Tensile deformation and failure of amyloid and amyloid-like protein fibrils

Nanotechnology

Volumn 25, Issue 10, 2014, Pages

  Solar, Max ^a   Buehler, Markus J ^a  

^a Massachusetts Institute of Technology   (United States)

Author keywords

amyloid; Hbond; hierarchical; mechanics; rotein; rupture

Indexed keywords

AMYLOID; NANOMATERIAL;

ARTICLE; BIOMECHANICS; CHEMICAL MODEL; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; TENSILE STRENGTH;

AMYLOID; BIOMECHANICAL PHENOMENA; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; NANOSTRUCTURES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; TENSILE STRENGTH;

EID: 84894124340     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/25/10/105703     Document Type: Article

References (50)

1. Aguzzi A 2009 Beyond the prion principle Nature 459 924-5
2. Berendsen H J C, Vanderspoel D and Vandrunen R 1995 Gromacs - a message-passing parallel molecular-dynamics implementation Comput. Phys. Commun. 91 43-56
3. Bernstein F C, Koetzle T F, Williams G J B, Meyer E F, Brice M D, Rodgers J R, Kennard O, Shimanouchi T and Tasumi M 1977 Protein data bank - computer-based archival file for macromolecular structures J. Mol. Biol. 112 535-42 (Pubitemid 8109216)
4. Brown K, Pompeo F, Dixon S, Mengin-Lecreulx D, Cambillau C and Bourne Y 1999 Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily EMBO J. 18 4096-107 (Pubitemid 29364113)
5. Buehler M J 2010 Strength in numbers Nature Nanotechnol. 5 172-4
6. Chiti F and Dobson C M 2006 Protein misfolding, functional amyloid, and human disease Annu. Rev. Biochem. 75 333-66 (Pubitemid 44118036)
7. Darden T, York D and Pedersen L 1993 Particle mesh ewald - an N ṡlog(N) method for ewald sums in large systems J. Chem. Phys. 98 10089-92
8. Dobson C M 1999 Protein misfolding, evolution and disease Trends Biochem. Sci. 24 329-32 (Pubitemid 29421804)
9. Dobson C M 2003 Protein folding and misfolding Nature 426 884-90 (Pubitemid 38056880)
10. Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 A smooth particle mesh Ewald method J. Chem. Phys. 103 8577-93
11. Goldschmidt L, Teng P K, Riek R and Eisenberg D 2010 Identifying the amylome, proteins capable of forming amyloid-like fibrils Proc. Natl Acad. Sci. USA 107 3487-92
12. Hess B 2008 P-LINCS: a parallel linear constraint solver for molecular simulation J. Chem. Theory Comput. 4 116-22
13. Hess B, Bekker H, Berendsen H J C and Fraaije J G E M 1997 LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1463-72 (Pubitemid 127637344)
14. Hess B, Kutzner C, van der Spoel D and Lindahl E 2008 GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 435-47
15. Hoover W G 1985 Canonical dynamics - equilibrium phase-space distributions Phys. Rev. A 31 1695-7
16. Humphrey W, Dalke A and Schulten K 1996 VMD: visual molecular dynamics J. Mol. Graphics 14 33 (Pubitemid 26152973)
17. Jaroniec C P, MacPhee C E, Bajaj V S, McMahon M T, Dobson C M and Griffin R G 2004 High-resolution molecular structure of a peptide in an amyloid fibril determined by magic angle spinning NMR spectroscopy Proc. Natl Acad. Sci. USA 101 711-6 (Pubitemid 38121022)
18. Keten S and Buehler M J 2008 Asymptotic strength limit of hydrogen-bond assemblies in proteins at vanishing pulling rates Phys. Rev. Lett. 100 198301 (Pubitemid 351671510)
19. Keten S and Buehler M J 2008 Geometric confinement governs the rupture strength of H-bond assemblies at a critical length scale Nano Lett. 8 743-8 (Pubitemid 351346050)
20. Keten S and Buehler M J 2008 Large deformation and fracture mechanics of a beta-helical protein nanotube: atomistic and continuum modeling Comput. Method Appl. M 197 3203-14
21. Keten S, Xu Z P and Buehler M J 2011 Triangular core as a universal strategy for stiff nanostructures in biology and biologically inspired materials Mater. Sci. Eng. C 31 775-80
22. Keten S, Z P Xu, Ihle B and Buehler M J 2010 Nanoconfinement controls stiffness, strength and mechanical toughness of beta-sheet crystals in silk Nature Mater. 9 359-67
23. 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 1900-3
24. Knowles T P J and Buehler M J 2011 Nanomechanics of functional and pathological amyloid materials Nature Nanotechnol. 6 469-79
25. 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 Nature Nanotechnol. 5 204-7
26. Kol N, Adler-Abramovich L, Barlam D, Shneck R Z, Gazit E and Rousso I 2005 Self-assembled peptide nanotubes are uniquely rigid bioinspired supramolecular structures Nano Lett. 5 1343-6 (Pubitemid 41084414)
27. Li C X, Adamcik J and Mezzenga R 2012 Biodegradable nanocomposites of amyloid fibrils and graphene with shape-memory and enzyme-sensing properties Nature Nanotechnol. 7 421-7
28. Lindahl E, Hess B and van der Spoel D 2001 GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model 7 306-17 (Pubitemid 36153547)
29. Luhrs T, Ritter C, Adrian M, Riek-Loher D, Bohrmann B, Doeli H, Schubert D and Riek R 2005 3D structure of Alzheimer's amyloid-beta(1-42) fibrils Proc. Natl Acad. Sci. USA 102 17342-7 (Pubitemid 41740868)
30. MacKerell A D et al 1998 All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 3586-616
31. Middleton A J, Marshall C B, Faucher F, Bar-Dolev M, Braslavsky I, Campbell R L, Walker V K and Davies P L 2012 Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site J. Mol. Biol. 416 713-24
32. Nose S 1984 A unified formulation of the constant temperature molecular-dynamics methods J. Chem. Phys. 81 511-9
33. Nose S and Klein M L 1983 Constant pressure molecular-dynamics for molecular-systems Mol. Phys. 50 1055-76
34. Nummelin H, Merckel M C, Leo J C, Lankinen H, Skurnik M and Goldman A 2004 The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll EMBO J. 23 701-11 (Pubitemid 38418738)
35. Paparcone R and Buehler M J 2009 Microscale structural model of Alzheimer A beta(1-40) amyloid fibril Appl. Phys. Lett. 94 1938301
36. Paparcone R and Buehler M J 2010 Failure of Alzheimer's A beta(1-40) amyloid nanofibrils under compressive loading JOM 62 64-8
37. Paparcone R, Keten S and Buehler M J 2010 Atomistic simulation of nanomechanical properties of Alzheimer's A beta(1-40) amyloid fibrils under compressive and tensile loading J. Biomech. 43 1196-201
38. Paparcone R, Sanchez J and Buehler M J 2010 Comparative study of polymorphous alzheimer's a beta(1-40) amyloid nanofibrils and microfibers J. Comput. Theor. Nanosci. 7 1279-86
39. Parrinello M and Rahman A 1981 Polymorphic transitions in single-crystals - a new molecular-dynamics method J. Appl. Phys. 52 7182-90 (Pubitemid 12456820)
40. Qiang W, Yau W M, Luo Y Q, Mattson M P and Tycko R 2012 Antiparallel beta-sheet architecture in Iowa-mutant beta-amyloid fibrils Proc. Natl Acad. Sci. USA 109 4443-8
41. Qin Z and Buehler M J 2010 Cooperative deformation of hydrogen bonds in beta-strands and beta-sheet nanocrystals Phys. Rev. E 82 061906
42. Ruiz L and Keten S 2012 Multi-scale modeling of elasticity and fracture in organic nanotubes J. Eng. Mech. at press
43. Ruiz L, VonAchen P, Lazzara T D, Xu T and Keten S 2013 Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force Nanotechnology 24 195103
44. Sawaya M R et al 2007 Atomic structures of amyloid cross-beta spines reveal varied steric zippers Nature 447 453-7 (Pubitemid 46816731)
45. Solar M and Buehler M J 2012 Comparative analysis of nanomechanics of protein filaments under lateral loading Nanoscale 4 1177-83
46. Solar M I and Buehler M J 2012 Composite materials: taking a leaf from nature's book Nature Nanotechnol. 7 417-9
47. Sotomayor M and Schulten K 2007 Single-molecule experiments in vitro and in silico Science 316 1144-8 (Pubitemid 46877468)
48. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A E and Berendsen H J C 2005 GROMACS: fast, flexible, and free J. Comput. Chem. 26 1701-18 (Pubitemid 43076182)
49. Van Melckebeke H, Wasmer C, Lange A, AB E, Loquet A, Bockmann A and Meier B H 2010 Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state nmr spectroscopy J. Am. Chem. Soc. 132 13765-75
50. Xu Z P, Paparcone R and Buehler M J 2010 Alzheimer's A beta(1-40) amyloid fibrils feature size-dependent mechanical properties Biophys. J. 98 2053-62