1. http://www.youtube.com/watch?v= BD2ZdVSe2vQ&feature=related

2. Serine Protease Mechanism: catalytic triad (AHS) Zac’s answer (+5): Hydrolysis may begin with a serine residue attacking the carbonyl carbon of a lysine and arginine residue (for trypsin) or an amino acid with an aromatic side chain (chymotrypsin). Serine engages in nucleophilic attack on the peptide bond to be cleaved, a proton is then donated by histidine to protonate the amino group. Nucleophilic attack on the carbonyl carbon by water then cleaves the bond. One H from H2O is accepted by histidine driving this step. Hsiao-Han’s answer (+5)

3. Outline What noncovalent interactions stabilize protein structure? What role does the amino acid sequence play in protein structure? What are the elements of secondary structure in proteins? How do polypeptides fold into three-dimensional protein structures? How do protein subunits interact at the quaternary level of protein structure?

4. Protein Structure and Function Are Tightly Linked The three-dimensional structures of proteins and their biological functions are linked by several overarching principles: Function depends on structure Structure depends on sequence and on weak, noncovalent forces The number of protein folding patterns is large but finite Structures of globular proteins are marginally stable Marginal stability facilitates motion Motion enables function

5. 6.1 What Noncovalent Interactions Stabilize the Higher Levels of Protein Structures? What are these “weak forces”? What are the relevant numbers? van der Waals: 0.4 - 4 kJ/mol hydrogen bonds: 12-30 kJ/mol ionic bonds: 20 kJ/mol hydrophobic interactions: <40 kJ/mol

6. Van der Waals Forces Although Van der Waals forces are weak, they are often the only attractive force between molecules. Two electrically neutral, closed-shell atoms Gives net attraction Temporary dipole resulting from quantum fluctuation Induced dipole, due to presence of other dipole  

7. H Bond F−H … :F (161.5 kJ/mol or 38.6 kcal/mol) O−H … :N (29 kJ/mol or 6.9 kcal/mol) O−H … :O (21 kJ/mol or 5.0 kcal/mol) N−H … :N (13 kJ/mol or 3.1 kcal/mol) N−H … :O (8 kJ/mol or 1.9 kcal/mol) HO−H … :OH 3+ (18 kJ/mol or 4.3 kcal/mol)

8. 6.1 What Noncovalent Interactions Stabilize the Higher Levels of Protein Structure? Secondary, tertiary, and quaternary structure of proteins is formed and stabilized by weak forces Hydrogen bonds are formed wherever possible Hydrophobic interactions drive protein folding Ionic interactions usually occur on the protein surface Van der Waals interactions are ubiquitous

9. Electrostatic Interactions in Proteins Figure 6.1 An electrostatic interaction between a positively charged lysine amino group and a negatively charged glutamate carboxyl group.

10. 6.3 What Are the Elements of Secondary Structure in Proteins, and How Are They Formed? The atoms of the peptide bond lie in a plane All protein structure is based on the amide plane The resonance stabilization energy of the planar structure is 88 kJ/mol A twist about the C-N bond involves a twist energy of 88 kJ/mol times the square of the twist angle. Twists can occur about either of the bonds linking the alpha carbon to the other atoms of the peptide backbone

11. Classes of Secondary Structure Secondary structures are local structures that are stabilized by hydrogen bonds Alpha helices Other helices Beta sheet (composed of "beta strands") Tight turns (aka beta turns or beta bends) Beta bulge

12. Hydrogen Bonds in Proteins Figure 6.5 Schematic drawing of a hydrogen bond between a backbone C=O and a backbone N-H.

13. The α-Helix First proposed by Linus Pauling and Robert Corey in 1951 (Read the box about Pauling on page 143) Identified in keratin by Max Perutz A ubiquitous component of proteins Stabilized by H bonds

14. The α-Helix Figure 6.6 Four different representations of the α-helix.

15. The α-Helix Has a Substantial Net Dipole Moment Figure 6.8 The arrangement of N-H and C=O groups (each with an individual dipole moment) along the helix axis creates a large net dipole moment for the helix. The numbers indicate fractional charges on respective atoms.

16. Amino acids can be classified as helix-formers or helix breakers I: indifferent C: random coil B: helix breaker H: helix former

17. The β-Pleated Sheet Figure 6.10 A “pleated sheet” of paper with an antiparallel β- sheet drawn on it.

18. The β-Pleated Sheet The β-pleated sheet is composed of β-strands Also first postulated by Pauling and Corey, 1951 Strands in a β-sheet may be parallel or antiparallel Rise per residue: – 3.47 Angstroms for antiparallel strands – 3.25 Angstroms for parallel strands – Each strand of a β-sheet may be pictured as a helix with two residues per turn

19. The β-Turn (aka β-bend, or tight turn) Allows the peptide chain to reverse direction Carbonyl C of one residue is H-bonded to the amide proton of a residue three residues away Proline and glycine are prevalent in β-turns

20. The β-Turn Figure 6.12 The structures of two kinds of β-turns (also called tight turns or β-bends). Four residues are required to form a β-turn.

21. 6.4 How Do Polypeptides Fold into Three-Dimensional Protein Structures? Several important principles: Secondary structures form wherever possible (due to formation of large numbers of H bonds) Helices and sheets often pack close together Peptide segments between secondary structures tend to be short and direct Proteins fold so as to form the most stable structures. Stability arises from: – Formation of large numbers of intramolecular hydrogen bonds – Reduction in the surface area accessible to solvent that occurs upon folding

22. 6.4 How Do Polypeptides Fold into Three-Dimensional Protein Structures? Two factors lie at the heart of these principles: – Proteins are typically a mixture of hydrophilic and hydrophobic amino acids – The hydrophobic groups tend to cluster together in the folded interior of the protein

24. Denaturation Leads to Loss of Protein Structure and Function The cellular environment is suited to maintaining the weak forces that preserve protein structure and function External stresses – heat, chemical treatment, etc. – can disrupt these forces in a process termed denaturation – the loss of structure and function The cooking of an egg is an everyday example Ovalbumin, the principal protein in egg white, remains in its native structure up to a characteristic melting temperature, T m Above this temperature, the structure unfolds and function is lost

25. Denaturation Leads to Loss of Protein Structure and Function Protein 6.30 Proteins can be denatured by heat, with commensurate loss of function.

26. Denaturation Leads to Loss of Protein Structure and Function Figure 6.31 Proteins can be denatured (unfolded) by high concentrations of guanidine- HCl or urea. The denaturation of chymotrypsin is plotted here.

27. Marginal Stability of the Tertiary Structure Makes Proteins Flexible A typical folded protein is only marginally stable It is logical to think that stability is important to function, so why are proteins often only marginally stable? The answer appears to lie in flexibility and motion It is becoming increasingly clear that flexibility and motion are important to protein function

28. Motion is Important for Globular Proteins Figure 6.36 The cis and trans configurations of proline residues in peptide chains are almost equally stable. Proline cis-trans isomerizations, often occurring over relatively long time scales, can alter protein structure significantly.

29. Diseases of Protein Folding

30. 6.5 How Do Protein Subunits Interact at the Quaternary Level of Structure? Figure 6.45 Schematic drawing of an immunoglobulin molecule, showing the intermolecular and intramolecular disulfide bonds.

31. Open Quaternary Structures Can Polymerize Figure 6.46 The structure of a typical microtubule, showing the arrangement of the α- and β-monomers of the tubulin dimer.