1. CHMI 2227 - E.R. Gauthier, Ph.D. 1 CHMI 2227E Biochemistry I Proteins: - Tertiary structure

2. CHMI 2227 - E.R. Gauthier, Ph.D. 2 Tertiary structure

3. CHMI 2227 - E.R. Gauthier, Ph.D. 3 Tertiary structure Secondary structure:  Involves a single type of structure:  -helix  -pleated sheet  Presence of interactions between amino acids that are close together in the primary structure  Main type of interaction: H bonds.  Necessary but not sufficient to make a functional protein. Tertiary structure:  Involves the folding, in space, of the whole polypeptide chain;  Involves several elements of seconday structures, whichy interact together through different interaction forces/bonds: H bonds Electrostatic interactions Van der Waals interactions Hydrophobic interactions Disulfide-bonds  Absolutely required for a protein to be active.  Two main types of tertiary structures exist: Fibrous (e.g. collagen) Globular (e.g. myoglobin) myoglobin Collagen

4. CHMI 2227 - E.R. Gauthier, Ph.D. 4 Tertiary structure Interaction forces For proteins in an aqueous environment:  Hydrophobic amino acids are buried in the interior of the structure;  Hydrophilic amino acids are exposed to the solvent; Conversely, membrane- bound proteins are exposed to an hydrophobic environment:  Hydrophobic amino acids are exposed;  Hydrophilic amino acids are buried inside. http:// butane.chem.uiuc.edu/cyerkes/chem104A_S07/Lecture_Notes_104/lect28c.html Check this one out: http://www.elmhurst.edu/~chm/vchembook/567tertprotein.html

5. CHMI 2227 - E.R. Gauthier, Ph.D. 5 Tertiary structure Protein folding occurs in specific steps:  Some individual elements of secondary structure are first formed;  A few elements of secondary structure cluster together to form conserved folding motifs;  These bundles of secondary structure then form domains, which fold independently of the rest of the protein;  Finally, several domains interact to form the final, functional 3-D structure of the protein. Any given protein will always adopt the same functional 3-D structure. A B

6. CHMI 2227 - E.R. Gauthier, Ph.D. 6 Tertiary structure Folding motifs - 1

7. CHMI 2227 - E.R. Gauthier, Ph.D. 7 Tertiary structure Folding motifs - 2

8. CHMI 2227 - E.R. Gauthier, Ph.D. 8 Tertiary structure Protein domains – Pyruvate kinase Domain 1 Domain 2 Domain 3

9. CHMI 2227 - E.R. Gauthier, Ph.D. 9 Tertiary structure 1. Myoglobin Found in muscles Binds the oxygen required for aerobic metabolism; Associated with a heme group, which is actually responsible for binding oxygen;  -turn Proline

10. CHMI 2227 - E.R. Gauthier, Ph.D. 10 Tertiary structure 1. Myoglobin Cross-sectional view Hydrophilic amino acids: Blue Hydrophobic amino acids: Yellow

11. CHMI 2227 - E.R. Gauthier, Ph.D. 11 Tertiary structure 2. Porin – a membrane-bound protein Hydrophilic amino acids: Blue Hydrophobic amino acids: Yellow

12. CHMI 2227 - E.R. Gauthier, Ph.D. 12 Tertiary structure Chaperones For some proteins, folding requires the help of other proteins called chaperones; Chaperones generally work by binding to exposed hydrophobic patches on the unfolded protein, preventing aggregation and irreversible inactivation.

13. CHMI 2227 - E.R. Gauthier, Ph.D. 13 Tertiary structure Protein denaturation Proteins can be denatured by treatments that destroy the interaction forces required for the adoption of the proper 3-D structure:  Heat  pH  Solvent  Urea/guadinium: breaks up H-bonds   -ME Check this one out: http://www.elmhurst.edu/~chm/vchembook/568denaturation.html

14. CHMI 2227 - E.R. Gauthier, Ph.D. 14 Tertiary structure Protein denaturation The fact that ribonuclease can be reversibly denatured and renatured in vitro shows that the information required for the proper folding of a protein resides in its primary structure.

15. CHMI 2227 - E.R. Gauthier, Ph.D. 15 Examples of proteins 1. Green fluorescent protein Protein found in the jelly fish; Has the unique property to emit a green light; Different variants were produced by genetic engineering to produce red, yellow, cyan, blue light. Extremely useful in cell biology: one can tag it to her/his protein of interest and follow the protein in the cell using fluorescence microscopy.

16. CHMI 2227 - E.R. Gauthier, Ph.D. 16 Examples of proteins 1. Green fluorescent protein Light!

17. CHMI 2227 - E.R. Gauthier, Ph.D. 17 Examples of proteins 1. Green fluorescent protein Golgi apparatus Nucleus

18. CHMI 2227 - E.R. Gauthier, Ph.D. 18 Examples of proteins 1. Green fluorescent protein

19. CHMI 2227 - E.R. Gauthier, Ph.D. 19 Examples of proteins 2. Prion proteins Normal form = PrP c Toxic form = PrP sc http://en.wikipedia.org/wiki/Image:Prion.gif

20. CHMI 2227 - E.R. Gauthier, Ph.D. 20 Examples of proteins 2. Prion proteins Fiber aggregation

21. CHMI 2227 - E.R. Gauthier, Ph.D. 21 Important web site: http://www.pdb.org/pdb/home/home.do