1. Protein structure and folding Some facts and fundamental conepts Cherri Hsu 02-2789-8658 Institute of Chemistry B307 cherri@sinica.edu.tw

2. Goals and plans Understand basic facts of protein structures. Understand general concepts that determines structure and dynamics. Physics Evolution Go through Chapters 8 and 9 of V&V book. A few more stories I’ve learned. My own review in protein folding prediction and simulation.

3. Structural basis: Hierarchy of protein structures Primary: sequence Secondary: local structures Tertiary: 3-dimension structure of a peptide chain. Quaternary: assembly of protein subunits (multiple chains) Local structural characteristics:  -  angles; Ramachandran plots.  -Helixes  -Sheets Loops

6. Methods for determing protein structures X-ray diffraction NMR

7. Determining molecular structures MethodUsesLimits Infrared Absorption Assigning local bonding types and structures Small organic molecules. NMR Assigning local bonding types and structures; Measuring distances Small molecules Small proteins (< 40 kDa?) X-ray diffraction Atomic resolution of molecular structures Virtually no limit over the sizes of the molecules. Single crystals needed. Electron microscopy & 2-D diffraction Good for large proteins. No crystals needed. Large, low resolution structures.

8. IR (Absorption) Spectra Methanol: CH 3 OH Ethanol: C 2 H 5 OH C 2 H 6 O Methyl ether: CH 3 OCH 3 C 2 H 6 O

9. Nuclear Magnetic Resonance

10. NMR is an important tool in chemistry

11. 2D NMR? A table that lists different 2D NMR techniques. A table that lists different 2D NMR techniques. Can be used to determine distance between atoms. Will be further introduced in next semester.

12. X-ray diffraction

13. X-ray diffraction: Physics2000: wavePhysics2000: wave Physics2000: two slitsPhysics2000: two slits

14. http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html

15. Basic building blocks of protein structures

16. Are proteins sticky tapes?

17. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 8-1The trans-peptide group. Page 220

18. Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 8-2The cis-peptide group. Page 220

19. “trans” is more stable “cis” conformation is rarely seen. For the peptide bonds follow proline residue, ~10% are “cis”.

21. Fibrous proteins

22. Keratin A mechanically durable, chemically unreactive protein.  -keratin occur in mammals (hair)  -keratin occur in birds (feather) and reptiles.

23.  -Keratin From x-ray, structure expected:  -helix But, the pitch is 5.1Å, rather than normal 5.4 Å. Coiled coil is expected. Rich in Cys residues, form disulfide bonds and cross- link adjacent peptide chains. “hard” or “soft” : high or low in sulfur content. Hard: hair, horn, nail Soft: skin When disulfide bonds cleaved, an  -keratin can be streched to become a  -pleated sheet.

24.  -Keratin From x-ray, structure expected:  -helix But, pitch is 5.1Å, rather than normal 5.4 Å. Coiled coil is expected. Rich in Cys residues, form disulfide bonds and cross-link adjacent peptide chains. “hard” or “soft” : high or low in sulfur content. Hard: hair, horn, nail Soft: skin When disulfide bonds cleaved, an  -keratin can be streched to become a  -pleated sheet.

25. Collagen Occurs virtually in every tissue. Connective tissues. Mammals have at least 33 genetically distinct polypeptide chains. 20 distinct collagen types in different tissues.

26. Hyp: A special residue found in collagens

27. Collagen Nearly 1/3 of its residues are Gly. 15-30% are Hyp residues. Hyp are converted to Hyp after collagen polypeptides are synthesized. The conversion is through prolyl hudroxylase, and it requires Ascorbic acid (vit. C). Hyp offers extra H-bondings. (possibly to peptides and to water)

28. Globular proteins Enzymes Transport and receptor proteins Soluable proteins Membrane proteins

30. Physical forces determining protein structures H-bonding Electro-static interactions Hydrophobic forces

31. H-bonds D-H … A Assignment: if D…A < 3.7 Å in crystal structure. (normally 2.7-3.1 Å). Energy of stablization: -12~-40 kJ/mol) Tends to be linear. Only weakly stabilize proteins. (!?)

32. A survey over H-bonds in globular proteins (J. Mol. Biol. (1992) 226, 1143)

33. Most H-bonds are local. Most H-bonds are between beckbone atoms.