protein_structure_and_folding - Ch Chemistry 237 237...

Ch i t 237 Chemistry 237
Proteins 2: 3 dimensional Proteins 2: 3 dimensional
structures of proteins

Structure hierarchy
Primary 1 ˚ : chemical
structure
S d 2 ˚ L l Secondary 2 : Local
structural elements
Tertiary 3 ˚ : long range
interactions overall
fold single
polypeptide chain
Quaternary 4 ˚ :
Interactions
between between
polypeptide chains

Peptide bond
n-1
n

Peptide bond
The peptide bond exists as
a resonance hybrid. The
two structure contribute
to the structural
properties of the peptide
Restricted rotation means
that the atoms of the
tid b d t b peptide bond must be
co-planar .

the peptide bond can be in the
i t fi i cis or trans configuration:
Figure 8-1 The trans-peptide group.
Figure 8-2 The cis-peptide group.
Bond angles at the C and N are close to those e pected for sp 2 h brid atoms Bond angles at the C and N are close to those expected for hybrid atoms

the plane of each peptide bond shares one C
α
ith th t tid b d l with the next peptide bond plane
Amino acid
Figure 8-4 The torsional degrees of freedom in a peptide
unit.

Phi = psi = 0 phi = psi = 180

Rotation of the angles Φ and Ψ changes the relative
position of the amide planes.
Some configurations are not possible.
This causes steric hindrance ► BAD!
N+1
N-1
n
ramachandran animation
Figure 8-6 Steric interference between adjacent residues.

Ramachandran Plot (~1968): A plot of all of the possible
configurations of Φ and Ψ .
7 The Ramachandran diagram.
8 Conformation angles in proteins.
O l th h d d “ ll d” ( t i hi d ) Only the shaded areas are “allowed” (no steric hindrance)
Most known protein structures fit into the allowed regions
But peptide bonds to glycine or proline residues are sometimes
found in un-allowed regions due to the small size of glycine side
chain and the ring structure of proline.

Secondary structure elements
Alpha helix
Beta sheet
B t t Beta turns
Loops
The terms alpha helix and beta sheet were coined in 1930 by William Astbury
l ki t l fib Th fi t t t b d ll d th l h looking at wool fibres. The first structure observed was celled the alpha
helix and the second the beta sheet.

The α -Helix Structure predicted by Linus Pauling
(1951)
i t t t t l f t
C terminus
important structural features:
right handed helix with 3.6
residues per turn
pitch of 5.4 Å (0.54 nm) per turn
held together by H-bonds
between C=0 residue n to NH of between C=0 residue n to NH of
residue n+4
N terminus
The right-handed  helix.
http://www.pnas.org/cgi/reprint/100/20/11207

The amino acid side chains point outward from the
i axis
Not all sequences can form α -helices Not all sequences can form helices
proline residues (why?)
lots of (-) or (+) charged residues
lots of bulky residues
A f h li l Amount of α -helical structures
in a protein can vary
Phi -45 to -180
Psi -30 to -60

Beta sheets
Two separate sections of extended polypeptide interact via
H-bonds
Th t ibl i t ti ti ll l d There are two possible orientations: antiparallel and
parallel
Antiparallel strands: straight H-bonds:

Beta sheets
parallel strands: The H-bonds are not straight
nc.