Acknowledgement
Supported by : National Research Foundation of Korea (NRF), Korea Institute of Science and Technology Information (KISTI)
References
- 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. https://doi.org/10.1016/j.pmatsci.2008.06.002
- Bustamante, C., Bryant, Z. and Smith, S.B. (2003), "Ten years of tension: Single-molecule DNA mechanics", Nature, 421(6921), 423-427. https://doi.org/10.1038/nature01405
- Cherny, I. and Gazit, E. (2008), "Amyloids: Not only pathological agents but also ordered nanomaterials", Angew. Chem. Int. Ed., 47(22), 4062-4069. https://doi.org/10.1002/anie.200703133
- 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. https://doi.org/10.1039/C4CP03804E
- 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. https://doi.org/10.1073/pnas.0708354105
- 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. https://doi.org/10.1021/jp035178x
- 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. https://doi.org/10.1103/PhysRevE.71.021904
- 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. https://doi.org/10.1073/pnas.1309690110
- Gao, M., Wilmanns, M. and Schulten K. (2002), "Steered molecular dynamics studies of titin I1 domain unfolding", Biophys. J., 83(6), 3435-3445. https://doi.org/10.1016/S0006-3495(02)75343-5
- 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. https://doi.org/10.1021/cr3000994
- 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. https://doi.org/10.1056/NEJM200008103430607
- Humphrey, W., Dalke, A. and Schulten, K. (1996), "VMD: Visual molecular dynamics", J. Mol. Graph., 14(1), 33-38. https://doi.org/10.1016/0263-7855(96)00018-5
-
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. https://doi.org/10.1038/nmat2704 - 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. https://doi.org/10.1126/science.1150057
- Knowles, T.P.J. and Buehler, M.J. (2011), "Nanomechanics of functional and pathological amyloid materials", Nat. Nanotech., 6(8), 469-479. https://doi.org/10.1038/nnano.2011.102
- 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. https://doi.org/10.1038/nnano.2010.26
- 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. https://doi.org/10.1038/nnano.2012.62
-
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. https://doi.org/10.1002/adma.201400730 - 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. https://doi.org/10.1016/S0006-3495(98)77556-3
- Lu, H. and Schulten, K. (1999), "Steered molecular dynamics simulations of force-induced protein domain unfolding", Proteins: Struct. Funct. Bioinfo., 35(4), 453-463. https://doi.org/10.1002/(SICI)1097-0134(19990601)35:4<453::AID-PROT9>3.0.CO;2-M
- 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. https://doi.org/10.1021/jp973084f
- Muller, D.J. and Dufrene, Y.F. (2008), "Atomic force microscopy as a multifunctional molecular toolbox in nanobiotechnology", Nat. Nanotech., 3(5), 261-269. https://doi.org/10.1038/nnano.2008.100
- 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. https://doi.org/10.1002/ange.200804198
- 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. https://doi.org/10.1073/pnas.0603931103
-
Paparcone, R. and Buehler, M.J. (2011), "Failure of A
${\beta}$ (1-40) amyloid fibrils under tensile loading", Biomaterials, 32(13), 3367-3373. https://doi.org/10.1016/j.biomaterials.2010.11.066 - Pepys, M.B. (2006), "Amyloidosis", Annu. Rev. Med., 57, 223-241. https://doi.org/10.1146/annurev.med.57.121304.131243
- 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. https://doi.org/10.1002/jcc.20289
- 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. https://doi.org/10.1038/nature03989
- 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. https://doi.org/10.1073/pnas.0604035103
- Solar, M. and Buehler, M.J. (2012a), "Comparative analysis of nanomechanics of protein filaments under lateral loading", Nanoscale, 4(4), 1177-1183. https://doi.org/10.1039/C1NR11260K
- Solar, M.I. and Buehler, M.J. (2012b), "Composite materials: Taking a leaf from nature's book", Nat. Nanotechnology, 7(7), 417-419. https://doi.org/10.1038/nnano.2012.86
- Solar, M. and Buehler, M.J. (2014), "Tensile deformation and failure of amyloid and amyloid-like protein fibrils", Nanotechnology, 25(10), 105703. https://doi.org/10.1088/0957-4484/25/10/105703
- Sotomayor, M. and Schulten, K. (2007), "Single-molecule experiments in vitro and in silico", Science, 316(5828), 1144-1148. https://doi.org/10.1126/science.1137591
- 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. https://doi.org/10.1146/annurev-physchem-032210-103526
- 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. https://doi.org/10.1038/nature04922
-
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. https://doi.org/10.1016/j.bpj.2009.12.4317 - 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. https://doi.org/10.1063/1.4774296
- 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. https://doi.org/10.1002/adfm.201002493
- 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. https://doi.org/10.1371/journal.pone.0088502
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