Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force

Nanotechnology

Volumn 24, Issue 19, 2013, Pages

  Ruiz, L ^a   Vonachen, P ^a   Lazzara, T D ^b   Xu, T ^b   Keten, S ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

^b Lawrence Berkeley National Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC PEPTIDE NANOTUBES; EXPERIMENTAL OBSERVATION; NANOPOROUS THIN FILMS; NOVEL NANOCOMPOSITES; QUASI-STATIC DEFORMATION; SPATIAL AND TEMPORAL DISTRIBUTION; SUPRA-MOLECULAR NANO STRUCTURES; SUPRAMOLECULAR NANOTUBE;

ASPECT RATIO; BIOLOGICAL MATERIALS; BLENDING; CHEMICAL PROPERTIES; COMPUTER SIMULATION; ELASTIC MODULI; ELASTICITY; INDUSTRIAL APPLICATIONS; MECHANICAL ENGINEERING; NANOTUBES; PROTEINS; STOCHASTIC SYSTEMS;

SUPRAMOLECULAR CHEMISTRY;

CYCLOPEPTIDE; NANOTUBE;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL MODEL; CHEMISTRY; MECHANICAL STRESS; MOLECULAR DYNAMICS; MOLECULAR GENETICS; STATISTICS; ULTRASTRUCTURE; YOUNG MODULUS;

AMINO ACID SEQUENCE; ELASTIC MODULUS; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; NANOTUBES; PEPTIDES, CYCLIC; STOCHASTIC PROCESSES; STRESS, MECHANICAL;

EID: 84876468657     PISSN: 09574484     EISSN: 13616528     Source Type: Journal    
DOI: 10.1088/0957-4484/24/19/195103     Document Type: Article

References (65)

1. Ghadiri M R, Granja J R, Milligan R A, Mcree D E and Khazanovich N 1993 Self-assembling organic nanotubes based on a cyclic peptide architecture Nature 366 324-7 (Pubitemid 23349358)
2. Percec V et al 2004 Self-assembly of amphiphilic dendritic dipeptides into helical pores Nature 430 764-8 (Pubitemid 39071343)
3. Zhou M J, Kidd T J, Noble R D and Gin D L 2005 Supported lyotropic liquid-crystal polymer membranes: promising materials for molecular-size- selective aqueous nanofiltration Adv. Mater. 17 1850 (Pubitemid 41120185)
4. Davis J T and Spada G P 2007 Supramolecular architectures generated by self-assembly of guanosine derivatives Chem. Soc. Rev. 36 296-313
5. Sakai N, Kamikawa Y, Nishii M, Matsuoka T, Kato T and Matile S 2006 Dendritic folate rosettes as ion channels in lipid bilayers J. Am. Chem. Soc. 128 2218-9
6. Li H, Eddaoudi M, O'Keeffe M and Yaghi O M 1999 Design and synthesis of an exceptionally stable and highly porous metal-organic framework Nature 402 276-9 (Pubitemid 129516259)
7. Ghadiri M R 1995 Self-assembled nanoscale tubular ensembles Adv. Mater. 7 675-7
8. Liu J, Stace-Naughton A, Jiang X and Brinker C J 2009 Porous nanoparticle supported lipid bilayers (protocells) as delivery vehicles J. Am. Chem. Soc. 131 1354-5
9. Moore J S 1999 Supramolecular polymers Curr. Opin. Colloid Interface Sci. 4 108-16 (Pubitemid 29397162)
10. Percec V, Dulcey A E, Peterca M, Ilies M, Nummelin S, Sienkowska M J and Heiney P A 2006 Principles of self-assembly of helical pores from dendritic dipeptides Proc. Natl Acad. Sci. USA 103 2518-23
11. Percec V, Imam M R, Peterca M, Wilson D A and Heiney P A 2008 Self-assembly of dendritic crowns into chiral supramolecular spheres J. Am. Chem. Soc. 131 1294-304
12. Stupp S I, Pashuck E T and Cui H G 2010 Tuning supramolecular rigidity of peptide fibers through molecular structure J. Am. Chem. Soc. 132 6041-6
13. D'Alessandro D M, Smit B and Long J R 2010 Carbon dioxide capture: prospects for new materials Angew. Chem. Int. Edn 49 6058-82
14. Shannon M A, Bohn P W, Elimelech M, Georgiadis J G, Marinas B J and Mayes A M 2008 Science and technology for water purification in the coming decades Nature 452 301-10 (Pubitemid 351430783)
15. Jiang D-E, Cooper V R and Dai S 2009 Porous graphene as the ultimate membrane for gas separation Nano Lett. 9 4019-24
16. Jirage K B, Hulteen J C and Martin C R 1997 Nanotubule-based molecular-filtration membranes Science 278 655-8 (Pubitemid 27464957)
17. Baker R W 2002 Future directions of membrane gas separation technology Indust. Eng. Chem. Res. 41 1393-411 (Pubitemid 34225901)
18. Koros W J and Mahajan R 2000 Pushing the limits on possibilities for large scale gas separation: which strategies? J. Membr. Sci. 175 181-96 (Pubitemid 30398567)
19. Xu T, Zhao N N, Ren F, Hourani R, Lee M T, Shu J Y, Mao S and Helms B A 2011 Subnanometer porous thin films by the co-assembly of nanotube subunits and block copolymers ACS Nano 5 1376-84
20. Hourani R, Zhang C, van der Weegen R, Ruiz L, Li C Y, Keten S, Helms B A and Xu T 2011 Processable cyclic peptide nanotubes with tunable interiors J. Am. Chem. Soc. 133 15296-9
21. Ruiz L and Keten S 2012 Multi-scale modeling of elasticity and fracture in organic nanotubes J. Eng. Mech. 1 371
22. Ruiz L and Keten S 2011 Atomistic modeling and mechanics of self-assembled organic nanotubes Int. J. Appl. Mech. 3 1-18
23. Keten S and Buehler M J 2010 Nanostructure and molecular mechanics of spider dragline silk protein assemblies J. R. Soc. Interface 7 1709-21
24. Keten S and Buehler M J 2010 Atomistic model of the spider silk nanostructure Appl. Phys. Lett. 96 153701
25. Keten S, Xu Z, 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
26. 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
27. Keten S and Buehler M J 2008 Large deformation and fracture mechanics of a beta-helical protein nanotube: atomistic and continuum modeling Comput. Methods Appl. Mech. Eng. 197 3203-14
28. 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
29. Knowles T P J and Buehler M J 2011 Nanomechanics of functional and pathological amyloid materials Nature Nanotechnol. 6 469-79
30. Diaz J A C and Cagin T 2010 Thermo-mechanical stability and strength of peptide nanostructures from molecular dynamics: self-assembled cyclic peptide nanotubes Nanotechnology 21 115703
31. Keten S, Rodriguez Alvarado J, Müftü S and Buehler M 2009 Nanomechanical characterization of the triple β-helix domain in the cell puncture needle of bacteriophage T4 virus Cell. Mol. Bioeng. 2 66-74
32. Smith J F, Knowles T P J, 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 15806-11 (Pubitemid 44657548)
33. 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
34. Aggeli A, Nyrkova I A, Bell M, Harding R, Carrick L, McLeish T C B, Semenov A N and Boden N 2001 Hierarchical self-assembly of chiral rod-like molecules as a model for peptide β-sheet tapes, ribbons, fibrils, and fibers Proc. Natl Acad. Sci. USA 98 11857-62 (Pubitemid 32959792)
35. Adamcik J, Lara C, Usov I, Jeong J S, Ruggeri F S, Dietler G, Lashuel H A, Hamley I W and Mezzenga R 2012 Measurement of intrinsic properties of amyloid fibrils by the peak force QNM method Nanoscale 4 4426-9
36. vandenAkker C C, Engel M F M, Velikov K P, Bonn M and Koenderink G H 2011 Morphology and persistence length of amyloid fibrils are correlated to peptide molecular structure J. Am. Chem. Soc. 133 18030-3
37. Xu Z and Buehler M J 2010 Mechanical energy transfer and dissipation in fibrous beta-sheet-rich proteins Phys. Rev. E 81 061910
38. Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, Chatenay D and Caron F 1996 DNA: an extensible molecule Science 271 792-4 (Pubitemid 26058929)
39. Evans E, Leung A, Hammer D and Simon S 2001 Chemically distinct transition states govern rapid dissociation of single L-selectin bonds under force Proc. Natl Acad. Sci. USA 98 3784-9 (Pubitemid 32249849)
40. Ackbarow T, Chen X, Keten S and Buehler M J 2007 Hierarchies, multiple energy barriers, and robustness govern the fracture mechanics of {alpha}-helical and beta-sheet protein domains Proc. Natl Acad. Sci. USA 104 16410-5 (Pubitemid 350211030)
41. Schlierf M, Li H and Fernandez J M 2004 The unfolding kinetics of ubiquitin captured with single-molecule force-clamp techniques Proc. Natl Acad. Sci. USA 101 7299-304 (Pubitemid 38638027)
42. Wartell R M and Benight A S 1985 Thermal denaturation of DNA molecules: a comparison of theory with experiment Phys. Rep. 126 67-107
43. Smith S B, Cui Y and Bustamante C 1996 Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 795-9
44. Hoff A J and Roos A L M 1972 Hysteresis of denaturation of DNA in the melting range Biopolymers 11 1289-94
45. Bouchiat C, Wang M D, Allemand J F, Strick T, Block S M and Croquette V 1999 Estimating the persistence length of a worm-like chain molecule from force-extension measurements Biophys. J. 76 409-13 (Pubitemid 29202467)
46. Marko J F and Siggia E D 1995 Stretching DNA Macromolecules 28 8759-70
47. Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kalé L and Schulten K 2005 Scalable molecular dynamics with NAMD J. Comput. Chem. 26 1781-802 (Pubitemid 43078511)
48. MacKerell A D, Brooks B, Brooks C L, Nilsson L, Roux B, Won Y and Karplus M 2002 Encyclopedia of Computational Chemistry (New York: Wiley)
49. Martyna G J 1994 Remarks on constant-temperature molecular dynamics with momentum conservation Phys. Rev. E 50 3234-6
50. Feller S E, Zhang Y, Pastor R W and Brooks B R 1995 Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 4613-21
51. Hibbeler R C and Hibbeler R 1999 Structural Analysis (New York: Prentice-Hall)
52. Mofrad M R K and Kamm R D 2006 Cytoskeletal Mechanics: Models and Measurements in Cell Mechanics (Cambridge: Cambridge University Press)
53. Schellman J A 1974 Flexibility of DNA Biopolymers 13 217-26
54. Israelachvili J 1992 Intermolecular and Surface Forces, Second Edition: With Applications to Colloidal and Biological Systems (Colloid Science) (New York: Academic)
55. Jones J E 1924 On the determination of molecular fields. II. From the equation of state of a gas Proc. R. Soc. A 106 463-77
56. Bell G 1978 Models for the specific adhesion of cells to cells Science 200 618-27
57. Theodor A and Markus J B 2009 Alpha-helical protein domains unify strength and robustness through hierarchical nanostructures Nanotechnology 20 075103
58. Zhao Q, Laurent K and Markus J B 2009 Nanomechanical properties of vimentin intermediate filament dimers Nanotechnology 20 425101
59. Kolmakov G V, Matyjaszewski K and Balazs A C 2009 Harnessing labile bonds between nanogel particles to create self-healing materials ACS Nano 3 885-92
60. Barber A H, Andrews R, Schadler L S and Wagner H D 2005 On the tensile strength distribution of multiwalled carbon nanotubes Appl. Phys. Lett. 87 203106 (Pubitemid 41611428)
61. Lee C, Wei X, Kysar J W and Hone J 2008 Measurement of the elastic properties and intrinsic strength of monolayer graphene Science 321 385-8 (Pubitemid 352029970)
62. Buehler M J and Yung Y C 2009 Deformation and failure of protein materials in physiologically extreme conditions and disease Nature Mater. 8 175-88
63. Rief M, Gautel M, Oesterhelt F, Fernandez J M and Gaub H E 1997 Reversible unfolding of individual titin immunoglobulin domains by AFM Science 276 1109-12 (Pubitemid 27218118)
64. Sotomayor M and Schulten K 2007 Single-molecule experiments in vitro and in silico Science 316 1144-8 (Pubitemid 46877468)
65. Lantz M A, Jarvis S P, Tokumoto H, Martynski T, Kusumi T, Nakamura C and Miyake J 1999 Stretching the α-helix: a direct measure of the hydrogen-bond energy of a single-peptide molecule Chem. Phys. Lett. 315 61-8 (Pubitemid 129549524)