Protein Secondary Structures

1
Protein Secondary Structures
2
Degrees of Freedom
3
1
4
2

3
Hydrogen Bond
Hydrogen bonds in water
Backbone hydrogen bonds
acceptor
O
O, acceptor, -
O
C
H, donor,
N
H
donor
4
Protein Secondary Structures

• Helices
• Strands
• Turns

5
Helices (1)
Cter
Nter
Hydrogen bonds O (i) lt-gt N (i4)
6
Helices (2)
7
Helices (3)
Thin 3.0 residues /turn 4 of all helices
Fat 4.2 residues /turn instable
Right 3.6 residues /turn 5.4 Å /turn most
helices
8
Identify Helix Type
1. Find one hydrogen bond loop
11
4
12
10
2. Count number of residues (by number of C
atoms in the loop). Here 4
13
3
8
9
7
2
1
5
6
4
2
3. Count number of atoms in the loop
(including first O and last H). Here 13
1
3
413 helix a-helix
9
a-Helix Dipole
-0.4e
The peptide bond has a strong dipole moment due
to the partial charges on the NH and CO groups
0.4e
-0.3e
0.3e
10
a-Helix Dipole
-0.5e
1. In the a-helix, peptide dipoles align and
give the helix a large dipole
2) This dipole is equivalent to having a
charge of 0.5e at the N-terminus and -0.5e at the
C-terminus
0.5e
11
Preferred Backbone Conformation in Helices
12
The b-strand
N-H---O-C Hydrogen bonds
Real b-strand is twisted
Extended chain is flat
13
Two types of b-sheets
Anti-parallel
Parallel
14
Preferred backbone conformation in b-sheets
Parallel j -119 y 113 Antiparallel j
-139 y 135
15
b-sheets are twisted
b-sheets organized as a barrel in TIM
16
The b-hairpin
17
b-turns
Type I
Type II
O is down
O is up
3
3
2
2
4
4
1
1
The chain changes direction by 180 degrees
18
b-turns
Type III
3
2
1
4
1 turn 310 helix
19
Preferred backbone conformations in turns
20
Favorable and Unfavorable Residues In Turns
21
Ramachandran Plot
b-sheets
helix-L
y
a-helices
f
22
Summary

• There are 3 major types of secondary structures
• a-helices, b-sheets and b-turns.
• 2) Most helices are a-helices, stabilized through
• a network of CO (i) --- HN (i3) hydrogen bonds
• 3) Helices have a large dipole
• 4) There are two types of b-sheets parallel and
• anti-parallel
• 5) b-turns correspond to 180 change in the
  backbone
• direction.