Amino acisd structure Peptide bond formation Analysis of protein Structure- X-ray Crystallography Different structural levels of proteins with examples. Importance of protein structure Creutzfeldt-Jacob-Disease due to changes in normal protein conformation.

1. Structure of Protein
W ROSEYBALA & GARETH LAWRENCE
MSC BIOINFORMATICS, FIRST SEMESTER,
JSS ACADEMY OF HIGHER EDUCATION AND RESEARCH, MYSURU.

2. Proteins
• First described by the Dutch chemist
Gerardus Johannes Mulder and named by
the Swedish chemist Jöns Jacob Berzelius in
1838.
• High molecular weight mixed polymers of α-
amino acids joined together with peptide
linkage (-CO-N H-).

3. Basic Structure
• Each protein is made up of a unique number and order of amino acids,
produced based on the genetic information in a cell.
• Each amino acid has an amino group at its core with a carboxyl group
and a side chain attached, which determines which amino acid it is
• A peptide bond:- formed when the carboxyl group of one molecule
reacts with the amino group of the other molecule, releasing a molecule
of water (H2O)
• Proteins have a unique three-dimensional structure, which allows it to
perform its various functions.

4. Analysing protein structure
• The Diffraction of X-rays by Protein Crystals Can
Reveal a Protein's Exact Structure : X-ray
crystallography.
• protein crystallization - proteins are dissolved in
an aqueous environment and sample solution until
they reach the supersaturated state
• Principle : when a beam of X-ray is incident on the
protein crystal, the incident X-ray is diffracted into
many directions.
• By measuring the angles and intensities of these
diffracted rays, 3D image of the protein sample is
produced.

5. • Protein crystal is placed on the
goniometer.
• Exposed to X-ray.
• Diffraction occurs. The spots
produced are called reflections.
• First 2D image is obtained.
• The process is repeated for different
orientations of the crystal.
• 2D images at different orientations
are converted into 3D image.
X-ray crystallography

6. Levels of protein structure
 The four levels of protein structure are primary, secondary, tertiary, and quaternary, distinguished from
one another by the degree of complexity in the polypeptide chain.

7. • Proteins are constructed from a set of 20 amino acids
• The simplest level of protein structure, primary structure, is
simply the sequence of amino acids in a polypeptide chain.
• because the final protein structure ultimately depends on this
sequence, this was called the primary structure of the
polypeptide chain.
• Unique sequence of amino acids.
• Sequence determined by DNA.
• Amino acids are covalently linked by peptide bonds.the
structure of protein starts from the amino-terminal (N) and
ends in the carboxyl-terminal C end.
Primary structure

8. Primary structure : Insulin
• The pancreatic hormone insulin has two poly-peptide chains, A and B, and they are linked together by
disulfide bonds.
• The N terminal amino acid of the A chain is glycine, whereas the C terminal amino acid is asparagine.
• The sequences of amino acids in the A and B chains are unique to insulin.

9. Secondary structure
The two most important secondary structures of protein: the
alpha helix and the beta sheet was predicted by Linus Pauling
in the early 1950s..
• The orderly arrangement of the peptide backbone was first
studied by examining fibrous proteins called keratins.
• Alpha keratin: hair, skin, wool.
• Beta Keratin: spider web or silkmoth silk.
• The most common type of secondary structure of protein is
the alpha helix.

10. Alpha helix
• Linus Pauling was the first to predict the existence
of α-helices.
• Coiling of the primary structure of protein such that
the peptide bond making up the protein backbone
form H-bonds between each other.
• involves regularly spaced H‐bonds between
residues along a chain. The amide hydrogen and
the carbonyl oxygen of a peptide bond are H‐bond
donors and acceptors respectively.
• H-bonds are directed along the axis of the helix.

11. Example of alpha helix
.
• E.g., collagen forms part of the matrix upon which cells
are arranged in animal tissues.
• Keratin -forms structures such as hair and fingernails.

12. Alpha keratin structure

13. Beta-pleated sheet
• Forms when two or more poly-peptide chains line up side by side.
• Consist of several β-strands, stretched segments of the polypeptide
joined by a network of hydrogen bonds between adjacent strands.
• A single chain forms H‐bonds with its neighboring chains, with the
donor (amide) and acceptor (carbonyl) atoms pointing sideways rather
than along the chain, as in the alpha helix.
• Can be either parallel, where the chains point in the same direction
when represented in the amino‐ to carboxyl‐ terminus, or antiparallel,
where the amino‐ to carboxyl‐ directions of the adjacent chains point in
the same direction.

14. • Can be either parallel, where the chains
point in the same direction when
represented in the amino‐ to carboxyl‐
terminus,
• or antiparallel, where the amino‐ to
carboxyl‐ directions of the adjacent chains
point in the different direction.
• Example of beta pleated sheet structure:
silk fibroin

15. Beta-pleated sheet example
Structure of silk fibroin

16. Tertiary Structure of protein
• 3D structure at which polypeptide chains become functional.
• Presents functional groups on its outer surface to interact with
other molecules, and giving it its unique function. The
arrangement is made with the help of chaperones.
• Main interactions that guide the bending and twisting that help
the protein molecule achieve a stable state are:
Hydrophobic Interactions, disulfide bridges, ionic bonds and
hydrogen bonds.

17. Types of tertiary Structure of protein
 Globular Proteins: Globular proteins form a compact ball shape,
where hydrophobic amino acids are found in the centre of the
structure and hydrophilic on the surface.
 Examples of globular proteins: myoglobin
 Fibrous Proteins: Fibrous proteins are made of fibers often consisting
of repeated sequences of amino acids, resulting in a highly ordered,
elongated molecule.
 Example of fibrous protein: collagen.

18. Quaternary Structure of protein
• Quaternary structure describes the joining of two or more
polypeptide subunits.
• The subunits each have their own tertiary structure and are
held together by the same forces involved in tertiary
structure.
• Eg. Hemoglobin is a globular protein, consisting of four
subunits: of two different types. Each subunit contains a
heme group for oxygen binding.

19. Importance of protein structure
• The function of a protein is directly dependent on its
threedimensional structure.
• The structure of protein sets the foundation for its interaction with
other molecules in the body.
• If a protein loses its shape at any structural level, it may no longer
be functional.
• The 3-dimensional conformation of proteins brings remote regions
of the amino acid sequence into close proximity creating active
sites on enzymes and antigen-binding sites on antibodies..
• Diseases caused by changes in protein structure: mad cow
diseases in cattle and Creutzfeldt-Jakob-disease in men.
• Sickle cell anemia: single amino acid change in hemoglobin.

20. Creutzfeldt-Jacob disease
• Degenerative brain disorder -> dementia and death.
• 5000 cases in India per year.
• Caused by prion proteins. Conformational changes in
normal cellular proteins.
• Characteristics: sponge like lesions in the brain, shrinking
and deterioration of the brain.
• Symptoms: personality changes, anxiety, depression and
memory loss within a few months and leads to coma.

21. Diagnosis,Treatment and prevention
• Fatal – death within a year.
• Diagnosis: brain biopsy or autopsy and MRI.
• No cure, treatment: reduces symptoms and
progression.
• Prevention:
• - cover cuts and wounds with waterproof dressings.
• - use surgical gloves while handling tissue and body
fluids.
• - use of disposable bed clothes in hospitals or
bleaching in chlorine.