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Protein: Linear chain of amino acids called residues (4 in this toy protein)

Leu. Ser. O. O. H. H. H. C. C. C α. N. N. C α. C α. C α. N. C. N. C. O. H. H. O. O. Trp. Lys. Protein: Linear chain of amino acids called residues (4 in this toy protein). The backbone (red) is the same for all residues. The side-chains (green) vary.

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Protein: Linear chain of amino acids called residues (4 in this toy protein)

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  1. Leu Ser O O H H H C C Cα N N Cα Cα Cα N C N C O H H O O Trp Lys Protein: Linear chain of amino acidscalled residues (4 in this toy protein) The backbone (red) is the same for all residues. The side-chains (green) vary.

  2. The 20 amino acids found in nature

  3. Patrice Koehl

  4. The Peptide Bond Peptide bond H Rn H O N Ca C C Ca N H O R H n+1 The peptide bond is planar Patrice Koehl

  5. Degrees of Freedom in Proteins Bond length Bond angle Dihedral angle 1 2 3 1 4 2 + Patrice Koehl

  6. Torsion angles avoid eclipsing

  7. Torsion angles characterize residue conformation φ ψ Backbone: 3 angles per residue :f,ψandw Sidechain: 1 to 7 angles,c; eachchas 3 favored values: 60o, -60o, 180o. Patrice Koehl

  8. Proteins fall to lowest free energy conformation Protein Folding in the Landscape Perspective: Chevron Plots and Non-Arrhenius Kinetics Hue Sun Chan and Ken A. Dill,Proteins: Structure, Function, and Genetics, 30:1 Free energy (vertical axis) as a function of conformation. The two horizontal axes represent torsional degrees of freedom.

  9. RAMACHANDRAN PLOTS y y f f All residues, but glycine Glycine Acta Cryst. (2002). D58, 768-776

  10. Small Amino acids: Glycine H CA C Highly flexible Patrice Koehl

  11. Hydrophobic Amino acids (1) CH3 CH3 CG2 CG1 CH3 CH CB CB CA C C CA Ala Val Patrice Koehl

  12. Hydrophobic Amino acids (2) CD2 CD CH3 CH3 CH3 CD1 CH CH2 CH3 CG2 CG CG1 CH CH2 CB CB CA C C CA Ile Leu Patrice Koehl

  13. Hydrophobic Amino acids (3) CG H CE1 CB C CZ CH CH CD1 CD CH CH CE2 CG N CA C CD2 CH2 CB CH2 CH2 CH2 CA C N C Phe Pro Patrice Koehl

  14. Hydrophobic Amino acids (4) CH CZ2 H H CE CH3 C CE2 NE1 N CZ3 HC C S CD2 CH SD CD1 HC C CE3 CH2 C C CG CG H CB CH2 CH2 CB C C CA CA Met Trp Patrice Koehl

  15. Polar Amino acids (1) CG2 OG1 OH CH3 CB CB OH CH CH2 OG C C CA CA Ser Thr Patrice Koehl

  16. Polar Amino acids (2) OH OH C CE2 CZ CH CH CD2 CE1 CH CH CD1 C CG CB CH2 CA C Patrice Koehl

  17. Polar Amino acids (3) OE1 OD1 O NH2 O NH2 C CD NE2 ND2 C CB CG CB CH2 CG CH2 CH2 C CA C CA Asn Gln Patrice Koehl

  18. Polar Amino acids: Cysteine SG S CB pKa sidechain: 8.3 CH2 C CA SG1 CB2 Can form disulphide bridges in proteins CB1 CA1 SG2 CA2 Patrice Koehl

  19. Polar Amino acids: Histidine NE2 CD2 CE1 N C H CH N H ND1 C CB CG CH2 C pKa sidechain: 6.04 CA Patrice Koehl

  20. Different ionic states of the Histidine sidechain H + N C H CH N H C H CH2 N C H N C H C CH N CH N H C C H CH2 CH2 N C H + C C CH N H C CH2 C Patrice Koehl

  21. Charged Amino acids (1) OD1 OE1 - - O O O O OE2 CG OD2 C C CD CG CB CH2 CB CH2 CH2 C CA CA C pKa sidechain: 3.9 pKa sidechain: 4.25 Asp Glu Patrice Koehl

  22. Charged Amino acids (2) NH2+ NH2 NZ NH3+ NH1 CZ NH2 CZ CH2 NE CE CD CD CH2 NE CH2 CG CG CH2 CH2 CB CH2 CB CH2 CA C CA C pKa sidechain: 9.2 pKa sidechain: 12.5 Lys Arg Patrice Koehl

  23. Molecular Visualization Software • Pymol: the standard for publications youtube tutorial at: http://www.youtube.com/watch?v=vDlyfk2zC-k A more complete tutorial can be found at: http://www.ebi.ac.uk/~gareth/pymol/ • Jmol • DS Visualizer displays rotamers off of a common mainchain

  24. Summary • Proteins in nature are a string of residues, each of which is one of the 20 amino acids. • Amino acids all have a backbone made of atoms N-Cα-CO in a conformation characterized by the torsion angles , , and • The remaining atoms form side-chains whose conformations are characterized by their torsion angles. Side-chains can be hydrophobic, polar or charged. • Hydrophobic amino acids: GLY,ALA,VAL,ILE,LEU,PHE,PRO,MET,TRP • Polar amino acids: CYS, SER, THR, HIS, ASN, GLN, TYR • Charged amino acids: ASP, GLU, ARG, LYS f y 

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