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Chapter 6
Protein Structure and Folding
1.  Secondary Structure
2.  Tertiary Structure
3.  Quaternary Structure
and Symmetry
4.  Protein Stability
5.  Protein Folding
Myoglobin
Introduction
1.  Proteins were long thought to be colloids of
random structure
2.  1934, crystal of pepsin in X-ray beam produces
discrete diffraction pattern -> atoms are ordered
3.  1958 first X-ray structure solved, sperm whale
myoglobin, no structural regularity observed
4.  Today, approx 50’000 structures solved
=> remarkable degree of structural regularity
observed
Hierarchy of Structural Layers
1.  Primary structure: amino acid sequence
2.  Secondary structure: local arrangement of peptide
backbone
3.  Tertiary structure: three dimensional arrangement
of all atoms, peptide backbone and amino acid side
chains
4.  Quaternary structure: spatial arrangement of
subunits
1) Secondary Structure
A)  The planar peptide group limits polypeptide
conformations
The peptide group ha a rigid, planar structure as a
consequence of resonance interactions that give
the peptide bond ~40% double bond character
The trans peptide group
The peptide group assumes the trans conformation
8 kJ/mol mire stable than cis
Except Pro, followed by cis in 10%
Torsion angles between peptide groups
describe polypeptide chain conformations
The backbone is a chain of planar peptide groups
The conformation of the
backbone can be described
by the torsion angles
(dihedral angles, rotation
angles) around the Cα-N (Φ)
and the Cα-C bond (Ψ)
Defined as 180° when
extended (as shown)
+ = clockwise, seen from Cα
Not all combinations of torsion angles are possible,
some result in collision of N-H with O=C or R
The
Ramachandran
diagram
indicates allowed
conformations of
polypeptides
• Pro limits Φ to -60°
• Gly allows more
freedom
B) The most common regular secondary
structures are the α Helix and the β Sheet
•  Two structures are widespread: α Helix and β
Sheet = regular secondary structures
• The α helix is a coil: structure
with allowed angles and stabilized
by hydrogen bonding
• Linus Pauling, 1951, model building
• Right-handed turn
• Pitch 3.6 Aa/turn = 5.4 Å
• Average length 12 Aa = 3 turns
~18 Å
• Bonding of C=O with N-H at n+4
• R point outwards, downwards
β sheets are formed from extended
chains
•  like α helix, β sheets are stabilized by hydrogen
bonding
• Bonding occurs between neighboring chains rather
than within the structure as is the case with α helix
• Parallel and antiparallel
Pleated appearance of a
β sheet
•  From 2 to 22 strands
•  Average 6 strands in protein
•  Exhibit right-handed twist
7-stranded
Bovine carboxypeptidase A
Coils
Helices
β-sheet
Turns connect some units of
secondary structure
•  topology = connectivity of β sheets can be
complex or made by a simple turn/loop
•  reverse turns or β bends, occur at the
protein surface, connect β sheets
Reverse turns in polypeptide chains
•  Require 4 Aa
•  180° flip of Aa 2
C) Fibrous proteins have repeating
secondary structure
Historical classification of proteins as globular of
fibrous
Fibrous proteins often have protective, connective,
or supportive role in living organisms
examples: keratin and collagen
α keratin is a coiled coil
Keratin, in all higher vertebrates
- horny outer epidermal layer
- hair, horn, nails, feathers
- α in mammals
- β in birds and reptiles
- Humans, over 50 α genes
- tissue specific expression
Forms coiled coil structure
- helix pitch 5.1 Å (rather than
5.4 Å as in α-helix)
- Parallel N->C, 81 residues long
Coiled coil has a pseudo-repeating structure:
a-b-c-d-e-f-g in which residues a and d are
predominately nonpolar.
Helical wheel
representation Higher order α keratin structure
-> Macrofibril
-> single hair
α keratin
α  keratin is rich in Cys residues, form disulfide
bonds that crosslink adjacent chains
α  keratins are classified “hard” and “soft” depending
on whether they have high or low sulfur content
Hard keratins in hair, horn, and nails are less pliable
than soft keratins such as in skin and callus (hornhaut)
Reductive cleavage of disulfide bonds results in
“curled hairs”
Collagen is a Triple Helix
Collagen occurs in all multicellular organism,
- Is the most abundant vertebrate protein
- Strong insoluble fibers
- Stress bearing component of connective tissues
(bone, teeth, cartilage, tendon)
One collagen molecule consists of three polypeptide
chains
-  Mammals have at least 33 genetically distinct chains
- Assembled in 20 different collagen varieties
- One of the most common is Type I collagen:
-  two α1(I) chains and one α2(I) chain
Collagen has a distinctive amino acid composition:
- 1/3 of its residues is Gly
-  15 to 30% are Pro and 4-hydroxyprolyl (Hyp)
These non-standard amino acids are formed after
collagen is synthesized
- Pro - > Hyp conversion by prolyl hydroxylase,
Vitamin C-dependent (ascorbic acid)
Collagen Diseases
Scurvy (Skorbut) results from Vitamin C-deficiency,
- Lack of newly synthesized functional collagen,
- Skin lesion, fragile blood vessels, poor wound healing
-  Sailors on long trips, lack of fresh food
-  Captain James Cook “limely” introduced limes to diet
Several rare genetic
collagen disorders
-  tend to be dominant
The Collagen Triple Helix
Collagen amino acid sequence consists of a
repeating triplet: Gly-X-Y over some 1000
residues, X often Pro, Y often Hyp
-  Pro prevents formation of α helix
-  Collagen forms left-handed superhelix with ~3
amino acids per turn
-  Three parallel chains wind around each other to
form right-handed triple-helical structure
-  Every third residue of each chain
passes through the center if the triple
helix, only Gly can pass
-  Three chains are staggered, Gly at each level
-  Inter-chain hydrogen bonding
Structure of collagen model peptide
Hydrogen bonding from Gly N- to
Pro O-atoms of adjacent chain
Collagen Crosslinking
Collagens well-packed, rigid, triple-helical
structure is responsible for its
characteristic tensile strength
Collagens assemble to form loose
networks or thick fibrils arranged in
bundles or sheets, depending on the
tissue
Collagen is internally covalently cross
linked which makes it insoluble, not by
Cys but by Lys and His reactions
Lysyl oxidase reaction:
D) Most proteins include nonrepetitive
structures
Majority of proteins are globular and may contain
several types of regular secondary structures,
including α helices and β sheets and coils (≠ random
coils, which are completely unstructured)
The sequence affects the secondary structure:
-  Pro is helix breaking, induces kink in helix and β
sheet
-  Large amino acids such as Tyr and Ile induce steric
clashes
-  Peter Chou and Gerald Fasman revealed the
propensity of amino acids to form helical or sheet
structures -> Chou-Fasman prediction
2) Tertiary Structure
Tertiary structure of a protein describes the folding
of its secondary structural elements and specifies
the position of every atom in the protein
This information is deposited in protein structure
database (pdb)
Experimentally determined by X-ray crystallography
or NMR
Protein crystals
A) Most proteins structures are determined by Xray crystallography or nuclear magnetic resonance
X-Ray crystallography: technique that directly
images molecules
-  X-ray wave length is short, ~1.5 Å, equivalent to
distance of atoms (visible light 4000 Å)
-  Crystal: repetitive arrangement of the same
structure => diffraction pattern (darkness of spot
is function of crystals electron density)
-  X-ray interact with electrons (not with nuclei) ->
X-ray structure is thus an electron density map of
a given protein -> represents contours of atoms
A thin section through a 1.5 Å resolution electron
density map of a protein that is contoured in three
dimensions
Most protein crystal structures exhibit less than
atomic resolution
Crystal is build up by repeating units, containing
protein in native conformation,
-  highly hydrated (40-60% water)
-  soft, jellylike consistency, unlike NaCl crystals
-  molecules are slightly disordered and display
Brownian motion -> this determines the resolution
limit of a given protein crystal (typical 1.5 – 3 Å)
-  inability to crystallize a protein to form crystals of
sufficiently high resolution is a major limiting factor
in structure determination
Electron density maps of diketopiperazine at
different resolution levels
- Electron density map alone is not sufficient to determine
the structure if the protein,
- Amino acid sequence is also required
- Computerized fitting algorithm of atoms into the
experimentally determined electron density map results in
protein structure determination of up to 0.1 Å resolution
Most crystallized proteins maintain their
native conformations
Key question: does the structure of protein in a crystal
accurately reflect the structure of the protein in solution,
where it normally functions ?
1.  The protein in the crystal is hydrated like it is in
solution
2.  X-ray structure is similar to NMR structure, which is
determined from proteins that are in solution
3.  Many enzymes remain catalytically active in the crytsal
Protein structures can be determined by
NMR
Nuclear magnetic resonance, NMR, an atom nucleus
resonates if a magnetic field is applied. This resonance is
sensitive to the electronic environment of the nucleus and
its interaction with nearby nuclei
- Developed since 1980, Kurt Wüthrich (ETH-Z), to
determine protein structures in solution
-  Because there are many nuclei in a protein that would
crowd in a conventional one-dimensional NMR -> twodimensional (2D) NMR was developed to measure atomic
distances of chemically linked atoms (COSY) or of
spatially close atoms (NOESY)
-  Size limit of about 40 kD, may reach 100 kD soon
-  Dynamic, can follow protein motion or folding
B) Side chain location varies with polarity
Since Kendrew solved the first protein structure, nearly
50’000 protein structures have been reported
No two are the same, but they exhibit some remarkable
consistency: globular structures lack the repeating
sequences that support the conformation of fibrous
proteins
Amino acid side chains in globular proteins are distributed
according to their polarity:
1.  Nonpolar residues Val, Leu, Ile, Met and Phe occur mostly in the
interior of a protein, excluded from the contact with water,
hydrophobic core, compact packing (no empty room)
2.  Charged amino acids Arg, His, Lys, Asp, Glu are located on the
surface, never in hydrophobic core
3.  Uncharged polar groups Ser, Thr, Asn, Gln, Tyr are usually on the
surface but are also found inside but then are hydrogen bonded
Side chain locations in an α helix and a β
sheet
polar
Surface
of protein
nonpolar
Side chain distribution in horse heart cytochrome c
Hydrophilic amino acids
Hydrophobic amino acids
C) Tertiary structures contain combinations
of secondary structure
Globular proteins are build from combinations of secondary
structure elements
These combinations of secondary structure elements form
protein motifs = supersecondary structures
1.  Most common is βαβ motif, α helix connects two parallel
strands of a β sheet
2.  Equally common is a β hairpin, antiparallel strands
connected by tight reverse turn
3.  αα motif, two successive antiparallel α helices packed
against each other
4.  Greek key motif, β hairpin is folded over to form 4stranded antiparallel β sheet
Most proteins can be classified as α, β, or
α/β
Secondary structural elements occur in globular proteins in
varying proportions
- E. coli cytochrome b562 for example consists only of α
helices => α protein
-  Immunoglobulins contain the immunoglobulin fold => β
proteins, contain large proportion of β sheets
-  Most proteins, including lactate dehydrogenase and
carboxypeptidase A are α/β proteins (average ~31% α helix,
28% β sheet)
-  Further subdivision of proteins by their topology: that is
connection of secondary structural elements
Selection of protein structures
Cytochrome b562
with heme Immunoglobulin
fragment
Lactate
dehydrogenase
Structures of β barrels
Human retinol
binding protein
Peptide
amidase F
Triose
phosphate
isomerase
Large polypeptides form domains
Polypeptides of more than 200 amino acids usually fold into
more than one domain in eukaryotes, prokaryotes can only
fold mono-domain proteins -> bi or multilobal appearance
Most domains consist of 40 to 200 Aa, average diameter of
~25 Å
Many domains are structurally independent units that have
the characteristic of globular proteins
Individual domains often have specific function, i.e. binding
of the dinucleotide NAD+ by nucleotide binding site:
Rossmann fold: 2 (βαβαβ)
Glyceraldehyde-3-phosphate dehydrogenase
2 globular domains
Dinucleotide binding
in N-term domain
Rossmann fold
D) Structure is conserved more than sequence
-  Grouping structures into families of high similarity,
- 50’000 structures define 1’400 protein domain families
- 200 different folding patterns account for about half of all
known structures
-  the protein domain is the evolutionary unit, not its sequence
-  comparison of c-type cytochromes
E) Structural bioinformatics provides tools for
storing, visualizing, and comparing protein
structural information
Structural data obtained by X-ray or NMR describing the
room coordinates of atoms is deposited into database,
similar to sequence information of DNA or proteins
Bioinformatics, structural bioinformatics takes advantage of
this information to address biological questions
Major structural database: Protein Data Bank (PDB), each
structure is assigned a unique identifier (PDBid), i.e.,
sperm whale myoglobin is 1MBO
Molecular graphics program interactively show
macromolecules in three dimensions
-  Jmol is a Web browser-based application that
allows you to directly visualized structures in PDB
-  Example potassium channel (KCSA)
http://www.pdb.org/pdb/explore/jmol.do?
structureId=1F6G
-  Swiss PDB viewer = Deep View allows protein
modeling and superimposition of two structures
Structure comparisons reveal evolutionary
relationships
-  Since evolution tends to conserve structure rather than
sequence, programs have been developed to search for
structurally related protein
-  CATH, classifies proteins in a four level hierarchy:
1. Class: mainly α / β structure
2. Architecture: gross arrangement of secondary structure
3. Topology: shape of protein domains and interconnectivity
4. Homologous superfamily, group of common ancsestor
-  CE (combinatorial extension of the optimal path) finds all
proteins in PDB that can be structurally aligned with the query
structure
-  FSSP (Family of Structurally Similar Proteins)
-  SCOP (Structural Classification of Proteins)
-  VAST (Vector Alignment Search Tool)
3) Quaternary Structure and
Symmetry
-  Many proteins, particularly those of > 100 kD consist of
more than one polypeptide chain. Multi-subunits associate
into defined structure = quaternary structure
-  For example collagen, assembly of multiple subunits is easier
than synthesizing one very large polypeptide chain….
-  Site of synthesis can differ from site of assembly
-  Damaged components can be replaced
-  Less genetic information required to encode self-assembling
subunits
-  Multi-subunit enzymes have multiple catalytic sites that can
be co-regulated
Subunits usually associate noncovalently
-  Multi-subunit protein may consist of identical or
nonidentical subunits (homo-, hetero-oligomeric)
-  oligomers, protomers
-  Example: hemoglobin is a dimer of αβ protomers
-  Contact region between subunits resembles the interior of a
single subunit protein: closely packed nonpolar residues,
hydrogen bonding, interchain disulfide bridges, but generally
less hydrophobic than the hydrophobic core of a single
subunit protein (they are synthesized as monomers and need
to be soluble each one before assembly…)
Quaternary structure of hemoglobin
heme
Subunits are symmetrically arranged
-  In the majority of oligomeric proteins, the subunits are
symmetrically arranged
-  That is: protomers occupy geometrically equivalent positions
-  No inversion or mirror symmetry because this would require
D-amino acids
-  Thus proteins can have only rotational symmetry
-  Simples case, cyclic symmetry, single axis of rotation (2-,3-,
4-,n-fold). C2 is most common
-  Dihedral symmetry (Dn): n-fold rotational axis intersects
with a twofold rotational axis. D2 most common
-  Tetrahedron, cube, and icosahedron, for example spherical
viruses
Symmetries of oligomeric proteins
Rotational symmetry
Symmetries of oligomeric proteins
Dihedral symmetry
Symmetries of oligomeric proteins
4) Protein Stability
-  Native proteins are only marginally stable under
physiological conditions -> high turnover
-  Free energy required for denaturation is ~0.4 kJ/mol/
residue -> fully folded 100 residue protein is ~40 kJ/mol
more stable than its unfolded form = energy of 2 hydrogen
bonds
-  But energy of all noncovalent interactions within a protein is
in the order of thousands of kJ/mol
=> native structure results from a delicate balance of
powerful counteracting forces
A) Proteins are stabilized by several
forces
-  Protein structures are governed mainly by hydrophobic
effects and to lesser extend by interactions between polar
residues
-  The hydrophobic effect causes nonpolar substances to
minimize their contact with water (degree of order, entropy,
of water is decreased because water has not to form “cages”
around the hydrophobic groups)
-  Relative hydropathy of residues: energy required to
solubilize a given amino acid in water
Hyrdopathic index plot for bovine
chymotrypsinogen
interior
exterior
Sum of hydropathie of 9 consecutive residues is plotted
Electrostatic interactions contribute to
protein stability
-  Relatively week van der Waals forces are nevertheless
important to stabilize the protein in its native state
-  But hydrogen bonds, which are a central feature of protein
structures, particularly secondary structures, make only a
minor contribution to the overall stability of a protein
-  Because of extensive hydrogen bonding of surface residues
to water, difference between native and unfolded energy of
hydrogen bonding is ~-2 to 8 kJ/mol
-  Ion pairing / salt bridges, i.e. between Lys+ and Asp75% of ionized residues are paired, mostly on surface, but
they have only a small stabilizing effect (paid by loss of
entropy and loss of solvation free energy) => poorly conserved
Examples of ion pairs in myoglobin
-  Oppositely charged side chains from groups that are far
apart in sequence closely approach each other through the
formation of ion pairs
Disulfide bonds cross-link extracellular
proteins
-  Intrachain or inter-chain disulfide bonds form during
folding of the protein
-  While they are not necessary for the structure/function of
most proteins, they “lock in” a particular backbone fold
- Disulfide bonds are rarely in cytoplasmatic protein because
the cytosol is a reducing environment that would cleave the
disulfide bridges
-  Most disulfide bridges occur in secreted proteins, i.e. they
are stable in the more oxidizing extracellular environment
Metal ions stabilize some small domains
-  Metal ions, bound within a protein, can also serve to
stabilize the protein structure, through internal cross-linking
-  For example zing fingers are motifs that frequently occur
in DNA binding proteins
-  Zn2+ is tetrahedrally coordinated by side chain Cys, His and
occasionally Aps and Glu
-  Zn2+ allows short stretches of polypeptides, 25-60 residues,
to fold into stable units
-  Zinc fingers are not stable in the absence of Zn2+
-  Zn2+ is stable and not oxidized/reduced (unlike Cu, or Fe)
A zing finger motif
Coordinated
by Cys and
His
Proteins are dynamic structures
-  Plethora of forces that act to stabilize a protein leave room
for mobility/movement of structural elements
-  Proteins are flexible and rapidly fluctuating molecules
-  Mobility is important for protein function
-  Conformational flexibility = breathing
Molecular dynamics of myoglobulin
Snapshots at
intervals of
5 x 10-12 sec
Hem
B) Proteins can undergo denaturation
and renaturation
-  Low conformational stability of native proteins makes them
susceptible to denaturation:
through alterations in the balance of weak bonding forces
-  Denaturation by:
-  Heat, cooperative melting of the structure
-  pH variation, alters ionization state of side chains
-  Detergents, break hydrophobic interactions
-  Chaotropic agents, guanidium ion, urea (5-10 M). Small
organic molecules that increase the solubility of nonpolar
substances in water, disrupt hydrophobic interactions
Many denatured proteins can be
renatured
-  1957, Christian Anfinson could denature and renature
ribonuclease A (RNase A), 124 Aa single chain protein
-  Denaturation in 8 M urea
-  Renaturation by dialysis, full enzymatic activity
⇒  Protein must spontaneously fold into active conformation,
including proper re-formation of 4 Cys-bridges
⇒  Even correct Cys bridges form spontaneously:
1/7 x 1/5 x 1/3 x 1/1 = 1/105 (less than 1%)
⇒  The primary structure if the protein dictates its three
dimensional conformation
Denaturation and renaturation of RNase A
Thermostable Proteins
-  Thermophilic and hyperthermophilic bacteria can grow at
near 100°C
-  Live in hot springs or submarine hydrothermal vents
-  But have the same metabolic pathways as mesophilic
organisms
-  No striking differences in overall structures
-  Difference of stability of corresponding thermophilic
proteins is ~100 kJ/mol = few noncovalent interactions
-  Network of salt bridges at surface
-  Increased hydrophobic contribution, but also only ~0.4 kJ/
mol/residue
=> low stability is important for function !! Breathing of
structure
5) Protein Folding
-  Protein folding is directed largely by residues that occupy
the interior of the folded protein
-  How does a protein fold into its three dimensional structure
-  Does not occur through sampling of all possible
conformations ! This would take longer than the universe
exists
(n residues -> 2n torsion angles, each has 3 stable
conformations ->32n = ~10n possible conformations, 10-13 sec
for each conformation -> t = 10n/1013
=> for n=100 residues t = 1087 sec,
20 Mia years = 6 1017 sec)
A) Proteins follow folding
pathways
-  Many proteins fold into their native
conformation in less than a few seconds
-  They follow directed pathways, not random
-  Folding occurs locally by the formation of
secondary structures
-  Followed by a hydrophobic collapse of the
structure to adopt a molten globule
= has most of the secondary structures
formed but not yet the proper tertiary
structure
-  Proteins fold in a hierarchical manner
-  Cooperative process
Energy-entropy diagram for protein folding
Folding funnel
Temporary
folding
traps
Protein structure prediction and
protein design
-  Sequence of 1 Mio proteins is know, but structure
has been determined for only 50’000
-  How is the structure encoded in the primary
sequence ? -> ab initio prediction of structure
-  Homology modeling of new sequence against existing
structure
-  Structural genomics, determine X-ray structure for
all the representative protein domains in a genome
-  Chou & Fasman predictions does not take into
account the influence of the neighboring residues
Protein structure prediction and protein
design
-  Protein design, inverse of structural prediction
-  Design an amino acid sequence that will form the
target structure or even target function
-  28 residue peptide that forms ββα structure
Protein disulfide isomerase acts during
protein folding
-  Proteins fold more slowly in vitro than they fold in
vivo
-  This is frequently due to the formation of nonnative disulfide bridges which are then slowly
exchanged to the native ones
-  In vivo, disulfide bond formation is catalyzed by and
enzyme: protein disulfide isomerase (PDI)
-  PDI binds a variety of unfolded proteins via a
hydrophobic patch to form a mixed disulfide
Mechanism of protein disulfide
isomerase
Mechanism of protein disulfide
isomerase
B) Molecular chaperones assist protein
folding
-  Proteins begin to fold as they are synthesized and
grow on the ribosome
-  In vivo, a peptide chain folds in the presence of a
very high concentration of other proteins
-  Molecular chaperones are essential proteins that
help to fold newly synthesized or partially unfolded
proteins to re-fold correctly
-  Many molecular chaperones were first described as
heat shock proteins (Hsp), their expression is
strongly induced upon heat treatment of cells
Chaperone activity requires ATP
Classes of molecular chaperones in prokaryotes and
eukaryotes
1. Hsp70 family, function as monomers with the
cochaperone Hsp40, folds newly made proteins
2. Chaperonins, large multisubunit proteins (see below)
3. Hsp90 proteins, folding of proteins in signal
transduction such as steroid receptors
4. Trigger factor, associate with ribosome and
prevent improper folding of newly made
All of them operate by binding to solvent-exposed
hydrophobic surfaces and subsequent release
All are ATPases
The GroEL/ES chaperonin forms closed
chambers in which proteins fold
The chaperonins in E. coli consist of two types of
subunits, GroEL and GroES
Structure: 14 identical 549-residue GroEL subunits
arranged in two stacked rings of seven subunits each
Complex is capped at one end by domelike heptameric
ring of 97 Aa GroES subunits
Bullet-shaped complex with C7 symmetry
Central chamber of ~45 Å in which peptides fold
X-ray structure of the GroEL-GroES-(ADP)7
complex
GroES (cap)
GroEL
(cis)
GroEL
(trans)
Note the larger size of
The cavity formed by the
cis ring
ATP binding and hydrolysis drive the
conformational changes in GroEL/ES
Each GroEL subunit can bind and hydrolyze ATP which
induces a conformational change -> movement -> work
All 7 subunits acts in concert to work on the unfolded
substrate protein
Exposure (ATP) or hiding (ADP) the hydrophobic
patch domain, to allow the protein to refold within an
isolated hydrophilic microenvironment
Eukaryotic counterpart: TRiC
Reaction cycle of the GroEL/ES
chaperonin
Some diseases are caused by protein
misfolding
At least 20 – usually fatal – human diseases are
associated with extracellular deposition of normally
soluble proteins as insoluble fibrous aggregates =
amyloids (starch-like)
Amyloidoses: set of rare inherited diseases in which
mutant forms of normally soluble proteins, such as
lysozyme or fibrinogen, accumulate as amyloids
Symptoms usually become apparent only later in life
(30-70 years) progress over 5-15 years till death
Amyloid-β protein accumulation in
Alzheimer’s disease
• Alzheimer’s disease is a neurodegenerative
condition, mainly in elderly ~10% of >65; 50% >85
• Amyloid plaque in brain tissue, surrounded by dead
and dying neurons
• Plaques consist of fibrils of a 40- to 42-residue
protein, amyloid-β protein (Aβ)
• Aβ is a fragment from a 770-residue membrane
protein, Aβ precursor protein (βPP) whose normal
function is unknown
Amyloid-β protein accumulation in
Alzheimer’s disease (2)
• Aβ is excised from βPP in a multistep process through
the action of two proteolytic enzymes: β- and γsecretase
• The age-dependence suggest that Aβ deposition is an
ongoing process
• Rare mutations in βPP result in early onset of the
disease
• Similar to Down’s syndrome patients (trisomy of Chr
21), which invariably develop Alzheimer’s by their 40th
• β- and γ-secretase inhibitors are being developed and
tested
Brain tissue from an individual with
Alzheimer’s disease
Prion diseases are infectious
• Scrapie, neurological disorder in sheep and goats,
thought to be due to “slow viruses”
• Bovine spongiform encephalopathy (BSE, mad cow
disease), and kuru (degenerative brain disease in
human, cannibalism on Papua New Guineas),
Kreutzfeld-Jakob disease (CJD), sporadic
(spontaneously arising)
• Neurons develop large vacuoles that give brain
tissue a spongelike microscopic appearance
• All are known as transmissible spongiform
encephalopathies (TSEs)
Prion diseases are infectious (2)
• TSEs are not caused by virus or microorganism
• Infectious agent is a protein = prion (proteinaceous
infectious particle), TSE = prion diseases
• The scrapie prion is named PrP (prion protein), 208 Aa,
many hydrophobic residues, aggregates to clusters of
rodlike particles that resemble amyloid fibrils
• How are prion diseases transmitted ? Scrapie form of
PrP, PrPSc is identical to PrPC in sequence but differs in
secondary and tertiary structure
• PrPSc catalyzes conformational change of PrPC to
become PrPSc which becomes insoluble and forms
rodlike particles
Electron micrograph of a cluster of
partially proteolyzed prion rods
• PrPSc is insoluble and protease
resistant
• Transmission of BSE to human,
new variant CJD in UK (160
cases)
• BSE due to feeding meat-andbone meal Amyloid fibrils are β sheet structures
• PrPC mostly α helical, PrPSc β sheet structures
• β sheet perpendicular to fibril axis
• Almost any protein can be induced to form
aggregates
PrPC
PrPSc
Model of an amyloid
fibril
• Catalyzed formation from
a nucleus/template (rare,
slow)
• Chain/fibril growth (fast)
• β sheet growth mostly
stabilized by inter-chain
hydogen bonds