Protein structure and_stability-1

1. Protein Structure and Stability
by Mahwish Kazmi

2. Overview of Protein Structure
• Primary Structure - The sequence of amino acids in the
polypeptide chain
• Secondary Structure - The formation of α helices and β
pleated sheets due to hydrogen bonding between the
peptide backbone
• Tertiary Structure - Folding of helices and sheets
influenced by R group bonding
• Quaternary Structure - The association of more than
one polypeptide into a protein complex influenced by R
group bonding

3. Primary Styructure
• The sequence of amino acids in the primary
structure determines the folding of the molecule.

4. Peptide Bond
• Two or more amino acids are joined by condensation
reaction i.e, removal of water molecule forms peptide
bond
• The partial double-bond character of the peptide bond
defines the conformations a polypeptide chain may
assume.
• It is shorter then a single bond
• Rigid & planar.

5. Protein Secondary Structure
• The primary sequence must organize itself to form a
compact structure. This is done in an elegant fashion by
forming secondary structure elements.
• The peptide backbone has areas of positive charge and
negative charge
• These areas can interact with one another to form
hydrogen bonds
• The result of these hydrogen bonds are two types of
structures:
α- helices
β- pleated sheets

6. Alpha Helix
• It is the most common confirmation.
• It is a spiral structure.
• Tightly packed coiled polypeptide backbone, with
extending side chains, R groups protrude outward from
the helical back bone.
• Height of single turn of helix is 5.4Å with 3.6 amino acid
residue.
• Right-handed α-helix predominates in nature.
• It is stabilized by H-bonding between amide hydrogens
and carbonyl oxygens of peptide bonds.

7. Alpha Helix

8. β- pleated sheets
• The backbone of the polypeptide chain is extended into
a zigzag rather than helical structure.
• The zigzag polypeptide chains can be arranged side by
side, hydrogen bonds are formed between adjacent
segments.
• The adjacent sheets can be either parallel or antiparallel

10. Tertiary Structure
• Folding of helices and sheets influenced by R group
bonding classified as
1. Fibrous Protein- chains aarranged to form long strands
and usually consist largely of a single type of secondary
structure. Structures that provide support, shape, and
external protection to vertebrates are made of fibrous
proteins.
2. Globular protein- chains arranged to form spherical
shapes and often contain several types of secondary
structures. Enzymes are mostly globular in nature.

11. Tertiary Structure
Factors influencing tertiary structure include:
• Hydrophobic interactions
• Hydrogen bonding
• Disulphide bridges
• Ionic bonds

12. Fibrous protein
1. α- Keratin
• is a right-handed α-helix.
• Two strands of α-keratin, oriented in parallel are
wrapped about each other to form a supertwisted coiled
coil.
• α-keratin is rich in the hydrophobic residues Ala, Val,
Leu, Ile, Met, and Phe.
• Many coiled coils can be assembled into large
supramolecular complexes,such as the arrangement of
α- keratin to form the intermediate filament of hair.

13. α- Keratin

14. 2. Collagen
• It is found in connective tissue such as tendons, cartilage,
the organic matrix of bone, and the cornea of the eye.
• Collagen helix is a unique secondary structure quite distinct
from the α- helix.
• It is left-handed and has three amino acid residues per
turn.
• Collagen is also a coiled coil but three separate
polypeptides, called α-chains, are supertwisted about each
other.
• The superhelical twisting is right-handed in collagen.
• Typically, they contain about 35% Gly, 11% Ala, and 21%
Pro and 4-hydroxyproline, an uncommon amino acid,

15. Collagen
structure of collagen

16. Globular Protein
• Different segments of a polypeptide chain fold back on each
other generates a compact form.
• It includes enzymes, transport proteins, regulatory proteins,
immunoglobulins etc.
• 3-D structure of Myoglobin revealed its a globular preotein,
comprises of a single polypeptide chain.
• The backbone of the myoglobin molecule is made up of eight
relatively straight segments of α-helix interrupted by bends,
some of which are β-turns.
• All helices are right-handed.
Tertiary structure of whale myoglobin

17. Quaternary structure
• Quaternary structure results from the interaction of
independent polypeptide chains
Factors influencing quaternary structure include:
• Hydrophobic interactions
• Hydrogen bonding
• The shape and charge distribution on amino acids of
associating polypeptides.
e.g., Haemoglobin made up of
4 polypeptide chains.

18. Protein stability
• Stability can be defined as the tendency to maintain a
native conformation.
• Chemical interactions that stabilize the native
confirmation includes
• Disulphide bonds
• Noncovalent interaction
• Hydrogen bonds
• Hydrophobic interactions
• Ionic interaction
Numerous weak interactions predominates as a
stabilizing force in protein structure.

19. Protein Folding
• The peptide bond allows for rotation around it and
therefore the protein can fold and orient the R groups in
favorable positions
• Weak non-covalent interactions will hold the protein in its
functional shape.
• Proteins shape is determined by the sequence of the
amino acids.
• α-helix turns like a spiral – fibrous proteins.
• β-sheet folds back on itself as in a ribbon –globular
protein

20. Some Proteins Undergo Assisted Folding
• Molecular chaperones are proteins that interact with
partially folded or improperly folded polypeptides,
facilitating correct folding pathways or providing
microenvironments in which folding can occur.

21. Protein Denaturation
• A loss of three-dimensional structure sufficient to cause
loss of function is called denaturation.
• Alterations in the environment (pH, salt concentration,
temperature etc.) disrupt bonds and forces of attraction.

22. Renaturation
• Native structure and biological activity of some globular
proteins can be regained if the denaturing agent will be
removed.
• Ribonucleases presents a classical example of this
property.