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Nanomechanical behaviors and properties of amyloid fibrils
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 Title & Authors
Nanomechanical behaviors and properties of amyloid fibrils
Choi, Bumjoon; Lee, Sang Woo; Eom, Kilho;
Amyloid fibrils have recently been considered as an interesting material, since they exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is larger than that of other protein materials. Despite recent findings of these excellent mechanical properties for amyloid fibrils, it has not been fully understood how these excellent mechanical properties are achieved. In this work, we have studied the nanomechanical deformation behaviors and properties of amyloid fibrils such as their elastic modulus as well as fracture strength, by using atomistic simulations, particularly steered molecular dynamics simulations. Our simulation results suggest the important role of the length of amyloid fibrils in their mechanical properties such that the fracture force of amyloid fibril is increased when the fibril length decreases. This length scale effect is attributed to the rupture mechanisms of hydrogen bonds that sustain the fibril structure. Moreover, we have investigated the effect of boundary condition on the nanomechanical deformation mechanisms of amyloid fibrils. It is found that the fracture force is critically affected by boundary condition. Our study highlights the crucial role of both fibril length and boundary condition in the nanomechanical properties of amyloid fibrils.
amyloid fibrils;mechanical deformation mechanisms;molecular dynamics simulation;fracture property;boundary condition;
 Cited by
Nanomechanical Characterization of Amyloid Fibrils Using Single-Molecule Experiments and Computational Simulations, Journal of Nanomaterials, 2016, 2016, 1  crossref(new windwow)
Buehler, M.J., Keten, S. and Ackbarow, T. (2008), "Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture", Prog. Mater. Sci., 53(8), 1101-1241. crossref(new window)

Bustamante, C., Bryant, Z. and Smith, S.B. (2003), "Ten years of tension: Single-molecule DNA mechanics", Nature, 421(6921), 423-427. crossref(new window)

Cherny, I. and Gazit, E. (2008), "Amyloids: Not only pathological agents but also ordered nanomaterials", Angew. Chem. Int. Ed., 47(22), 4062-4069. crossref(new window)

Choi, B., Yoon, G., Lee, S.W. and Eom, K. (2015), "Mechanical deformation mechanisms and properties of amyloid fibrils", Phys. Chem. Chem. Phys., 17(2), 1379-1389. crossref(new window)

Engel, M.F.M., Khemtemourian, L., Kleijer, C.C., Meeldijk, H.J.D., Jacobs, J., Verkleij, A.J., de Kruijff, B., Killian, J.A. and Hoppener, J.W.M. (2008), "Membrane damage by human islet amyloid polypeptide through fibril growth at the membrane", Proc. Natl. Acad. Sci. USA., 105(16), 6033-6038. crossref(new window)

Eom, K. (2011), Simulations in Nanobiotechnology, CRC Press, Boca Raton, FL, USA.

Eom, K., Li, P.C., Makarov, D.E. and Rodin, G.J. (2003), "Relationship between the mechanical properties and topology of cross-linked polymer molecules: Parallel strands maximize the strength of model polymers and protein domains", J. Phys. Chem. B., 107(34), 8730-8733.

Eom, K., Makarov, D.E. and Rodin, G.J. (2005), "Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single-molecule pulling experiments", Phys. Rev. E., 71(2), 021904. crossref(new window)

Fitzpatrick, A.W.P., Park, S.T. and Zewail, A.H. (2013), "Exceptional rigidity and biomechanics of amyloid revealed by 4D electron microscopy", Proc. Natl. Acad. Sci. U.S.A., 110(27), 10976-10981. crossref(new window)

Gao, M., Wilmanns, M. and Schulten K. (2002), "Steered molecular dynamics studies of titin I1 domain unfolding", Biophys. J., 83(6), 3435-3445. crossref(new window)

Gere, J.M. (2003), Mechanics of Materials, (6th Edition), Thomson Learning, Belmont, CA, USA.

Gosline, J., Guerette, P., Ortlepp, C. and Savage, K. (1999), "The mechanical design of spider silks: From fibroin sequence to mechanical function", J. Exp. Biol., 202(23), 3295-3303.

Hamley, I.W. (2012), "The amyloid beta peptide: A chemist's perspective role in Alzheimer's and Fibrillization", Chem. Rev., 112(10), 5147-5192. crossref(new window)

Hoppener, J.W.M., Ahren, B. and Lips, C.J.M. (2000), "Islet amyloid and type 2 diabetes mellitus", New England J. Med., 343(6), 411-419. crossref(new window)

Humphrey, W., Dalke, A. and Schulten, K. (1996), "VMD: Visual molecular dynamics", J. Mol. Graph., 14(1), 33-38. crossref(new window)

Keten, S., Xu, Z., Ihle, B. and Buehler, M.J. (2010), "Nanoconfinement controls stiffness, strength, and mechanical toughness of ${\beta}$-sheet crystals in slik", Nat. Mater., 9(4), 359-367. crossref(new window)

Knowles, T.P., Fitzpatrick, A.W., Meehan, S., Mott, H.R., Vendruscolo, M., Dobson, C.M. and Welland, M.E. (2007), "Role of intermolecular forces in defining material properties of protein nanofibrils", Science, 318(5858), 1900-1903. crossref(new window)

Knowles, T.P.J. and Buehler, M.J. (2011), "Nanomechanics of functional and pathological amyloid materials", Nat. Nanotech., 6(8), 469-479. crossref(new window)

Knowles, T.P.J., Oppenheim, T.W., Buell, A.K., Chirgadze, D.Y. and Welland, M.E. (2010), "Nanostructured films from hierarchical self-assembly of amyloidogenic proteins", Nat. Nanotech., 5(3), 204-207. crossref(new window)

Li, C., Adamcik, J. and Mezzenga, R. (2012), "Biodegradable nanocomposites of amyloid fibrils and graphene with shape-memory and enzyme-sensing properties", Nat. Nanotech., 7(7), 421-427. crossref(new window)

Ling, S., Li, C., Adamcik, J., Shao, Z., Chen, X. and Mezzenga, R. (2014), "Modulating materials by orthogonally oriented ${\beta}$-strands: Composites of amyloid and silk fibroin fibrils", Adv. Mater., 26(26), 4569-4574. crossref(new window)

Lu, H.B., Isralewitz, B., Krammer, A., Vogel, V. and Schulten, K. (1998), "Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation", Biophys. J., 75(2), 662-671. crossref(new window)

Lu, H. and Schulten, K. (1999), "Steered molecular dynamics simulations of force-induced protein domain unfolding", Proteins: Struct. Funct. Bioinfo., 35(4), 453-463. crossref(new window)

MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D. and Karplus, M. (1998), "All-atom empirical potential for molecular modeling and dynamics studies of proteins", J. Phys. Chem. B., 102(18), 3586-3616. crossref(new window)

Muller, D.J. and Dufrene, Y.F. (2008), "Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology", Nat. Nanotech., 3(5), 261-269. crossref(new window)

Nielsen, J.T., Bjerring, M., Jeppesen, M.D., Pedersen, R.O., Pedersen, J.M., Hein, K.L., Vosegaard, T., Skrypstrup, T., Otzen, D.E. and Nielsen, N.C. (2009), "Unique identification of supramolecular structures in amyloid firbils by solid-state NMR spectroscopy", Angew. Chem. Int. Ed., 121(12), 2152-2155. crossref(new window)

Pampaloni, F., Lattanzi, G., Jonas, A., Surrey, T., Frey, E. and Florin, E.-L. (2006), "Thermal fluctuations of grafted microtubules provide evidence of a length-dependent persistent length", Proc. Natl. Acad. Sci. USA, 103(27), 10248-10253. crossref(new window)

Paparcone, R. and Buehler, M.J. (2011), "Failure of A${\beta}$(1-40) amyloid fibrils under tensile loading", Biomaterials, 32(13), 3367-3373. crossref(new window)

Pepys, M.B. (2006), "Amyloidosis", Annu. Rev. Med., 57, 223-241. crossref(new window)

Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L. and Schulten, K. (2005), "Scalable molecular dynamics with NAMD", J. Comput. Chem., 26(16), 1781-1802. crossref(new window)

Silveira, J.R., Raymond, G.J., Hughson, A.G., Race, R.E., Sim, V.L., Hayes, S.F. and Caughey, B. (2005), "The most infectious prion protein particles", Nature, 437(7056), 257-261. crossref(new window)

Smith, J.F., Knowles, T.P., Dobson, C.M. MacPhee, C.E. and Welland, M.E. (2006), "Characterization of the nanoscale properties of individual amyloid fibrils", Proc. Natl. Acad. Sci. USA, 103(43), 15806-15811. crossref(new window)

Solar, M. and Buehler, M.J. (2012a), "Comparative analysis of nanomechanics of protein filaments under lateral loading", Nanoscale, 4(4), 1177-1183. crossref(new window)

Solar, M.I. and Buehler, M.J. (2012b), "Composite materials: Taking a leaf from nature's book", Nat. Nanotechnology, 7(7), 417-419. crossref(new window)

Solar, M. and Buehler, M.J. (2014), "Tensile deformation and failure of amyloid and amyloid-like protein fibrils", Nanotechnology, 25(10), 105703. crossref(new window)

Sotomayor, M. and Schulten, K. (2007), "Single-molecule experiments in vitro and in silico", Science, 316(5828), 1144-1148. crossref(new window)

Straub, J.E. and Thirumalai, D. (2011), "Towards a molecular theory of early and late events in monomer to amyloid fibril formation", Annu. Rev. Phys. Chem., 62, 437-463. crossref(new window)

Tanaka, M., Collins, S.R., Toyama, B.H. and Weissman, J.S. (2006), "The physical basis of how prion conformations determine strain phenotypes", Nature, 442(7102), 585-589. crossref(new window)

Xu, Z., Paparcone, R. and Buehler, M.J. (2010), "Alzheimer's A${\beta}$(1-40) amyloid fibrils feature sizedependent mechanical properties", Biophys. J., 98(10), 2053-2062. crossref(new window)

Yoon, G., Kim, Y.K., Eom, K. and Na, S. (2013), "Relationship between disease-specific structures of amyloid fibrils and their mechanical properties", Appl. Phys. Lett., 102(1), 011914. crossref(new window)

Yoon, G., Kwak, J., Kim, J.I., Na, S. and Eom, K. (2011), "Mechanical characterization of amyloid fibrils using coarse-grained normal mode analysis", Adv. Funct. Mater., 21(18), 3454-3463. crossref(new window)

Yoon, G., Lee, M., Kim, J.I., Na, S. and Eom, K. (2014), "Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils", PLOS ONE, 9, e88502. crossref(new window)