1. Haixu Tang School of Inforamtics
Protein structures
Haixu Tang
School of Inforamtics

2. A covalent peptide bond

5. Protein conformation is specified by tts Amino Acid sequence
Steric interactions
Weak non-covalent bonds
hydrogen bonds
ionic bonds
van der Waals attractions
Hydrophobic interaction
distribution of its polar and nonpolar amino acids

8. Protein folding: lowest energy conformation

9. Protein denaturalization

10. Visualizing protein conformations
Protein structures in atomic level
Protein Data Bank (PDB)
Pymol:
Rasmol:

12. Protein secondary structure

14. Secondary structure prediction
Prefer a-helix: Ala, Leu, Met, Phe, Glu, Gln, His, Lys, Arg (sidechains cover and protect the backbone H-bonds)
Prefer b-sheet: Tyr, Trp, Phe, Ile, Val, Thr, Cys (large bulky sidechains)
Disrupt secondary structure: Gly, Pro, Ser, Asp, Asn (small, restrained, or sidechain hydrogen bonds)

15. Coiled coil

16. Protein Domains Independent structural unit Independent function
Independent folding
Independent evolve

17. Protein families

18. Class Folds Super-families Families
Protein structural classification (SCOP:
Class
Folds
Super-families
Families

20. Sulfur-sulfur (disulfur) bonds

21. Assembly of Large Structures

22. Experimental determination of protein structures
X-ray crystallography
NMR (Nuclear Magnetic Resonance) Spectroscopy

23. X-ray crystallography

24. NMR spectrum