Transcript structure-sheets-text

CHMI 2227E
Biochemistry I
Proteins:
Secondary Structure
- Beta Strands and Beta Sheets
- Loops and Turns
- A special case: Collagen
-
CHMI 2227 - E.R. Gauthier, Ph.D.
1
Beta Strands and Beta Sheets



The other common secondary structure is called the β
structure which includes β strands and β sheets
β strands are portions of the polypeptide chain that are
almost fully extended having a “zig-zag” shape
β strands are flexible but not elastic
CHMI 2227 - E.R. Gauthier, Ph.D.
2
Beta Sheets

When multiple β strands are
arranged side-by-side, they
form β sheets;

Proteins rarely contain isolated
β strands because the structure
by itself is not significantly more
stable than other conformations

However, β sheets are
stabilized by hydrogen bonds
between carbonyl oxygens and
amide hydrogens on adjacent β
strands.
CHMI 2227 - E.R. Gauthier, Ph.D.
3
Hydrogen Bonded Beta Strands


The H-bonded β strands can be on separate
polypeptide chains or on different segments of the same
chain
The β strands in a sheet can be either parallel (running
in the same N- to C- terminal direction) or antiparallel
(running in opposite N- to C- terminal direction)
N
C
N
C
N
C
N
C
CHMI 2227 - E.R. Gauthier, Ph.D.
4
Antiparallel Beta Strands


The hydrogen bonds are nearly perpendicular to the
extended polypeptide chains
The carbonyl oxygen and the amide hydrogen atoms of
one residue form hydrogen bonds with the amide
hydrogen and carbonyl oxygen of a single residue in the
other strand
http://dbs.umt.edu/courses/fall2006/bioc380/lectures/011/lecture.html
CHMI 2227 - E.R. Gauthier, Ph.D.
5
Parallel Beta Strands

In the parallel arrangement, the hydrogen bonds
are not perpendicular to the extended chains,
and each residue forms hydrogen bonds with
the carbonyl and amide groups of two different
residues on the adjacent strand
http://dbs.umt.edu/courses/fall2006/bioc380/lectures/011/lecture.html
CHMI 2227 - E.R. Gauthier, Ph.D.
6
Mixed Beta Sheets

Many strands, typically 4 or 5 but as many as 10 or
more, can come together in β sheets. Such sheets can
be purely antiparallel, purely parallel, or mixed
CHMI 2227 - E.R. Gauthier, Ph.D.
7
Beta Sheet Conformation

The R groups from the amino acids point
alternatively above and below the plane of the
sheet
http://dbs.umt.edu/courses/fall2006/bioc380/lectures/011/lecture.html
CHMI 2227 - E.R. Gauthier, Ph.D.
8
Beta Pleated Sheets

In certain proteins
adopting a β
conformation, small R
groups from amino acids
such as Ala, Gly and Ser
allow the β sheets to
stack closely together;

This β conformation is
responsible for the
flexible characteristic of
the silk filaments

Beta Pleated Sheets: Silk
Example: Silk Fibroin
CHMI 2227 - E.R. Gauthier, Ph.D.
9
Loops and Turns

In an α-helix or a β strand, consecutive
residues have a similar conformation that
is repeated throughout the structure;

Most of these regions of secondary
structures can be characterized as loops
and turns since they cause directional
changes in the polypeptide backbone;
CHMI 2227 - E.R. Gauthier, Ph.D.
10
Loops and Turns

Loops and turns connect α-helices and β strands
and allow the polypeptide chain to fold back on
itself, producing the compact 3D shape seen in
native structures;

Loops often contain hydrophilic residues and are
usually found on the surfaces of proteins where
they are exposed to solvent and form H-bonds
with water
CHMI 2227 - E.R. Gauthier, Ph.D.
11
Loops and Turns

Loops containing only a few
(up to 5) residues are referred
to as turns if they cause an
abrupt change in the direction
of a polypeptide change;

The most common types of
tight turns are called reverse
turns or β turns because
they usually connect different
antiparallel β strands
CHMI 2227 - E.R. Gauthier, Ph.D.
12
Beta turns

β turns contain 4 amino acid
residues and are stabilized by
hydrogen bonding between the
carbonyl oxygen of the first
residue and the amide hydrogen of
the fourth residue;

β turns produce an abrupt (usually
about 180°) change in the
direction of the polypeptide chain

Gly and Pro are often part of the β
turns

Pro is capable of forming a cis
peptide bond conformation which is
highly susceptible in forming β turns
http://web.chemistry.gatech.edu/~williams/bCourse_Information/6521/pro
 Glycine has a small R group which
tein/secondary_structure/beta_turn/down/beta_turn_1.jpg
is capable of generating unique psi
and phi angles permitting a high
degree of flexibility
13
CHMI 2227 - E.R. Gauthier, Ph.D.
A special case : collagen



Family of over 20 rod-like proteins;
Important part of connective tissue (1/3 of all proteins in
mammals);
Classified into 5 different types, according their amino
acid content, their primary structure and their sugar
content.
Type I
bone, tendon, fibrocartilage, dermis, cornea
Type II
nucleus pulposus, hyaline cartilage
Type III
intestinal and uterine wall
Type IV
endothelial, epithelial membranes
Type V*
cornea, placenta, bone, heart valve
* Found in small quantities
CHMI 2227 - E.R. Gauthier, Ph.D.
14
A special case : collagen


Consists in a triple helix: 3
polypeptide chains (each left
handed) are intertwined together to
form a right-handed superhelix;
For each left-handed helix:





Chain 1
Pitch: 0.94 nm
Rise: 0.31 nm per residue
3 residues per turn
1000 residues per chain
Chain 2
So: the collagen helix is more
extended than the a-helix
Chain 3
Triple helix
(from Kadler, 1996)
CHMI 2227 - E.R. Gauthier, Ph.D.
15
A special case : collagen
Type V collagen = 1839 a.a.!!
CHMI 2227 - E.R. Gauthier, Ph.D.
16
A special case : collagen

The collagen polypeptides
have a very specific amino
acid composition:




Hypro
1/3 Gly
1/4 Pro
1/4 Hypro (hydroxyproline)
and 5-Hylys (hydroxylysine)
These residues follow a
strict sequence where Gly
is always repeated every
third position – WHY??;
CHMI 2227 - E.R. Gauthier, Ph.D.
5-Hylys
17
A special case : collagen
13
CHMI 2227 - E.R. Gauthier, Ph.D.
18
A special case : collagen

The presence of Gly at every third
residue allows each collagen chains
to form a tightly wound helix that can
accommodate Pro/Hypro (which are
otherwise rarely included in helices);

Since the helix has 3 a.a. per turn,
having Gly at every third residue
means that Gly is always on the
same side of the helix;

It just so happens that Gly is always
positioned at the center of the triple
helix;

This allows close packing of the
three helices, which can interact and
yield a very strong, rope-like
structure.
CHMI 2227 - E.R. Gauthier, Ph.D.
19
Hydrogen bonds stabilize the
collagen triple helix
Gly of Chain 1
G
Glycine
Hypro
Pro
Pro of Chain 2
CHMI 2227 - E.R. Gauthier, Ph.D.
20
Formation of collagen fibers
Lysine
Collagen triple helix
(tropocollagen)
Lysine
Collagen triple helix
(tropocollagen)
CHMI 2227 - E.R. Gauthier, Ph.D.
21
Formation of collagen fibers
Transmission electron
microscopy of collagen
fibers
CHMI 2227 - E.R. Gauthier, Ph.D.
22
Collagen, Vitamin C and scurvy

The formation of Hypro requires
the enzymatic modification of Pro
in a reaction which involves:


Prolyl hydroxylase (an enzyme)
Fe+2

Ascorbic acid, a derivative of Vit C
and an antioxidant, keeps iron in
its reduced Fe+2 form, and not the
oxidized, more stable Fe+3 form.

Humans cannot make Vit C on
their own;

In the absence of Vit C, the
collagen triple helix cannot
assemble properly, leading to a
much softer connective tissue.
CHMI 2227 - E.R. Gauthier, Ph.D.
23