Three-Dimensional Structure of Proteins

1. Three-Dimensional Structure of Proteins

2. Rotation around the a-Carbon in a Polypeptide

3. A Sterically Nonallowed Conformation

4. The a Helix and b Pleated Sheet Conformationally allowable structures where backbone is optimally H- bonded (linear H- bonds). • Pleated Sheet: • Anti-parallel or parallel • 2.0 residues/”turn” • 0.34 nm/residue (anti-parallel) or 0.32 nm/residue (parallel) • a Helix (3.613 Helix): • 3.6 residues/turn • Rise = 0.15 nm/ residue • 13-atom hydrogen-bonded loop Linus Pauling and Robert Corey, 1950 Linus Pauling and Robert Corey, 1951

8. Antiparallel and Parallel b Pleated Sheets

11. Other Secondary Structures •  Helix (4.416 Helix): • 4.4 residues/turn • 0.12 nm/residue • 16-atom hydrogen- bonded loop • 310 Helix: • 3 residues/turn • 0.20 nm/residue • 10-atom hydrogen-bonded loop

12. Idealized Helices

13. Hydrogen Bonding Patterns for Different Helices

14. Ramachandran Plot G.N. Ramachandran, 1963

15. Fibrous Proteins*Proteins with an elongated or filamentous form, often dominated by a single type of secondary structure over a large distance. Most fibrous proteins are associated with connective tissue and help provide mechanical strength to the tissue. *vs. globular proteins

16. Structure of Keratin and Keratin-Type Intermediate Filaments Keratin is a principal component of hair, horn, nails and feathers. Adjacent polypeptide chains also crosslinked by disulfide bonds. Disulfide bond patterns between are what determine whether human hair is straight or curly.

18. Coiled-Coil a-Helical Dimer of a Keratin Amphipathic a helices: Residues a, d, a’ and d’ hydrophobic, other residues hydrophilic.

20. Structure of Silk Fibroin Silk made by silkworms and spiders. Composed of microcrystalline array of antiparallel b pleated sheets where each b strand has alternating Gly and Ala or Ser residues.

22. Structure of Collagen Fibers Collagen is the most abundant vertebrate protein and the major stress-bearing component of connective tissue (bone, teeth, cartilage, tendon) and fibrous matrix of skin and blood vessels. • 3 intertwined left- handed helices • 3.3 residues/turn • Repeating Gly-X-Y (X often Pro, Y often Pro or hydroxyPro)

25. The Collagen Triple Helix (Tropocollagen) Tropocollagen with Gly Ala substitution (yellow) Interactions between strands G.N. Ramachandran, 1955

26. Post-Translational Modifications in Collagen Collagen contains unusual, oxidized and crosslinked lysine residues. Lysyl oxidase is the enzyme that oxidizes lysine residues to the aldehyde allysine, which then forms the crosslinks. Hydroxyproline is also found in collagen. (Some lysine residues also hydroxylated.) The enzyme required for hydroxylation of proline residues is prolyl hydroxylase, a vitamin C-dependent enzyme. Scurvy is caused by reduced hydroxyproline in collagen as a result of vitamin C deficiency.

28. Biosynthesis and Assembly of Collagen

29. Globular ProteinsProteins with a compact folded structure (with an interior and exterior), generally containing different types of secondary structure elements as well as irregular regions. The vast majority of proteins are globular.

30. Ribbon Diagram Showing Secondary Structures in a Globular Protein

31. Some Globular Protein Structures Hemoglobin (complex of 4 polypeptide chains or subunits) Myoglobin Triose phosphate isomerase (complex of 2 subunits) 20S Proteasome (complex of 28 subunits)

33. Additional Elements of Structure: Turns R2 often Pro R3 never Pro Most common type of turn R2 often Pro R3 never Pro g turn b turns trans-Pro (above) or cis-Pro (in Type VI b turns) often found in turns.

35. Turns with cis-Proline: Type VI b turns Type VIa b turn Type VIb b turn

36. cis-trans Isomerization of Proline Residues Peptidyl-prolyl cis-trans isomerases (rotamases) accelerate the isomerization.

37. Irregularly structured elements • More disordered and flexible than turns • Connects secondary structure elements • Variable in length and shape • Frequently form binding sites and enzyme active sites Additional Elements of Structure: Loops The N- and C-terminal arms of proteins are also generally more disordered and irregularly structured.

38. Domain and Motifs in Globular Proteins: Supersecondary Structure

39. Some Common Motifs Found in Proteins b hairpin bab motif aa motif b barrels ab barrel

44. Solving 3-D Structure of Proteins X-ray crystallography Must crystallize protein. Structure solved is of protein packed in crystal and not protein in solution; however, protein crystals usually have high water content (and so solution-like in structure). Almost no limit to size of protein. Nuclear magnetic resonance (NMR) Solution structure. Can be used to look at dynamics. Only possible at this time for proteins with a Mr of < ~50,000.

45. X-Ray Crystallography Used to Solve First 3-D Protein Structures Max Perutz with model of hemoglobin and John Kendrew with model of myoglobin in 1962

46. X-Ray Crystallography to Solve Protein Structures Protein crystals 3-D structure of protein X-ray diffraction pattern Electron density map

48. Nuclear Magnetic Resonance (NMR)

49. Comparison of X-Ray and NMR Structures of Bovine Pancreatic Trypsin Inhibitor Both X-ray crystallography and NMR methods usually yield very similar structures. Crystallized proteins generally adopt a conformation very similar to the “averaged” NMR solution structure.

50. Molecular Motion in Proteins • Proteins are not static structures but are highly dynamic: • “Breathing” - molecular-scale vibrations and oscillations • Larger-scale conformational changes in both secondary structural elements and whole domains