Download Lecture 3 Proteins and Disease Protein structure summary… Recap…

10/21/10
Protein structure summary…
Lecture 3
Proteins and Disease
Recap…
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Proteins are polymers of amino acids (polypeptides)
Amino acid polymers are due to formation of peptide bonds
20 R groups = 20 aa’s – 4 subgroups
Protein structure has 4 levels:
Primary structure = aa sequence
Secondary structure = alpha helix
beta pleated sheet
(due to reactions within the polypeptide backbone)
•  Tertiary structure = hydrophobic bonds
Van der waals interactions
Ionic bonds
Hydrogen bonds
Disulphide bridges
(due to interactions between Reactive side chains)
•  Quaternary structure
•  X-ray crystallography
–  Is used to determine a protein’s threedimensional structure
How?
• X-ray hits a crystallised protein
• Diffracts into many different
directions, based on chemical
make-up of the protein
• 3D image of electrons in
protein
• Can calculate what atoms,
chemical bonds and their order
are present
X-ray
diffraction
pattern
Photographic film
Diffracted X-rays
X-ray
X-ray
beam
source
Crystal Nucleic acid Protein
(a) X-ray diffraction pattern
(b) 3D computer model
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Recap…
Proteins are encoded by genes
Inherited information
carried in genes
Controls the pattern or
sequence of mRNA
Functional protein
Proteins and Disease
"a disease gene is discovered, which leads
to the disease-causing protein, which
leads to a definition of the molecular basis
of the disease, which enables researchers
to develop compounds to cure the
disease"
Frank Gannon
Director SFI
Passage of information from gene sequence to protein structure
Proteins and Disease
Proteins and Disease
Disease
Gene
Disease
Gene
Disease
Message
Disease
Message
Disease
Protein
ONE GENE defect
eg. Huntington’s
disease, or cystic
fibrosis
Cells can
compensate
Disease
Protein
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Proteins and Disease
Proteins and Disease
Compensatory
Pathways
Disease
Gene
Disease
Message
Compensatory
Gene
Compensatory
Message
Disease
Gene
Multiple
Disease
Genes
Disease
Message
The real
story
Disease
Protein
Functional
Protein
Proteins and Disease
Disease
Gene
Multiple
Disease
Genes
Disease
Message
Disease
Fingerprint
Disease
Protein
Disease
Protein
Proteins and Disease
Disease
Fingerprint
Therapeutic
Intervention
• New drug targets
• New drugs
• Early treatment
Diagnostics
• New tests
• Early diagnosis
• Predict
response to
therapy
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Proteins and Disease
Sickle-Cell Disease:
A Simple Change in
Primary Structure
•  Humans are complex
•  Scientists use simple models to study
disease
–  Yeast
–  Drosophila (fruit fly)
–  Caenorhabditis elegans (worm-nematode)
One
Gene
•  Sickle-cell disease
–  Inherited blood disorder
–  Results from a single amino acid substitution in the Gene
protein hemoglobin (glutamic acid- valine)
Variants
–  Hemoglobin carries oxygen in red blood cells
–  Symptoms: sickle cell crises
•  Misshapen angular cells clog tiny blood vessels
•  Impede blood flow
•  Physical weakness, pain, organ damage and death
Hemoglobin function
•  All body cells require oxygen
for metabolism
-oxygen is non-polar and
not soluble in the aqueous
blood.
•  Hemoglobin has a group called
"heme", which is at the heart of
the protein structure.
•  Hemoglobin structure and sickle-cell
disease
Primary
structure
Normal hemoglobin
Val
His Leu Thr
Pro Glul Glu
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Sickle-cell hemoglobin
. . . Primary
Val
His
Leu Thr
α
β
Function
Molecules do
not associate
with one
another, each
carries oxygen.
Red blood
cell shape
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen
β
α
Pro
Val
Glu
structure 1 2 3 4 5 6 7
Secondary
β subunit and tertiary
structures
Quaternary Hemoglobin A
structure
•  At the center of the heme
group is the iron +2 metal ion.
•  The oxygen molecule will
ultimately bind to this iron ion
Disease
Protein
Quaternary
structure
...
β subunit
α
β
β
α
Function
10 µm
10 µm
Red blood
cell shape
Exposed
hydrophobic
region
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced.
Fibers of abnormal
hemoglobin
deform cell into
sickle shape.
•  Globular structure
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Sickle cell anemia
•  1/10 Africans have this trait
•  Selective advantage to the disease trait in
malarial regions
•  The malarial parasite remains at a lower density
in cells with sickle hemoglobin
•  Trade off
-Fewer malarial symptoms
vs
-sickle cell symptoms
Proteins and Disease
Disease
Gene
Multiple
Disease
Genes
Disease
Message
Disease
Fingerprint
Disease
Protein
Breast Cancer-mutant ER
receptor
•  Most common
malignancy in women
•  Estrogen receptors are
over-expressed in
around 70% of breast
cancer cases, referred
to as "ER-positive".
•  Constant growth of
Breast cells
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Breast Cancer-mutant ER
receptor
•  Tamoxifen -drug used
to reduce ER levels
•  Cancer cells depend
on ER and so die
–  Cell suicide called
‘apoptosis’
Drug
Gene mutations
•  Proteins are coded for by genes
The order of bases
along the length of
the DNA= genetic code
instructs what protein
is to be made
DNA
mRNA
•  Amino acid change is due to a gene defect
•  A single base change in the DNA of a
gene can give rise to a single amino acid
change (sickle cell anemia)
Each set of three
bases, or codon,
specifies a particular
amino acid. Amino
acids are the building
blocks of proteins.
Amino acid
Glutamic acid codon = GAG
valine codon = GUG
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Gene Mutations causing SNPs
- single nucleotide polymorphisms (SNPs) variations in DNA sequence of genes
-can cause an amino acid change
Disease
Cause
Trait
Retinitis Pigmentosa
Mutation in gene for
transducin
blindness
Spina Bifida
Mutation in gene for
Methylene Tetra
Hydra Folate
Reductase (MTHFR)
Neural tube defect
Spina Bifida
This enzyme MTHFR uses a nutrient called folic acid to help form the neural tube.
The variant requires more folic acid:
Normal MTHFR
Folic acid
Building blocks for neural tubes
Variant MTHFR
Protein Folding
Protein folding
•  Unique shape confers unique function
•  What are the key factors determining shape?
-primary structure - sequence
effects
-secondary structure – bonds in polypeptide backbone
-tertiary structure
- bonds between side chains
•  Is this the whole story? –NO!
-we don’t know all the rules
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Video
Chaperones
•  http://www.youtube.com/watch?
v=gFcp2Xpd29I&feature=related
•  Protein folding occurs
spontaneously in vitro
•  Physical and chemical conditions
of the cellular environment can
affect “native” conformation
• 
Hydrophilic environment
inside
pH changes / salt changes / temperature
changes
•  http://www.youtube.com/watch?
v=EZ1XuOgknuE&p=B1701B280DD86D3
F&playnext=1&index=46
Protein Folding
Solvent
•  Chaperone proteins assist protein
folding
-protect a new protein from the
external environment
-provide hydrophillic environment
for proper folding
Cylindrical in shape
Eg. TRiC
Chaperones
Hydrophobic
amino acids
Hydrophillic
amino acids
Amino Acid Sequence determines the way the protein will fold in a specific
environment using
•  Hydrophobic interactions
•  Hydrogen bonds
•  Van Der Waals forces
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Disease due to misfolded proteins
Prions- misfolded proteins
•  How can a protein which can not replicate itself be infectious?
- Many diseases are diseases of protein
conformation.
•  Prions are mis-shapen versions of normal brain proteins
– once a prion gets into the brain they interact with the normal
version of the protein and convert it to the misfolded- prion
version
- eg Creutzfeld Jacob disease
- Prions = infectious proteins, virtually
indestructible
•  This way Prions trigger a chain reaction which increase their
numbers
- There is no known cure for prion
diseases
•  These Prions then polymerise and are toxic to normal cells
- Prion proteins build up in the brain,
ultimately causing death
Prions
Normal
Disease-causing
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Prions
The mechanism:
PrPc (normal)
Disease due to misfolded or
aggregated proteins
Normal brain
PrPsc infects
Normal brain
PrPsc interacts with
PrPc
Normal brain
PrPc turned into PrPsc
Causing polymerisation
Neuronal death occurs
Symtoms begin and accelerate
Aggregates- misfolded proteins
Alzheimer’s Disease
•  Amyloid-related
disease-Amyloids are
insoluble fibrous
protein aggregates
•  Accumulation of
abnormally folded
proteins in the brain
called β-amyloid
plaques
•  Death of neurons
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Alzheimer’s Disease
(A) Senile plaques (SPs) and neuron loss in entorhinal cortex. SPs show dense cores and radially oriented
dystrophic neurites. (B) A typical neurofibrillary tangle in CA3. Bielschowsky silver stain. (C) Amyloid beta
protein immunohistochemistry demonstrates frequent plaques in posterior cingulate cortex, accompanied by
cerebral amyloid angiopathy (inset). Hematoxylin counterstain. (D) Immunohistochemical stains for
hyperphosphorylated tau show aggregation in NFTs and cortical dystrophic neurites
In summary…
•  A single amino acid change in the primary
structure of a protein can cause disease eg.
Sickle cell disease
•  Amino acid changes occur due to SNPs in the
DNA sequence of a gene
•  Chaperones assist protein folding
•  Many diseases are due to protein mis-folding eg.
CJD
•  Protein structure can be determined by X-ray
crystallography
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