Chapter 6 3-D Structure of Proteins

1. Chapter 6 3-D Structure of Proteins Chymotrypsin, a globular protein Glycine Proteins are large molecules. Each protein has a unique structure.

2. Overview of protein structure • For a protein numerous conformations are possible (without breaking a bond, by just rotation about single bonds) • However, a conformation existing under a given condition is the most stable thermodynamically having the lowest Gibbs free energy • Proteins in any of their functional folded conformations are called native protein

3. Peptide bond 1 3 2 Electric dipole

4. The peptide bond is rigid and planar C O C = N 1.27 Ao C N 1.47 Ao • 6 atoms lie in a single plane • Oxygen atom of the carbonyl group & the H of amide nitrogen are in trans • Bond between C and N has double bond character and is unable to rotate • Rotation is permitted between N – Ca and Ca– C • Polypeptide backbone: series of rigid planes with consecutive planes sharing a common point of rotation at Ca

5. Bond angles resulting from rotations at Ca C O Ca – C bond (psi) N – Ca bond (phi) • In the fully extended conformation f = y = 180o • y can have nay values between -180o to 180o • But many values are prohibited by steric interference

6. 2 peptide bonds are in the same plane • f = y = 0o • This conformation is not allowed in proteins due to steric overlap between a-carbonyl oxygen and a-amino hydrogen atom

7. C Ramachandran Plot for L-Ala No steric overlap & Allowed conformation Permissible If little flexibility is allowed in the bond angle

8. Levels of structure in proteins Linking of aa Stable arrangement of aa give rise to structural patterns 3-dimensional folding of polypeptides Arrangement in space of 2 or more polypeptide subunits

9. Protein Secondary Structure • Refers to the local conformation of some part of polypeptide • Prominent secondary structures that are stable and occur in proteins are 1) a helix 2) b conformation

10. a helix • f = -60o • y = -45o to-50o • Each helical turn includes 3.6 aa • a helix found in all proteins is right handed Shows the hydrogen bonds Imaginary axis

11. a helix Looking down the longitudinal axis

12. Atoms in the center of the a helix are in very close contact

13. a helix • Form more readily • Helical structure is very stable • Because of internal hydrogen bonds • Between H attached to N of peptide linkage & the electronegative carbonyl O of the 4th aa on the N-terminal side of the peptide bond • Within the helix every peptide bond participates in such H bonding (except the last 4 amino acids that are close to the end of the helix)

14. AA sequence affects helix stability • For example, polypeptide with long block of Glu residues will not form an a helix at pH 7 • Bulk shape of Cys, Ser, Thr can destabilize the helix if they are close together in a chain • Proline introduces destabilizing kink in a helix • Gly occurs infrequently as it is very flexible & takes coiled structure different from a helix Interactions between R groups of aas 3 residues apart in a helix Arg (103) side chain Asp(100) side chain

15. Electric dipole of a peptidebond is transmitted through the hydrogen bonds along an a helix resulting in an overall helix dipole Negatively charged amino acids near the end of the amino terminal stabilize the positive charge of the helix electric dipole Positively charged amino acids near the end of the N-terminal destabilize the helix

16. The b conformation of the polypeptide chains Hydrogen bonds cross-links between adjacent chains The backbone of the polypeptide chain is extended into a zigzag structure Zigzag structures arranges side by side to form a structure resembling a series of pleats (called b sheet)

17. Parallel b sheet

18. Most common structures of b turns (connecting elements) • Connects ends of 2 adjacent segments of an anti-parallel b sheet • 180o turn involving 4 amino acids • Gly and Pro occur in b turns (Gly at 3rd position) N H O C More common

19. Ramachandran plots for variety of structures Although theoretically possible, not observed in proteins

20. Relative probability that a given amino acid will occur in the 3 common types of secondary structure

21. Proteins are classified into 2 major groups: Globular proteins • Polypeptide folded into globular shape • Contain more than 1 type of secondary structure • Soluble in water Example: most enzymes Fibrous proteins • Polypeptide chain arranged in sheets or strands • Contain single type of secondary structure • Insoluble in water

22. Relationship between protein structure and biological function

23. Structure of hair (right-handed a helix) Higher order structures

24. A hair is an array of many a-keratin filaments

25. Collagen a chain Structure of collagen Unique secondary structure distinct from a helix Repeating tripeptide sequence Gly-X-Pro or Gly-X-HyPro Adapts a left-handed helical structure with 3 residues per turn 3 separate a chains are supertwisted

26. Collagen with a distinct tertiary and quaternary structure • Collagen is • 35% Gly • 11% Ala • 21% pro and hyPro • Gelatin is derived from collagen Gly 3 stranded collagen superhelix

28. Structure of silk • Silk or spider web made up of the protein fibroin Layers of Antiparallel b sheet Small R groups allow close packing

29. Globular protein structures are compact and varied Human serum albumin 585 residues Actual size of the protein

30. Tertiary structure of sperm whale myoglobin 8 a helix Some bends which are b turns

31. Tertiary structure of sperm whale myoglobin

32. Tertiary structure of sperm whale myoglobin Hydophobic residues (buried)

33. The heme group

38. 3-D structure of some small proteins Disulfide bonds a helix b sheet

40. Polypeptides (with more than few 100 aas) fold into 2 or more stable globular units called domains

41. Supersecondary structures (or motifs or folds) Stable arrangements of several elements of secondary structure and the connections between them Stable folding patterns in proteins

42. Stable folding patterns in proteins

43. Construction of large motifs from smaller ones

48. The quaternary structure of deoxyhemoglobin a subunits b subunits

49. Protein denaturation (loss of 3-D structure sufficient to cause loss of function)

50. Renaturation of unfolded, denatured ribonuclease