CH339K

1. CH339K Proteins: Higher Order Structure

2. Higher Levels of Protein Structure

3. Side chains hang off the backbone Repetitive background: -N-C-C-N-C-C-

4. The shape of the peptide chain can be defined by the three consecutive bond torsional anglesBond Rotation Torsion angle definedNH to Ca free phi Ca to C=O free psiC=O to NH rigid planaromega

5. Since w is constrained, only f and y can vary There are steric restrictions on what values they can assume

6. Permissable F-Y Angles(Ramachandran Plot)

7. Secondary Structures • Represent interactions among backbone atoms • Examples • a-helices • Other helices • b-sheets • b- and g-turns • These structures have characteristic f and y angles

8. a-helix H bonds between • carbonyl O of residue n • amide H of residue n+4

9. R/V Alpha Helix Woods Hole Oceanographic Institute 1966-2011

10. Helical parameters – Pitch and Rise

11. Backbone forms helix Side chains extend outwards f ≈ -57o • ≈ -47o 3.6 residues/turn

12. Helix Types a-helix: C=O H-bonded to NH of residue n+4 (aka 3.613 helix) 310 helix: C=O H-bonded to NH of residue n+3 • (f ≈ -49oy ≈ -26o) p-helix: C=O H-bonded to NH of residue n+5 (aka 4.116 helix) (f ≈ -57oy ≈ -80o)

13. Helix terminologyH-bond makes a closed loop from amide H through backbone through carbonyl ODefine helix by (a) Nbr of residues per turn (e.g. 3.6 for a -helix)(b) Nbr of atoms in the loop (e.g. 13 for a -helix)

15. b-Sheets • Can be thought of as helix with two residues per helix • Backbone atoms run in a plane • Side chains extend up and down from plane • f ≈ -110o to -140o • y ≈ +110o to +135o

20. C=O of residue n with N-H of residue n+3

21. Gamma Turns: C=O of residue n with N-H of residue n+2

22. F-y Angles for Secondary Structures NOTE: Left-handed a-helix has f = +57, y = +47

23. Ramachandran Plot: Blue areas are permitted F and Y angles

24. Ramachandran plot for pyruvate kinase

25. Tertiary Structures • Determined by side chaininteractions • Salt links • H-Bonds • Disulfides • Hydrophobic interactions • Fibrous Proteins • Globular Proteins

26. Fibrous Proteins Keratin a-keratin: hair, horns, and hoofs of mammals b-keratin: scales, claws and shells of reptiles, beaks and claws of birds, porcupine quills

27. a-keratin • Lots of Ala, Gly, Cys • All a-helix Right handed Left handed

29. Disulfides in the Barber Shop Sodium thioglycolate Various peroxides

30. Fibrous Proteins - Fibroin 75-80% Ala/Gly 15% Ser

33. Within a fiber: crystalline regions are separated by amorphous regions.

34. Fibrous Proteins - Collagen Left handed helix of tropocollagen forms right handed triple helix of collagen.

36. Hydroxyproline participates in H-bonding between tropocollagen chains

37. (1) (2) In the absence of vitamin C, reaction 2 oxidizes Fe2+ to Fe3+.

38. Lack of hydroxyls causes serious destabilization of the triple helix

39. Arrrrr… Scurvy • Weakness • Paleness • Sunken eyes • Tender gums and/or tooth loss • Muscular pain • Reopening of old wounds or sores • Internal bleeding • Loss of appetite • Bruising easily • Weight loss; inability to gain weight • Diarrhea • Increased heart rate • Fever • Irritability • Aching and swelling in joints • Shortness of breath • Fatigue

40. British Empire at its Peak • A healthy navy is a victorious navy (of course, my ancestors were less than thrilled…)

41. Protein structure cartoons a-helix Antiparallel b-sheet

42. Globular Proteins (examples)

44. Motifs – common stable folding patterns Found in proteins w/ different functions result from the physics and chemistry of the structure

45. More motifs

46. Domains – • Common patterns found in different proteins • Typically have similar function • Caused by evolution (gene recombination / duplication) Ricin B chain • Two domains • Each domain is a trefoil • 3 repeats of a sheet-loop structure • i.e. 6 repeats of a primitive fold

47. C-rich Domain of Earthworm Mannose Receptor Fibroblast Growth Factor

48. Domains can be shared among proteins

50. Quaternary Structure (Hemoglobin)