1. Levels of Protein Structure

2. Charged and polar R-groups tend to map to protein surfaces

3. Primary sequence reveals important clues about a protein
• Evolution conserves amino acids that are important to protein structure and function across species. Sequence comparison of multiple “homologs” of a particular protein reveals highly conserved regions that are important for function.
• Clusters of conserved residues are called “motifs” -- motifs carry out a particular function or form a particular structure that is important for the conserved protein.
motif
DnaG E. coli
...EPNRLLVVEGYMDVVAL...
DnaG S. typ
...EPQRLLVVEGYMDVVAL...
DnaG B. subt
...KQERAVLFEGFADVYTA...
gp4 T3
...GGKKIVVTEGEIDMLTV...
gp4 T7
...GGKKIVVTEGEIDALTV... : *
small hydrophobic
large hydrophobic
polar
positive charge
negative charge

4. Hydropathy index of amino acids
The hydropathy index of an amino acid is a number representing the hydrophobic or hydrophilic properties of its side-chain.
It was proposed by Jack Kyte and Russell Doolittle in 1982.
The larger the number is, the more hydrophobic the amino acid. The most hydrophobic amino acids are isoleucine (4.5) and valine (4.2). The most hydrophilic ones are arginine (-4.5) and lysine (-3.9).
This is very important in protein structure; hydrophobic amino acids tend to be internal in the protein 3D structure, while hydrophilic amino acids are more commonly found towards the protein surface.

5. Kyte Doolittle Hydropathy Plot(

6. Possible transmembrane fragment

7. Surface region of a protein
Window size – 9, strong negative peaks indicate possible surface regions

8. Prediction of transmembrane helices in proteins
(TMHMM)

9. 5-hydroxytryptamine receptor 2A (Mus musculus)

10. 5-hydroxytryptamine receptor 2A
(Grapical output)

11. Secondary structure of protein
Amino acid sequences fold onto themselves to become a biologically active molecule.
There are three types of local segments:
Helices: Where protein residues seem to be following the shape
of a spring. The most common are the so-called alpha helices
Extended or Beta-strands: Where residues are in line and successive residues turn back to each other
Random coils: When the amino acid chain is neither helical nor extended

12. Predicting secondary structure (PSIPRED)(

13. PSIPRED
Continued…

14. Typical PSIPRED and its explanation
The prediction (Pred) line, consisting of H, E and C characters, denoting the predicted conformation for each residue (H=Helical, E=Extended, and C=Random coil)
The confidence (Conf) line, consisting of digits 9 to 0 indicating the reliability of prediction for each position (9=high, 0=poor)

15. Typical PSI graphics (output in pdf format)

16. Tertiary structure of protein(

17. Selecting the FASTA input window in PDB

18. Adding FASTA sequence in PDB

19. PDB output

20. 3D structure of the protein

21. Output of the protein and receptor complex

22. 3D structure of the protein and receptor complex