Transcript 4.2 - Alfred State College

Chapter 4.2:
Protein Secondary
Structure
CHEM 7784
Biochemistry
Professor Bensley
CHAPTER 4.2
Protein Secondary Structure
Today’s Objectives -
To learn and understand:
– The structural hierarchy in proteins
– The various types of protein secondary structure
and why one type is favored over another
Secondary Structures
• Secondary structure refers to a local spatial
arrangement of the polypeptide chain
The  helix
The  helix: Top View
• The inner diameter of the helix (no side-chains) is
about 4 – 5 Å
Too small for anything to fit “inside”
• The outer diameter of the helix (with side chains)
is 10 – 12 Å
Happens to fit well into the major groove of
dsDNA
• Residues 1 and 8 align nicely on top of each other
Sequence Affects Helix Stability
• Not all polypeptide sequences adopt -helical
structures
• Small hydrophobic residues such as Ala and
Leu are strong helix formers
• Pro acts as a helix breaker because the
rotation around the N-Ca bond is impossible
• Gly acts as a helix breaker because the tiny Rgroup supports other conformations
The Helix Dipole
 Sheets
Parallel beta sheet
H-bonded strands
run in the same
direction
Anti-parallel beta
sheet
H-bonded strands run
in opposite directions
 Sheets
• Side chains point alternately above and
below the plane of the beta-sheet
• 2- to 15 beta-strands/beta-sheet
• Each strand made of ~ 6 amino acids
 Turns
Proline Isomers
• Most peptide bonds not involving proline are in the
trans configuration (>99.95%)
• For peptide bonds involving proline, about 6% are in
the cis configuration. Most of this 6% involve turns
• Proline isomerization is catalyzed by proline
isomerases