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Protein Chemistry Basics

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  1. Protein ChemistryBasics • Protein function • Protein structure • Primary • Amino acids • Linkage • Protein conformation framework • Dihedral angles • Ramachandran plots • Sequence similarity and variation

  2. Protein Function in Cell • Enzymes • Catalyze biological reactions • Structural role • Cell wall • Cell membrane • Cytoplasm

  3. Protein Structure

  4. Protein Structure

  5. Model Molecule: Hemoglobin

  6. Hemoglobin: Background • Protein in red blood cells

  7. Red Blood Cell (Erythrocyte)

  8. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen

  9. Heme Groups in Hemoglobin

  10. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen • Picks up oxygen in lungs, releases it in peripheral tissues (e.g. muscles)

  11. Hemoglobin – Quaternary Structure Two alpha subunits and two beta subunits (141 AA per alpha, 146 AA per beta)

  12. Hemoglobin – Tertiary Structure One beta subunit (8 alpha helices)

  13. Hemoglobin – Secondary Structure alpha helix

  14. β-Hairpin Motif • Simplest protein motif involving two beta strands [from Wikipedia] • adjacent in primary sequence • antiparallel • linked by a short loop • As isolated ribbon or part of betasheet • a special case of a turn • direction of protein backbone reverses • flanking secondary structure elements interact (hydrogen bonds) CS 882 course project

  15. Types of Turns • β-turn (most common) • donor and acceptor residues of hydrogen bonds are separated by 3 residues (ii +3 H-bonding) • δ-turn • ii +1 H-bonding • γ-turn • ii +2 H-bonding • α-turn • ii +4 H-bonding • π-turn • ii +5 H-bonding • ω-loop • a longer loop with no internal hydrogen bonding CS 882 course project

  16. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding

  17. Hydrogen Bonding • Involves three atoms: • Donor electronegative atom (D) (Nitrogen or Oxygen in proteins) • Hydrogen bound to donor (H) • Acceptor electronegative atom (A) in close proximity D – H A

  18. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation

  19. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation • Result: • Closer approach of A to H • Higher interaction energy than a simple van der Waals interaction

  20. Hydrogen Bonding And Secondary Structure beta-sheet alpha-helix

  21. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding • Covalent • Disulfide bonds

  22. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond

  23. Disulfide Bridge

  24. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond • Contribute to the stability of the folded state by linking distant parts of the polypeptide chain

  25. Disulfide Bridge – Linking Distant Amino Acids

  26. Hemoglobin – Primary Structure NH2-Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- Gly-Gly-Glu-….. beta subunit amino acid sequence

  27. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds

  28. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds • Amino Acid • Central carbon (Cα) attached to: • Hydrogen (H) • Amino group (-NH2) • Carboxyl group (-COOH) • Side chain (R)

  29. General Amino Acid Structure H H2N COOH Cα R

  30. General Amino Acid Structure At pH 7.0 H +H3N COO- Cα R

  31. General Amino Acid Structure

  32. Amino Acids • Chiral

  33. Chirality: Glyceraldehyde D-glyderaldehyde L-glyderaldehyde

  34. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain

  35. 20 Naturally-occurring Amino Acids

  36. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain • Classification: • Non-polar (hydrophobic) • Charged polar • Uncharged polar

  37. Alanine: Nonpolar

  38. Serine: Uncharged Polar

  39. Aspartic AcidCharged Polar

  40. GlycineNonpolar (special case)

  41. Peptide Bond • Joins amino acids

  42. Peptide Bond Formation

  43. Peptide Chain

  44. Peptide Bond • Joins amino acids • 40% double bond character • Caused by resonance

  45. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length

  46. Peptide Bond Lengths

  47. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length • Double bond disallows rotation

  48. Protein Conformation Framework • Bond rotation determines protein folding, 3D structure

  49. Bond Rotation Determines Protein Folding