1. Lecture 47: Structure II -- Proteins

2. Today’s Outline The monomers: amino acids – Side chain characteristics – Acid-base equilibria and pK a Peptide backbone – Peptide bond formation – Rotational degrees of freedom – Common folding motifs Side chain interactions in folding (Time permitting) Levinthal’s paradox

3. This is not intended as a Fischer projection!

4. isoleucine Covalent bond between side chain and backbone Bulkiest First AA in most proteins Smallest Isomers

5. These three are the most commonly phosphorylated residues in eukaryotes

6. Umami flavor of MSG Neurotransmitter

7. As appropriate a time as any: pK a

8. Rearranging, we get: When pH >> pK a, [A - ] >> [HA] When pH << pK a, [A - ] << [HA] When pH = pK a, [A - ] = [HA] Strong acids have low pK a s: HBr:-10 HCl:-7 Weaker acids have low-ish pK a s: H 2 PO 4 :2 HF:3 D/E:4

9. Umami flavor of MSG Neurotransmitter pK a = 3.9 pK a = 4.1

10. pK a = 10.5 pK a = 6.0 pK a = 12.5

11. Peptide bonds link amino acids

12. A protein’s folded shape can be roughly described by the path traced by its peptide backbone (ignoring sidechains)

13. Peptide bonds have limited rotational freedom The peptide bond has two conformations …but cis is less likely due to steric clash The peptide bond is planar:

14. Most backbone rotation occurs via phi (  ) and psi (  ) torsion angles

15. Some combinations of torsion angles are much more likely than others Ramachandran plot: shows frequency of ( ,  ) observed for residues in folded proteins

16. Ball-and-stick models provide some insight on infrequency of  >0

17. Glycine does adopt positive  values Less steric hindrance because side chain (green) is very small

18. Proline’s  value is (somewhat) fixed by its side chain’s bond to the backbone This side chain can clash sterically with the preceding amino acid, so the“pre- proline” Ramachandran plot is also unique

19. Pre-proline Ramachandran plot

20. Another trend for consecutive amino acids: correlation in position Amino acid n Amino acid n+1 What do we get if we repeat the same torsion angles many times in a row?

21. PyMOL interactive

22. These amino acids participate in the more common, right-handed form of helices

23. PyMOL interactive Other right-handed helices besides alpha helices have similar torsion angles  helix 3 10 helix  helix

24. PyMOL interactive

25. These amino acids are part of beta sheets

26. PyMOL non-interactive These amino acids participate in the less common, left-handed forms of helices

27. Most of the residues in most folded proteins participate in one of these motifs

28. Peptide backbone hydrogen bonding is the most common motif in folding The pattern of backbone hydrogen bonding is referred to as a protein’s secondary structure Some side chains inhibit formation of certain secondary structures (e.g. proline/  helices) With those exceptions, secondary structures are not dependent on amino acid sequence

29. Does hydrogen bonding in secondary structures drive protein folding?

30. What interactions between side chains drive sequence-specific protein folding? Hydrophobic effectSteric clash

31. What interactions between side chains drive sequence-specific protein folding?

32. These forces determine the relative orientation of a protein’s secondary structures, i.e., the protein’s tertiary structure

33. The same forces that drive tertiary structure formation can also hold two or more proteins together

34. Hydrophobic effect and vdW forces drive leucine zipper folding

35. Covalent disulfide bonds can form between cysteines Reduction potentials: Cysteines:-222 mV NADH:-320 mV

36. Formal collaboration policy This course encourages collaboration, which is a key to learning and the progress of science. You may talk together about approaches to problems and you may work together to perform calculations or write code. But any formal assignments that you are given must be written, rather than copied, by you and you only, with the exception of computer code, where the code may be written communally, but all code must be well commented, and all comments in graded code must be written by you, on your own. Since the goal of assignments is to help you and us assess your level of understanding of the material, we require that you understand both the conceptual structure and the details of each individual step of any answer you submit and we may ask you to answer questions, orally, about an assignment, to demonstrate that you have achieved this level of understanding.