Transcript Slide 1

LEARNING OBJECTIVES
•STRUCTURE OF PROTEINS
•HOW ARE PROTEINS DENATURED?
•CLINICAL APPLICATIONS
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Different proteins can be formed from 20 a.a in
diff sequences determined by the genetic code
Native conformation of a protein( unique 3D
structure) is determined by the sequence
Binding sites are formed after folding, dictating
function of the protein
Clinical consequences
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Changes in protein structure
Conformational changes in proteins that
affect solubility and degradability
E.g. Amyloidosis- IgG chains form an
insoluble protein aggregate called amyloid
in organs and tissues
Prion diseases result from misfolding and
aggregation of normal cellular protein
SCA, point mutation in Hb affects the 4°
structure and its solubility, not ability to
bind oxygen
Roles that proteins play:
Catalytic
Structural
Regulatory
Cell differentiation
Cell communication
Muscle contraction
Transport
Storage
Proteins rock!
Description of Protein Structure?
Levels of Structure
Primary
structure
- linear sequence of amino acids
- peptide bonds
Secondary
structure
- local folding( Regular arrangements of amino acids)
- H-bonding within the backbone
Tertiary
structure
- over all folding and 3D conformation
- mainly R group interactions within one chain
Quaternary
structure
- multi-chain interactions
- mainly R group interactions among polypeptide chains
Peptide Bond Formation
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a. Lack of rotation around the bond:
partial double bond rigid and planar bond
between -C and -amino or –CO group is
Non rotatable
b. Trans configuration:
(steric interference in cis position)
c. Uncharged but polar:
like all –CONH2 links, peptide bonds do not
protonate between pH 2-12
only side chains and N- and C- terminals
can ionize
peptide bond is polar (charged) and can be
involved in H-bonding.
Proteins
Polypeptides and Proteins
Proteins are polyamides.
When formed by amino acids, each amide group is called a peptide bond.
Peptides are formed by condensation of the -COOH group of one amino acid and the NH
group of another amino acid.
The acid forming the peptide bond is named first. Example: if a dipeptide is formed from
alanine and glycine so that the COOH group of glycine reacts with the NH group of alanine,
then the dipeptide is called glycylalanine.
Not broken when proteins are denatured
Prolonged exposure to acid or base at high temps is necessary to break bonds.
1. Naming the peptide
a. order of amino acids in a peptide
Left (N-terminal a.a.) is written first, C-terminal next
b. Naming of polypeptides
component a.a. in peptides called moieties or residues.
Except C-terminal, all moieties called –yl instead of –ine –ate, or -ic
E.g. valylglycylleucine
Characteristics of the peptide bond
3. Trans configuration
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minimizes steric hindrance
Characteristics of the peptide bond - summary
• partial double bond character
• rigid and planar
• trans configuration
• uncharged but polar
trans
config
amide
plane
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O
H
C
H3N
R1
C
R2
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N
H
O
C
C
H
O
This results in the formation of a series of
planes as indicated by the dotted lines
In this structure there is no rotation about
the bond:
Primary structure
gives the kind, number and sequence of
amino acids in the linear polypeptide
chain.
 basis for abnormality in genetic diseases
 starts with the N-terminus and ends with
the C-terminus
 amino acids ends are joined together by
peptide bonds in a polypeptide chain
Determining a protein’s primary structure by
DNA sequencing
Secondary structures
 locally folded structure/regular arrangements in
regions of the polypeptide
 mainly formed through hydrogen bonds between
backbone atoms
Types:
stable secondary structures (interior and surface)
alpha helices
beta-sheets
unstable secondary structures (surface)
bends, random coils, loops, turns
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Formed between the –CO group of one peptide bond
and the –NH group of an adjacent peptide bond
Helps to stabilize secondary structures
-if the H-bonds form between peptide bonds in the
same chain helical structure (α-Helix) or turns (β-Turns)
develops
-if the H-bonds form between peptide bonds in
different chain , extended structures are formed e.g.: βPleated sheets
-helix
right -handed helix
 H-bonding almost parallel to
main axis of helix (weak
bonds)
Each –CO is Hydrogen
bonded to –NH of a peptide
bond that is 4 residue away
from it
 allows extensibility
 PRO and GLY disrupt alpha
 Helix
Left-hand
 helix
Right-hand
 helix
Intrachain Hydrogen Bonding is important in maintaining secondary protein structure.
Here (in the α helix) the carbonyl oxygen from one amino acid is H-bonded to an alpha
nitrogen of the 4th distant amino acid in the polymer.
Hydrogen
bond
b Sheet
• “pleated”
• all peptide bond components involved in H-bonding
• strands visualized as broad arrows
N terminal
C terminal
• may be parallel or antiparallel
• Have a right handed curl , twisted sheets form core
of globular proteins
b Sheet
b-bends
Reverse the direction of a polypeptide chain,
helping it form a compact, globular shape
Often found on the surface of protein molecules
Generally composed of
four amino acids with Proline
and glycine as common
Components
 Stabilized by Hydrogen and Ionic
Bonds
SUPER Secondary structures
 combinations of secondary structures
 also called motifs
Tertiary structure
describes the packing of alpha-helices,
beta-sheets and random coils with
respect to each other on the level of one
whole polypeptide chain
due to R group or side chain
interactions or between R groups at a
distance and backbone
associated with domains
Tertiary structure
Side chain interactions (R groups) which
stabilize the tertiary structure
H-bonds – O or N bound H atoms of Ser,
Thr with COO- or carbonyl grp.↑ solubility
Disulfide bonds – Cysteine →Cystine e.g.
in Igs secreted by cells
Ionic Bonds – btw acidic n basic side
chains (salt bridges)
Hydrophobic interactions – non-polar side
chains on the interior and vice-versa
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Domains
Fundamental functional and 3-D structural
units of polypeptides
>200 amino acids  2 or more domains
folding within domain independent of
folding within other domains
each domain has characteristics of small,
compact, globular protein
Quaternary structure
only exists if there is more than one polypeptide
chain present in a complex protein
describes the spatial organization of the chains
associated with subunits
 assembled usually via electrostatic, H-bonding or
hydrophobic interactions(Non- Covalent
interactions)
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1)
In the cell folding is achieved by:
Protein Disulfide Isomerase
Catalyzes the formation of proper disulfide bond.
2) Chaperones
Chaperones (“heat shock” proteins)
Specialized group of proteins
•assists protein folding
•Catalyzes the proper folding of protein by
inhibiting improper folding and interactions with
other peptides
 prevent protein aggregation and misfolding
by limiting the number of unproductive
folding pathways
Why do proteins fold?
•To achieve a stable 3D
Conformation
•Flexible
•Able to function in the
correct
site of the cell
•Capable of being
degraded
by cellular enzymes
Protein Denaturation
•Unfolding and disorganization of the protein’s secondary,
tertiary and quaternary structures.
•Peptide bonds are not hydrolyzed. (Primary structure)
•Denaturing agents: heat, organic solvents, mechanical
mixing, strong acids or bases, detergents and heavy
metal ions lead and mercury
•Ideally, protein denaturation is reversible.
Folded
Protein
Unfolded
Protein
Protein Misfolding Diseases
When we boil or fry an egg, the
proteins in the white unfold. But when
the egg cools, the proteins do not
return to their original shapes.
Instead, they form a solid, insoluble
(but tasty) mass. This is misfolding !
When Proteins Go Unwell
• Mutation in the DNA so that the amino acid
sequence differs from normal.
• Lack of an enzyme or chaperone needed to
fold a protein.
• Correctly folded protein becoming
misfolded by accumulated damage due to
oxidation or other chemical reaction.
• Interaction with other misfolded proteins.
Amyloidosis
• a group of protein misfolding diseases characterized
by the accumulation of insoluble fibrillar protein that
leads to cell death and tissue degeneration
•The dominant component in amyloid plaque that
accumulates in Alzheimer's is Aβ
•The amyloid precursor protein is a single trans
membrane protein. In Alzheimer's there will be
accumulation of neurofibrillary tangles in the brain,
which contains a key an abnormal form of the tau
protein, which in its healthy form helps in assemble of
microtubular structure.
Amyloidoses
-antitrypsin
Ig light chain
Apolipoprotein
Cystatin C
Procalcitonin
Amylin
Bri-L
keratoepithelin
b-2-microglobulin
Ab peptide
-synuclein
Huntingtin
emphysema
myeloma
hereditary aortic disorder
cerebral hemorrhage
thyroid medullary cancer
diabetes type 2
familial British dementia
dystrophy of the cornea
dialysis related amyloidosis
Alzheimer Disease
Parkinsonism
Huntington Disease
Mad cow and other mad species
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are infectious diseases transmitted by prions
 A proteinaceous infectious particle, or prion is an
infectious agent composed primarily of protein
 known as TSE transmissible spongiform
encephalopathies - creutzfeldt-jakob disease CJD,
Scrapie and BSE bovine spongiform encephalopathy
 transmitted by inoculation, cannibalism, genetic
inheritance
PrP
Non-infectious
PrPSc
Infectious
FIBRILS
Prions propagate by transmitting a mis-folded protein
state: so as with viruses the protein cannot replicate by
itself. Instead, when a prion enters a healthy organism
the prion form of a protein induces pre-existing normal
forms of the protein to convert into the rogue form.
Since the new prions can then go on to convert more
proteins themselves, this triggers a chain reaction that
produces large amounts of the prion form.
All known prions induce the formation of an amyloid
fold, in which the protein polymerizes into an aggregate
consisting of tightly packed beta sheets.
Amyloid aggregates are fibrils, growing at their ends,
and replicating when breakage causes two growing
ends to become four growing ends.