1. Twisted by freedom: The structure of an amyloid-like fibril GNNQQNY from SUP35 Xavier Periole, Aldo Ramponi, MicheleVendruscolo

2. Jimenez, J.L., Guijarro, J.I., Orlova, E., Zurdo, J., Dobson, C.M., Sunde, M. and Saibil, H. (1999) EMBO J 18, 815-821 Cryo-electron microscopy structure of an SH3 amyloid fibril and model of the molecular packing. Twisted fibrils 4 subunits

3. Twisted fibrils Ivanova, MI, Sawaya, M.R., Gingery, M., Attinger, A., Eisenberg, D. (2004) PNAS 101, 10584-9 An Amyloid-forming segment of b2-microglobulin suggests a molecular model for the fibril

4. Amyloid-like fibril: X-ray structure Planar Structure GNNQQNY from SUP35

5. 90 o t=0 20 pair-of-peptides t=10ns X-raycrystalaqueous

6. 90 o t=0 20 pair-of-peptides t=10ns microcrystal envir. aqueousX-ray

7. 90 o t=0 20 pair-of-peptides t=10ns microcrystal envir. aqueous envir. X-ray

8. Twisted  -sheets:  -sandwich  -barrel What drives the Twist? Solvation effects,hydrogen bonding,increase in side-chain entropy etc

9. Only small structural changes associated with twist phi/psi H-bonds bb-bb sc-sc 90 o

10. Hydrogen bond #12345  Rosetta Water-12.6-5.9-16.7-11.1-12.9-59.2 Crystal-18.9-19.3-16.5-15.1-14.9-84.7 Water-Crystal+6.3+13.3-0.13+4.1+2.1+25.6 GROMOS Water-9.6-8.5-9.6-8.6-9.5-45.9 Crystal-10.5-10.8-10.4-9.3-9.7-50.6 Water-Crystal+0.8+2.3+0.7+0.6+0.2+4.7 Hydrogen Bonding Energy (kJ/mole per peptide) Hydrogen bonds favor planar forms (shown previously) Aside: Rosetta and GB model both favor planar forms

11. Energetic Analysis (kJ/mol per peptide) Release of position restraints

12. Energetic Analysis (kJ/mol per peptide) Interactions of charged termini dominate energetics. Neutralized termini: System still twists. Remove termini: Energetics almost identical.

13. Solvent Accessible Surface Area Effectively no change on twist (0.16 nm 2 per peptide). (one water ~0.25 nm 2 )

14. Remove Solvent Simulate in Vacuum (neutral ends)  Still twists (almost the same as in water)

15. What drives the twist? - Energy profile almost flat. -Charged termini (slightly) increase twist. -Hydrogen bonds favor planar form. -Solvent not required but favors twist -Implict solvent models favor planar form. -Solvent ordering effects?

16. Estimation of Side Chain Entropy Correlation effects ignored (upper estimate) Difference planar (position restrained) Twisted < 2 kJ/mol per peptide)

17. Solvent Ordering Water Density Map Planar Twisted