Organisers

• Nick Quirke (University College Dublin & Imperial College London, Ireland)
• Nicolae-Viorel Buchete (University College Dublin, Ireland)
• Suzanne P. Jarvis (University College Dublin, UCD Conway Institute, Ireland)
• Anika Mostaert (University College Dublin, UCD Conway Institute, Ireland)

Supports

Science Foundation Ireland

University College Dublin

Atlantic Centre for Atomistic Modelling - ACAM

Description

This workshop will bring together both experimentalists and theorists with the goal to identify and discuss the state-of-the-art, emerging techniques that could be used to characterize and control molecular aggregation processes and the formation of nanoscale biomolecular structures, with a focus on peptide and protein aggregation. Current and future applications of these structures will be explored by the inclusion of representatives from relevant industries.

References

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2. Buchete NV, Tycko R and Hummer G, "Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments," J. Mol. Biol. 353:804-821 (2005)
3. Luca S, Yau WM, Leapman R, and Tycko R. "Peptide conformation and supramolecular organization in amylin fibrils: Constraints from solid-state NMR", Biochemistry, 46:13505-13522 (2007)
4. Wickner RB, Dyda F, Tycko R. "Amyloid of Rnq1p, the basis of the [PIN+] prion, has a parallel in-register beta-sheet structure" PNAS 105:2403-2408 (2008)
5. Mostaert AS, and Jarvis SP."Beneficial characteristics of mechanically functional amyloid fibrils evolutionarily preserved in natural adhesives". Nanotechnology 18:044010 (2007)
6. Mostaert AS, Higgins MJ, Fukuma T, et al. "Nanoscale mechanical characterisation of amyloid fibrils discovered in a natural adhesive" J. Biol. Phys 32:393-401 (2006)
7. Tarus B, Straub JE, and Thirumalai D. "Structures and free-energy landscapes of the wild type and mutants of the Abeta(21-30) peptide are detennined by an interplay between intrapeptide electrostatic and hydrophobic interactions". J. Mol. Biol., 379:815-829 (2008)
8. Nguyen PH, Li MS, Stock G, Straub JE, and Thirumalai D "Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism", PNAS, 104: 111-116 (2007)
9. Thirumalai D, Klimov DK, Dima RI, "Emerging ideas on the molecular basis of protein and peptide aggregation", COSB 13:146-159 (2003)
10. Vaiana SM, Ghirlando R, Yau WM, Eaton WA, and Hofrichter J. "Sedimentation studies on human amylin fail to detect low-molecular-weight oligomers", Biophys J. 94: L45-L47 (2008)
11. Eaton WA, Henry ER, Hofrichter J, et al. "Evolution of allosteric models for haemoglobin", IUBMB LIFE 59:586-599 (2007)
12. Petkova AT, Leapman RD, Guo Z, Yau WM, Mattso MP, and Tycko R. "Self-propagating molecular-level polymorphism in Alzheimer"s "-Amyloid Fibrils", Science 307: 262-265 (2005)
13. Ryadnov MG, and Woolfson DN "MaP peptides: Programming the self-assembly of peptide-based mesoscopic matrices", JACS 127: 12407-12415 (2005)
14. Papapostolou D, Smith AM, Atkins EDT, Oliver SB, Ryadnov MG, Serpell LC, and Woolfson DN "Engineering nanoscale order into a designed protein fiber", PNAS 104: 10853-10858 (2007)
15. Smith AM, Acquah SFA, Bone N, Kroto HW, Ryadnov MG, Stevens MSP, Walton DRM, and Woolfson DN " Polar assembly in a designed protein fiber", Angew. Chem. Intl. Ed. 44: 325-328 (2005)
16. Jahn T, Parker M, Homans SW, and Radford SE " Amyloid formation under physiological conditions proceeds via a native-like folding intermediate", Nat. Struct. Mol. Biol. 13: 195-201 (2006)
17. Antzutkin ON, Balbach JJ, and Tycko R "Site-specific identification of non-beta-strand conformations in Alzheimer's beta-amyloid fibrils by solid-state NMR", Biophys. J. 84: 3326"3335 (2003)
18. Tycko R "Progress towards a molecular-level structural understanding of amyloid fibrils", Curr. Opin. Struct. Biol. 14: 96-103 (2004)
19. Makin OS, Atkins E, Sikorski P, Johansson J, and Serpell LC "Molecular basis for amyloid fibril formation and stability", PNAS 102: 315-320 (2005)
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21. Cleary J, Walsh DM, et al. "Oligomers but not monomers of the amyloid " protein transiently disrupt learned behavior", Nat. Neurosci. 8:79-84 (2005)
22. Keten S, and Buehler MJ, "Geometric Confinement Governs the Rupture Strength of H-bond Assemblies at a Critical Length Scale", Nano Lett. 8: 743-748 (2008)
23. Carny O, Shalev D, and Gazit E (2006) "Fabrication of Coaxial Metal Nanowires Using Self-Assembled Peptide Nanotube Scaffold", Nano Lett. 6: 1594-1597 (2006)
24. Reches M, and Gazit E "Controlled Patterning of Aligned Self-Assembled Peptide Nanotubes", Nature Nanotech. 1: 195-200 (2006)
25. Colmbo G, Soto P, and Gazit E "Self Aggregating Systems and Peptides and their Possible Use", Trends Biotechnol. 25: 211-218 (2007)
26. Ackbarow T, Cheng X, Keten S, and Buehler MJ, "Hierarchies, multiple energy barriers and robustness govern the fracture mechanics of alpha-helical and beta-sheet protein domains ", PNAS 104: 16410-16415 (2007)
27. Silva GA, Czeisler C, Niece KL, Beniash E, Harrington DA, Kessler JA and Stupp SI "Selective differentiation of neural progenitor cells by high-epitope density nanofibers", Science 303: 1352-1355 (2004)
28. Scheibel T, Parthasarathy R, Sawicki G, Lin XM, Jaeger H, and Lindquist SL "Conducting nanowires built by controlled self-assembly of amyloid fibers and selective metal deposition", PNAS 100: 4527-4532 (2003)
29. Supple S, and Quirke N "Short range united atom potentials for alkanes: Decane and nonane", Molecular Simulation 29: 77-82 (2003)
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