This document discusses the hierarchical structure of proteins. It describes the four levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure is the amino acid sequence. Secondary structures include alpha helices and beta sheets formed by hydrogen bonds between amino acids in the chain. Tertiary structure refers to the overall 3D shape of a single polypeptide chain. Quaternary structure involves the spatial arrangement of subunits in a multi-chain protein. Common techniques to determine protein structures are X-ray crystallography and NMR spectroscopy. Understanding protein structure is important for functions like oxygen transport by hemoglobin.

1. Science of Living
System (BS20001)
• SOUMYA DE
• Office: 2nd Floor, Sir JC Bose Laboratory Complex
• Phone: 03222-260514
• E-mail: somde@iitkgp.ac.in
• Research interests:
Biophysics
Nuclear Magnetic Resonance (NMR) Spectroscopy
Protein Engineering
Signal Transduction and Gene Expression
Enzymology

2. Hierarchy of Protein
Structure

3. Protein Molecules are Organized in a Structural
Hierarchy
Secondary
Tertiary
Primary
Quaternary

4. Secondary Protein Structure
Beta Sheet
Alpha helix
Characterized by main chain NH and CO groups participating in H-bonds

5. Alpha Helix
Every 3.6 residues make one turn
The distance (pitch of helix)
between two turns is 5.4 Å
The C=O of residue ‘n’ is hydrogen
bonded to N-H of residue ‘n+4’
n n+1 n+2 n+3 n+4 n+5

6. The Alpha-Helix has a Dipole Moment
n n+1 n+2 n+3 n+4 n+5
The dipoles of peptide units are aligned along the
α helical axis

7. Less Preferred:
Pro, Gly, Tyr, Ser
Some Amino Acids are Preferred in α-Helices
Good helix formers:
Ala , Glu, Leu , Met

8. Alpha helix can be – Right-
handed or Left handed
BUT, left handed helix is not
possible for L-amino acids
due to close approach of
the side chains and CO
group.
Right handed – most
commonly observed in
proteins.
Alpha Helix: Right-handed or Left-handed?

9. Helical Wheel Plot
N
C

10. Helical Wheel: Each
residue can be
plotted every
360/3.6=100° around
a circle or spiral
Hydrophobic
Hydrophilic
Charged
Totally buried Partially buried
Exposed

11. β-sheet
(Number of β-Strands are Involved)
β-sheet from several regions of the
chain; Each β-strand, typically 5-10
residues long
α-helix: from one
continuous region
H-bonds are perpendicular to strands

12. β-pleated sheet: ‘pleated’ because
side chains point up and down
alternatively
Parallel and Antiparallel β-sheet

13. Mixed β-sheet

14. Loop regions mostly occur at the surface
of protein molecules

15. Hair Keratin

16. Hair Keratin

17. Chemistry of Straight and Curl Hair

18. Polypeptide Chains Fold into Several Domains
•Fundamental unit of tertiary structure – DOMAIN
•Domain: polypeptide chain or a part of polypeptide chain that can
independently fold into a stable tertiary structure
•Domains are also units of function
Tertiary structure refers to the spatial arrangement of amino acid residues
that are far apart in the sequence and to the pattern of disulfide bonds.

19. Quaternary Structure
Proteins containing more than one polypeptide chain exhibit a fourth level of
structural organization. Each polypeptide chain in such a protein is called a
subunit. Quaternary structure refers to the spatial arrangement of subunits
and the nature of their interactions.
The simplest quaternary structure is a dimer, consisting of two identical
subunits.

20. Quaternary Structure (higher order)
Complex Quaternary Structure. The
coat of rhinovirus comprises 60 copies
of each subunits
The α2β2 tetramer of human
haemoglobin. The structure of the two
identical α subunits (red) is similar to
but not identical with that of the two β
subunits (yellow).

21. • Structure Function
• Structure Mechanism
• Structure Origins/Evolution
• Structure-based Drug Design
• Solving the Protein Folding Problem
Solving Protein Structures
Only 2 kinds of techniques allow one to get atomic resolution
pictures of macromolecules
QHTAWCLTSEQHTAAVIWDCETPGKQNGAYQEDCA
HHHHHHCCEEEEEEEEEEECCHHHHHHHCCCCCCC
H: α-helix
E: β-strand
C: unstructured

22. Methods to study protein structures
X-ray crystallography
NMR spectroscopy
• Prof. Amit K Das
(http://www.iitkgp.ac.in/department/BT/faculty/bt-amitk)
• Prof. Dibyendu Samanta
(http://iitkgp.ac.in/department/BS/faculty/bs-dibyendu.samanta)
• Nuclear magnetic resonance (NMR) spectroscopy
• Prof. Soumya De
(http://iitkgp.ac.in/department/BS/faculty/bs-somde)
Structure-guided protein engineering

23. Hemoglobin A: Val-His-Leu-Thr-Pro-Glu-Glu-Lys-
Hemoglobin S: Val-His-Leu-Thr-Pro-Val-Glu-Lys-
“sticky patch” causes hemoglobin S to agglutinate (stick together) and
form fibers which deform the red blood cell
Importance of Protein Structure