Download Protein Structure

Secondary Structure
a helix
Discovered by Linus Pauling
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2 Nobel prizes.
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Discovered folding while sick in bed!
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Treated poorly as a result of his antinuclear stands - 2nd NB prize
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Pushed high doses of vitamin C
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The helix is a right handed twist of the
backbone - notice when we are looking at
this the side groups are NOT considered
Notice where the amino acids are.
Hydrogen bonding occurs between the
carbonyl and the amino group four residues
away. The bonding takes place within the
same chain.
A run of proline residues lead to breaking the
helix structure. Why?
And there are always exceptions!
Proline –Cyclic side chain limits the range of
rotation
It is the most conformationally restricted
amino acid residue
Glycine- The only amino acid without a beta
carbon atom is the smallest of the amino
acids
Has almost unlimited rotational freedom and
can fit into almost any conformation
Specifics on helical descriptions:
Pitch: the vertical distance per turn. Think of
a screw, if you turned a screw one turn
this is how far the screw would penetrate
n = residues per turn. This depends on the
helix. If it is stretched out (n=2) if it is
compressed (n=12) the most stable is 3.6
or nearly 4 amino acids per turn. This is
where the best H bonding can occur.
(think of the alignment of the donor and
acceptor
nth residue: This means any residue in the
helix as a reference point
nth + 4 residue: Indicates the residue 4
positions in with n taken as the first. The
+sign does not mean add 4 residues to n,
just you are looking at a residue 4 amino
acids away from the nth residue.
nm: n refers to the residue position, m is the
number of atoms in the loop formed by
hydrogen bonding. The a helix has an nm
of 413 m
b Pleated sheet
Formed when the peptide chain is lined up
side by side. This is an extended
formation of the backbone
The structure is stabilized by hydrogen
bonds between two different chains
 -C=O and -NH
 Same donors and acceptors as in
the helix but not within the same
chain
Each strand of the b pleated sheet is
from 6 to 15 residues
2 arrangements of
sheets parallel and
anti parallel. Look
at the N to C
terminus directions
2 arrangements of sheets
parallel and anti parallel.
Look at the N to C
terminus directions
Anti parallel conformations
are stronger - alignment
of H bonding.
 Often found in silk
 R groups can
interact - glycine
and alanine
H bonding within 3 residues
can disrupt the sheets causes bend or turn in
the chain.
Unique structure of collagen
A special helical protein
– biological significance - fibrous, structural component
– Type I collagen is found in bone, tendon and skin, II in cartilage
and III in blood vessels
– very different amino acid sequence from alpha helix
– 3 residues / turn
– 1/3 amino acids are glycine Gly X Y
Unique structure of collagen
A special helical protein
– Glycine R group face inside others outside
– up to 30% are proline or hydroxyproline - important for maintaining
secondary structure
– hydroxyprolines involved in H bonding of three strands together
– helical structure formed by three left handed helices twisted to form
a right handed superhelix (gives strength)
– hydrogen bonding between 3 helices
(thus the glycine)
– covalent bonding of lysine between
strands necessary for strength
Unique structure of collagen
A special helical protein
Hydroxylations on pro are performed
by an enzyme called prolyl hydroxylase,
which is an enzyme that requires
vitamin C as a cofactor in the reaction.
Absence of vitamin C in the diet
reduces hydroxylation of pro, and
collagen fibres begin to break down and
new collagen not formed properly.
Lack of vitamin C causes scurvy
because collagen fibres are not formed
properly, and this causes skin lesions,
weakened gums so teeth fall out etc.
Unique structure of collagen
A special helical protein
Equally important is hydroxy-lys catalysed by lysine hydroxylase.
Attached to the lys residues are three sugars gal-gal-glu, and
these enable H-bonding to occur between triple helices, which is
essential for stability of the greater complex that binds fibers
together to form a matrix bed to binds cells to the matrix and form
a tissue.
Collagen Related Disease
Loss of flexibility with age is likely due to increased amount crosslinked collagen compared to younger tissue
Scurvy
meats.
– problems with sea voyages, lack of food other than salted
Collagen Related Disease
Loss of flexibility with age is likely due to increased amount cross-linked
collagen compared to younger tissue
 Scurvy – problems with sea voyages, lack of food other than salted meats.
– Symptoms include, swollen gums, loose teeth, small black-and-blue
spots on the skin, and bleeding from small blood vessels are among
the characteristic signs of scurvy.
– Caused when vitamin C (ascorbic acid) is lost from diet
– Vit C is needed to keep Iron reduced in the active site of prolyl
hydroxylase. This is the enzyme responsible for conversion of proline
to hydroxyproline. The H bonding of hydroxyproline is vital for the
connective protein’s function
– In 1795, the British Royal Navy provided a daily ration of lime or lemon
juice to all its men. English sailors to this day are called "limeys", for
lime was the term used at the time for both lemons and limes.
Collagen Related Disease
Several
heritable diseases result from mutations in the
collagen
Brittle Bone
Disease –
results from a
Gly-Ala
mutation –
Consider the
consequences
of this
mutation, both
in the protein’s
triple helix and
the strength of
the bone!
Collagen Related Disease
Several heritable diseases result from mutations in the
collagen
Marfan’s Syndrom and
Ehler’s-Danlos syndromes inherited disorder of
connective tissue which
affects many organ systems,
including the skeleton,
lungs, eyes, heart and blood
vessels.
All resulting from various
mutation in collagen and
other fibril associated
proteins, ultimately affecting
the structure and molecular
interaction.
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Tertiary structure
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–
–
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overall final 3 D shape of a protein assumes
aa side chain interactions responsible for 3 D structures
hydrophobic interactions
salt bridges
hydrogen bonds (know donors and acceptors)
sulfhydryl bonds
Tertiary structure
–
–
–
–
–
–
overall final 3 D shape of a protein assumes
aa side chain interactions responsible for 3 D structures
hydrophobic interactions
salt bridges
hydrogen bonds (know donors and acceptors)
sulfhydryl bonds
Domain - an amino segment of folded protein showing conformational
integrity. Or…
Tertiary structure
–
–
–
–
–
–
overall final 3 D shape of a protein assumes
aa side chain interactions responsible for 3 D structures
hydrophobic interactions
salt bridges
hydrogen bonds (know donors and acceptors)
sulfhydryl bonds
Domain - an amino segment of folded protein showing conformational
integrity. Or…
A region of the protein that has its own identifiable function. There are
dozens of domains identified. A protein can have more than one domain.
– Can be made of the whole protein or just part of the protein.
– Often coded by their own section of DNA (exon)
Quaternary structure
Proteins with 2 or more peptide chains or subunits
Proteins with 2 or more peptide chains or
subunits can be different or identical subunits
loss of quaternary or tertiary (native) structure
is called denaturation. Examples include
- Heat – to unravel the folding by adding
energy – eg. egg whites
- Detergent – interfere with hydrophobic
interactions
- Changes in pH - ionization of R groups
Reducing agents – chemicals which break sulfhydryl
bonds by changing the redox state of cys amino
Mad Cow Disease
All known prion diseases are fatal. Since
the immune system does not recognize
prions as foreign, no natural protection
develops. Scrapie in sheep was first
described during the18th century. It has
been transmitted to other animals such
as mink and cats, and more recently to
cows (mad cow disease or bovine
spongiform encephalopathy, BSE) through
contaminated feedstuff.
In New Guinea, the Fore-people contracted kuru by
eating the brains of deceased people. CreutzfeldtJakob Disease (CJD) frequently arises spontaneously,
while fatal familial insomnia (FFI) GerstmannSträussler-Scheinker GSS) disease, and 10-15% of CJD
are caused by mutations in the gene encoding the prion
protein. A new variant CJD, diagnosed in some 20
patients, may have arisen through transmission of BSE
to humans.
The Nobel Foundatioin
BSE - Mad Cow; A protein gone wrong
The prion protein exists in two forms. The normal, protein
(PrPc) can change its shape to a harmful, disease-causing
form (PrPSc). The conversion from PrPc to PrPSc then
proceeds via a chain-reaction. When enough PrPSc proteins
have been made they form long filamentous aggregates that
gradually damage neuronal tissue. The harmful PrPSc form is
very resistant to high temperatures, UV-irradiation and
strong degradative enzymes.
Prions and protein folding
Prions affect
different regions of
the brain. A spongelike appearance
results when nerve
cells die. Symptoms
depend on which
region of the brain is
affected.
A precise diagnosis of a prion disease can
only be made upon autopsy. The figures
show thin sections of diseased brains.
FFI, with typical proliferation of
astrocytes, the support cells of the
brain, is shown to the left (arrows).
CJD, with the characteristic spongiform
appearance with vacuoles (arrows) is
shown to the right.
Cerebral cortex -loss of memory
and mental acuity (CJD).
Thalamus Damage results in
insomnia (FFI).
Cerebellum Damage results in
problems to coordinate body
movements and difficulties to
walk (kuru, GSS).
Brain stem In the mad cow
disease (BSE).
Prion diseases arise in three different ways
1. Through horizontal transmission from e.g. a sheep
to a cow (BSE).
2. In inherited forms, mutations in the prion gene are
transmitted from parent to child.
3. They can arise spontaneously.
Route of infection
When cows are fed with offals prepared from infected
sheep, prions are taken up from the gut and
transported along nerve fibers to the brain stem.
Here prions accumulate and convert normal prion
proteins to the disease-causing form, PrPSc. Years
later, BSE results when a sufficient number of nerve
cells have become damaged, affecting the behavior
of the cows.