification Protein structures basics where to find them how to look at them what they can tell you structural and evolutionary comparisons PDB ID: 1HCL Schulze-Gahmen, U., J. Brandsen, H. D. Jones, D. O. Morgan, L. Meijer, J. Vesely, S. H. Kim. "Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine." Proteins 22 (1995): 378. The Protein Data Bank (PDB - http://www.pdb.org/) is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. The Protein Data Bank. Nucleic Acids Research 28 (2000): 235-242 . (PDB Advisory Notice on using materials available in the archive: http://www.rcsb.org/pdb/advisory.html) Review of protein structure hierarchy Primary structure MAAAAAAGPEMVRGQVF 20 amino acids hydrophobic/hydrophilic acidic/basic large/small specialized (Gly,Pro,Cys) C C O- O H Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) H H 3 N + C C O- O H CH 3 CH 3 CH 3 H 3 N + C C O- O H CH H 3 N + C C O- O H CH H 3 N + H 3 C OH CH 3 CH 3 CH 3 C C O- O H CH 2 CH 2 CH 3 C C O- O H H 3 N + CH 2 CH 2 C C O- O H H 3 N + CH 2 S CH 3 H 3 N + C C O- O H H 3 N + CH 2 C C O- O O H H 3 N + CH 2 C C O- O H H 3 N + CH 2 CH 2 C NH 2 C C C O- O H H 3 N + CH 2 C C O- O H H 2 N + H 2 C C C O- O O H H 3 N + CH 2 C C O- O H H 3 N + CH 2 CH 2- O C O C C O- O H H 3 N + CH 2 CH 2 CH 2 CH 2 NH 3 + NH 2 + NH + NH C C O- O H H 3 N + CH 2 C C O- O H H 3 N + CH 2 CH 2 CH 2 C NH NH 2- O C O NH 2 CH 2 CH 2 NH C C O- O H H 3 N + CH 2 C C O- O H H 3 N + CH 2 SH OH C C O- O H H 3 N + CH OH Leucine (Leu, L) Isoleucine (IIe, I) Methionine (Met, M) Serine (Ser, S) Aspartic acid (Asp, D) Glutamic acid (Glu, E) Lysine (Lys, K) Arginine (Arg, R) Histidine (His, H) Threonine (Thr, T) Cysteine (Cys, C) Tyrosine (Tyr, Y) Asparagine (Asn, N) Glutamine (Gln, Q) Acidic Basic Phenylalanine (Phe, F) Tryptophan (Trp, W) Proline (Pro, P) Electrically charged Polar, Hydrophillic R-groups Nonpolar, Hydrophobic R-groups O N N O N N O N N N O O N N S Representations of Protein Structure Review of protein structure hierarchy Secondary structure - why do you get regular secondary structure?...
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791_ak_lecture1 - Protein Structure Outline of the next...

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