1. Types of Proteins Proteomics - study of large sets of proteins, such as the entire complement of proteins produced by a cell E. coli has about 4000 different polypeptides (average size 300 amino acids, M r 33,000) Fruit fly (Drosophila melanogaster) about 16,000, humans, other mammals about 40,000 different polypeptides

2. Globular Proteins Usually water soluble, compact, roughly spherical Hydrophobic interior, hydrophilic surface Globular proteins include enzymes,carrier and regulatory proteins

3. Fibrous Proteins Provide mechanical support Often assembled into large cables or threads  -Keratins: major components of hair and nails Collagen: major component of tendons, skin, bones and teeth

4. Four Levels of Protein Structure: Primary structure - amino acid linear sequence Secondary structure - regions of regularly repeating conformations of the peptide chain, such as  -helices and  -sheets Tertiary structure - describes the shape of the fully folded polypeptide chain Quaternary structure - arrangement of two or more polypeptide chains into multisubunit molecule

5. Four Levels of Protein Structure:

6. Resonance Structures of the Peptide Bond (a) Peptide bond shown as a C-N single bond (b) Peptide bond shown as a double bond (c) Actual structure is a hybrid of the two resonance forms. Electrons are delocalized over three atoms: O, C, N

7. Planarity Rotation around C-N bond is restricted due to the double-bond nature of the resonance hybrid form Peptide groups (blue planes) are therefore planar

8. “trans” and “cis” conformations Nearly all peptide groups in proteins are in the trans conformation

9. Rotation around the N-C  and C  -C bonds that link peptide groups

10. The  -Helix Each C=O (residue n) forms a hydrogen bond with the amide hydrogen of residue n+4 Helix is stabilized by many hydrogen bonds (which are nearly parallel to long axis of the helix) All C=O groups point toward the C-terminus (entire helix is a dipole with (+) N, (-) C-termini) The  and  angles of each residue are similar: near -57 o (  ) and near -47 o (  )

11. The  -Helix Pitch is 0.54nm (recurrence of equivalent positions) Rise - Each residue advances by 0.15nm along the long axis of the helix There are 3.6 amino acid residues per turn Most  helices in proteins are right handed (backbone turns clockwise when viewed along the axis from the N terminus)

13. Stereo view of right-handed  helix

14. Helix in horse liver alcohol dehydrogenase Helical wheel diagram

15.  Strands and  Sheets  Strands - polypeptide chains that are almost fully extended  Sheets - multiple  strands arranged side-by-side  Strands are stabilized by hydrogen bonds between C=O and -NH on adjacent strands

16. Parallel and antiparallel  -strands  Strands in a sheet are parallel or antiparallel Parallel  sheets - strands run in the same N- to C- terminal direction Antiparallel  sheets - strands run in opposite N- to C- terminal directions In antiparallel  sheets the H-bonds are nearly perpendicular to the chains (more stable than parallel chains with distorted H-bonds)

17.  -Sheets (a) parallel, (b) antiparallel

18. Loops and Turns Loops and turns connect  helices and  strands and allow a peptide chain to fold back on itself to make a compact structure Loops - often contain hydrophilic residues and are found on protein surfaces Turns - loops containing 5 residues or less  Turns (reverse turns) - connect different antiparallel  strands

19. Reverse turns

20. Tertiary Structure of Proteins Tertiary structure results from the folding of a polypeptide chain into a closely-packed three- dimensional structure Amino acids far apart in the primary structure may be brought together Stabilized primarily by noncovalent interactions (e.g. hydrophobic effects) between side chains Disulfide bridges also part of tertiary structure

21. Supersecondary Structures (Motifs)

22. Domains Independently folded, compact units in proteins Domain size: ~25 to ~300 amino acid residues Domains are connected to each other by loops, bound by weak interactions between side chains Domains illustrate the evolutionary conservation of protein structure

23. Protein Denaturation and Renaturation Denaturation - disruption of native conformation of a protein, with loss of biological activity Energy required is small, perhaps only equivalent to 3-4 hydrogen bonds Proteins denatured by heating or chemicals Some proteins can be refolded or renatured

24. Urea and guanidinium chloride (chaototropic agents)

25. Hydrogen Bonding Contributes to cooperativity of folding Helps stabilize secondary structures and native conformation

26. Examples of hydrogen bonds

27. Van der Waals and Charge-Charge Interactions VDW contacts occur between nonpolar side chains and contribute to the stability of proteins Charge-charge interactions between oppositely charged side chains in the interior of a protein also may stabilize protein structure

28. Protein Folding Is Assisted by Chaperones Molecular chaperones increase rate of correct folding and prevent the formation of incorrectly folded intermediates Chaperones can bind to unassembled protein subunits to prevent incorrect aggregation before they are assembled into a multisubunit protein Most chaperones are heat shock proteins (synthesized as temperature increases)

29. Stereo view of human Type III collagen triple helix

30. Collagen triple helix Multiple repeats of -Gly-X-Y- where X is often proline and Y is often 4-hydroxyproline Glycine residues are located along central axis of a triple helix (other residues cannot fit) For each -Gly-X-Y- triplet, one interchain H bond forms between amide H of Gly in one chain and -C=O of residue X in an adjacent chain No intrachain H bonds exist in the collagen helix

31. 4-Hydroxyproline and 5-hydroxylysine Formed by enzyme hydroxylation reactions (require vitamin C) after incorporation into collagen Vitamin C deficiency (scurvy) leads to lack of proper hydroxylation and defective triple helix (skin lesions, fragile blood vessels, bleeding gums) Unlike most mammals, humans cannot synthesize vitamin C