Protein folding and misfolding

Protein
Definition:
Proteins are complex biomolecules (organic compounds) composed of many
amino acids linked together through peptide bonds.

Peptide bond????
Peptide bond

A peptide bond is a chemical bond formed

between two molecules when the carboxyl
group of one molecule reacts with amino
group of other molecule, releasing the
molecule of water (H2O).

This is a condensation reaction and usually

occurs between amino acids.

Prolong exposure to strong acid or base at elevated temperature is required to these

bonds non-enzymatically
 Peptide: A molecule formed by the joining of two or more amino acids
through peptide bond is called peptide

Peptide names for the number of amino acids

Dipeptide: Two amino acid molecules covalently joint through a

substituted amide linkage termed as peptide bond to yield a
dipeptide

Oligopeptide: When few amino acids joint covalently is called oligopeptide (10-
15 amino acids)

Polypeptide: Several amino acid molecules join to make a polypeptide chain

(more than 15 amino acids)

Protein: have more than 50 amino acids

 Characteristics of the peptide bond

➢ Lack of rotation around the bond

The peptide bond has partial double bond characteristics

(rigid and planar)

➢ Peptide bonds are uncharged but polar

• Polar hydrogen atoms of α-amino group, polar oxygen atoms of carboxyl

group and any ionized group present in the side chain presents charge

• This allows Hydrogen bonds to form between peptide bonds in different parts
of the chain

➢ Trans configuration
 Protein synthesis

⚫ Protein is synthesized via the following processes:

DNA RNA Protein

Gene Function

Each protein is made from the 20 standard amino acids

and fold into a specific 3-D structure.
 Protein structure

Proteins have different levels of structural organization

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quaternary structure

Specific protein structure required for its specific biological function or

activity
 Primary structure
◆ Sequence of amino acids in the polypeptide chain

◆ The peptide bonds are responsible for the primary structure

◆ Peptide chain has left side N-terminal, right side C-terminal and
remaining amino acids in the chain called residues

◆ Precise sequence is determined by the genes

Changing one amino acid in the sequence can change all the protein

◆ Polypeptide chain can be 50-1000 amino acids in length

Example: Lysozyme has 129 amino acids, all in a very specific order
Hemoglobin—577 amino acids. (E-V) causes sickle cell anemia
 Secondary structure
Describes the shape of the protein
Three type: α-helix and β- pleated sheets, beta bends

Alpha helix
➢ It has spiral structure, consist of
▪ Polypeptide back bone
▪ Side chains of amino acids extended outward
➢ Formed and Stabilized by
▪ Hydrogen bonding between the peptide-bond carbonyl oxygen and
hydrogen atoms of amide group of fourth amino acid in the chain

➢ Amino acids per turn

▪ Each turn of an α-helix contains 3.6 amino acids (amino acid
residues spaced three or four apart in the primary structure)
➢ Amino acids that disrupt an α-helix
▪ Proline (imino group is not geometrically compatible, insert a kink in
the chain)
 β- sheets
In β-sheets peptide bond components are involved in hydrogen bonding.

β-sheets are composed of two or more peptide chains

Hydrogen bonds are perpendicular to the polypeptide backbone

β-sheets can be formed from two or more separate polypeptide chains that are
arranged either parallel or antiparallel

Inter-chain bonds: When hydrogen

bonds formed between the polypeptide
backbone of separate polypeptide
chains

Intrachain bonds: When a single

polypeptide chain folds back to form a
β-sheet
 β-bends

❑ Reverse turn or hairpin turn

❑ β-bends reverse the direction of polypeptide chain to
get a folded structure
❑ It helps to form a compact, globular shape rather than
linearity.
❑ H-bonds stabilizes β-bends
❑ It contains proline and glycine residues
❑ β-bend promotes the formation of anti-parallel beta
sheets
❑ They generally composed of 4 amino acids
 Tertiary structure
❖ Three dimension structure
(conformation) of a polypeptide chain
(globular or fibrous)

❖ It is folding and coiling due to

interactions among R-groups and
between R-groups and surrounding
water.

❖ Alpha helix and beta sheets are folded

into specific 3-dimentional shapes
Bonding involved includes
- Covalent bonding----disulphide bridges
- Hydrogen bonding
- Ionic bonding
- Hydrophobic bonding
 Function of the protein depends on its tertiary structure
 Protein looses its activity if it gets disturbed
 Quaternary Structure
Result from combination of two or more polypeptide subunits attached with each
other by non-covalent interactions like H-bonding, ionic or hydrophobic
interaction

Examples of proteins having quaternary structure

Collagen: Fibrous protein of three polypeptide chains

(trimeric), supercoiled like a rope

Hemoglobin: globular protein with four polypeptide

chains (tetrameric).

Insulin: Dimeric protein having two polypeptide chains

Amino acids--------functional proteins
Four levels of protein structure
 Protein misfolding

Protein misfolding:

Failure to fold into native structure generally produces

inactive proteins, but in some instances misfolded proteins
have modified or toxic functionality

Many allergies are due to misfolded proteins as immune

system develops no antibodies for it, tendency of proteins to
self aggregate increases and amyloids are formed, no
clearance from body → proteopathy develops(class of
disease that arise due structurally abnormal proteins→
disturb cells, tissues and organ functions) like parkinson’s
disease due to α-synuclein
 α-helix
β-sheet
Conformational change

➢the starting point is the

➢the end-point is the same
natural protein folded in the
protein adopting prevalent β-
native and active conformation
sheets structure
➢normal protein is rich in α-
➢it is disease-associated
helix conformations (folded
protein (misfolded structure)
structure)

Aggregation

Loss of biological
Gain of toxic activity function
The conformational change
➢ a change in the secundary or tertiary structure of a
normal protein without alteration of the primary structure

➢ the biological function of a protein depends on its

tridimensional structure

Protein conformatinal disorders (PCD)

➢ diverse diseases arise from protein misfolding

➢ the conformational change may promote the disease by

either gain of a toxic activity or by the lack of biological
function of the natively folded protein
Protein misfolding causes disease!

➢ the hallmark event in PCD (protein conformational

disorder) is a formation of β-sheet conformations

➢ the production of β-sheets is usually stabilized by

protein oligomerization and aggregation

➢ the misfolded protein self-associates and becomes

deposited in amyloid-like aggregates in diverse
organs, inducing tissue damage and organ dysfunction
Diseases Protein involved
Alzheimer‘s disease Amyloid-β
Parkinson disease α-Synuclein
Diabetes type 2 Amylin
Amyotrophic lateral sclerosis Superoxide dismutase
Haemodialysis-related amyloidosis β2-microglobulin

Cystic fibrosis Cystic fibrosis transmembrane

regulator
Sickle cell anemia Hemoglobin
Hungtington disease Huntingtin
Creutzfeldt-Jakob disease Prion protein
Amyloidosis Ten other proteins
 Implication of protein misfolding
1. Gain of toxicity
The harmfull effect of the misfolded protein may be due to
deleterious gain of function as seen in many neurodegenerative
disorders (Alzheimer disease, Parkinson disease, Hungtington
disease), in which protein misfolding results in the formation of
harmfull amyloid. Neurodegenerative diseases are characterized by
the accumulation of misfolded proteins and formation of aggregates

2. Loss of function
Other effect of the misfolded protein may be due to loss of function,
as observed in cystic fibrosis. There is a mutation in the
CFTR(cystic fibrosis transmembrane conductance regulator)
sequence

3. Accumulation
Protein aggregates are sometimes converted to a fibrillar structure.
Fibrils themselves are not toxic but insoluble. Their
accumulation cause tissue damage (amyloidoses)