Lecture 47: Structure II -- Proteins

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

This is not intended as a Fischer projection!

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

These three are the most commonly phosphorylated residues in eukaryotes

Umami flavor of MSG Neurotransmitter

As appropriate a time as any: pK a

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

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

pK a = 10.5 pK a = 6.0 pK a = 12.5

Peptide bonds link amino acids

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

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:

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

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

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

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

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

Pre-proline Ramachandran plot

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?

PyMOL interactive

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

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

PyMOL interactive

These amino acids are part of beta sheets

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

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

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

Does hydrogen bonding in secondary structures drive protein folding?

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

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

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

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

Hydrophobic effect and vdW forces drive leucine zipper folding

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

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