html5-img
1 / 74

CH339K

CH339K. Proteins: Higher Order Structure. Higher Levels of Protein Structure. Side chains hang off the backbone. Repetitive background: -N-C-C-N-C-C-.

cosmo
Télécharger la présentation

CH339K

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 characteristicfandyangles

  8. a-helix Pauling, Corey, and Branson (1951) H bonds between • carbonyl O of residue n • amide H of residue n+4 Each amino acid is rotated 100o from the previous one. 3.6 amino acids per turn

  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)

  14. Idealized Helices

  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

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

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

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

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

  20. Ramachandran plot for pyruvate kinase

  21. Tertiary Structures • Three dimensional folding • Determined by side chaininteractions • Salt links • H-Bonds • Disulfides • Hydrophobic interactions • Fibrous Proteins • Globular Proteins

  22. 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

  23. a-keratin • Lots of Ala, Gly, Cys • All a-helix (well, almost) Right handed Left handed

  24. Disulfides in the Barber Shop Sodium thioglycolate Various peroxides

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

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

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

  28. Hydroxyproline participates in H-bonding between tropocollagen chains

  29. (1) (2) In the absence of vitamin C, reaction 2 oxidizes Fe2+ to Fe3+.

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

  31. 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

  32. The Brits Found the Link Between Fruits and Veggies and Healthy Sailors Walk wide o' the Widow at Windsor, For 'alf o' Creation she owns: We 'ave bought 'er the same with the sword an' the flame, An' we've salted it down with our bones. (Poor beggars! -- it's blue with our bones!) The Widow at Windsor – Kipling We broke a King and we built a road --A court-house stands where the reg'ment goed.And the river's clean where the raw blood flowedWhen the Widow give the party.(Bugle: Ta--rara--ra-ra-rara!) The Widow’s Party - Kipling

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

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

  35. Globular Proteins (examples)

  36. Structural Motifs – “supersecondary structures” common stable folding patterns Formed from consecutive sequences Found in proteins w/ different functions result from the physics and chemistry of the structure

  37. Greek Key Motif (antiparallel b-sheets) • Schematic of motif • Staphylococcus nuclease protein

  38. More motifs

  39. Domains – • Stable, independently folded, globular units • Common patterns found in different proteins • Typically have similar function • Caused by evolution (gene recombination / duplication) • Frequently (not always!) correspond to exons in genes 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

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

More Related