Toward intelligent materials

Molecular Self-Assembly: Advances and Applications

Volumn , Issue , 2012, Pages 1-36

  Childers, W Seth ^a   Mehta, Anil K ^a   Bui, Thinh Q ^a   Liang, Yan ^a   Lynn, David G ^a  

^a EMORY UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84871335229     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4032/9789814364317     Document Type: Chapter

References (127)

1. Bromley EH, Channon K, Moutevelis E, Woolfson DN (2008) Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems. ACS Chem Biol 3: 38-50.
2. Daw R, Tonzani S (2009) Biomaterials. Nature 462: 425.
3. Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA, Smith HO, Venter JC, Glass JI (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325: 1693-1696.
4. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, III, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329: 52-56.
5. Darwin C (1859) On the origin of species by means of natural selectio.n. London: John Murray.
6. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737-738.
7. Hunding A, Kepes F, Lancet D, Minsky A, Norris V, Raine D, Sriram K, Root-Bernstein R (2006) Compositional complementarity and prebiotic ecology in the origin of life. Bioessays 28: 399-412.
8. Capra F (1996) The web of life. New York: Doubleday.
9. Mansy SS, Schrum JP, Krishnamurthy M, Tobe S, Treco DA, Szostak JW (2008) Template-directed synthesis of a genetic polymer in a model protocell. Nature 454: 122-125.
10. Joyce GF, Inoue T, Orgel LE (1984) Non-enzymatic template-directed synthesis on RNA random copolymers - Poly (C,U) Templates. J Mol Biol 176: 279-306.
11. Ertem G, Ferris JP (1996) Synthesis of RNA oligomers on heterogeneous templates. Nature 379: 238-240.
12. Orgel LE (1992) Molecular replication. Nature 358: 203-209.
13. Goodwin JT, Lynn DG (1992) Template-directed synthesis: use of a reversible reaction. J Am Chem Soc 114: 9197-9198.
14. Li X, Lynn DG (2002) Polymerization on solid supports. Angew Chem Int Ed Engl 41: 4567-4569.
15. Zhan Z-YJ, Lynn DG (1997) Chemical amplification through templatedirected synthesis. J Am Chem Soc 119: 12420-12421.
16. Li X, Hernandez AF, Grover MA, Hud NV, Lynn DG (2010) Step-growth control in template-directed polymerization. Heterocycles 82: 1477- 1488.
17. Li X, Zhan ZY, Knipe R, Lynn DG (2002) DNA-catalyzed polymerization. J Am Chem Soc 124: 746-747.
18. Benner SA (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37: 784-797.
19. Chernoff YO (2004) Amyloidogenic domains, prions and structural inheritance: rudiments of early life or recent acquisition. Curr Opin Chem Biol 8: 665-671.
20. Inge-Vechtomov SG, Zhouravleva GA, Chernoff YO (2007) Biological roles of prion domains. Prion 1: 228-235.
21. Lu K, Jacob J, Thiyagarajan P, Conticello VP, Lynn DG (2003) Exploiting amyloid fibril lamination for nanotube self-assembly. J Am Chem Soc 125: 6391-6393.
22. Childers WS, Anthony NR, Mehta AK, Berland KM, Lynn DG (2012) Phase networks of cross-β peptide assemblies. Langmuir 28: 6386- 6395..
23. Mehta AK, Lu K, Childers WS, Liang Y, Dublin SN, Dong J, Snyder JP, Pingali SV, Thiyagarajan P, Lynn DG (2008) Facial symmetry in protein self-assembly. J Am Chem Soc 130: 9829-9835.
24. Childers WS, Mehta AK, Ni R, Taylor JV, Lynn DG (2010) Peptides organized as bilayer membranes. Angew Chem Int Ed 49: 4104-4107.
25. Miller SL (1953) A production of amino acids under possible primitive earth conditions. Science 117: 528-529.
26. Fox SW (1980) Metabolic microspheres: origins and evolution. Naturwissenschaften 67: 378-383.
27. Woolfson DN, Ryadnov MG (2006) Peptide-based fibrous biomaterials: some things old, new and borrowed. Curr Opin Chem Biol 10: 559- 567.
28. Ulijn RV, Woolfson DN (2010) Peptide and protein based materials in 2010: from design and structure to function and application. Chem Soc Rev 39: 3349-3350.
29. Gao R, Lynn DG (2007) Integration of rotation and piston motions in coiled-coil signal transduction. J Bacteriol 189: 6048-6056.
30. Bryson JW, Betz SF, Lu HS, Suich DJ, Zhou HXX, Oneil KT, Degrado WF (1995) Protein design - a hierarchical approach. Science 270: 935- 941.
31. Lovejoy B, Choe S, Cascio D, McRorie DK, Degrado WF, Eisenberg D (1993) Crystal structure of a synthetic triple-stranded a-helical bundle. Science 259: 1288-1293.
32. Lupas A (1996) Coiled coils: new structures and new functions. Trends Biochem Sci 21: 375-382.
33. DeGrado WF, Summa CM, Pavone V, Nastri F, Lombardi A (1999) De novo design and structural characterization of proteins and metalloproteins. Annu Rev Biochem 68: 779-819.
34. Venkatraman J, Shankaramma SC, Balaram P (2001) Design of folded peptides. Chem Rev 101: 3131-3152.
35. Zimenkov Y, Conticello VP, Guo L, Thiyagarajan P (2004) Rational design of a nanoscale helical scaffold derived from self-assembly of a dimeric coiled coil motif. Tetrahedron 60: 7237-7246.
36. Zimenkov Y, Dublin SN, Ni R, Tu RS, Breedveld V, Apkarian RP, Conticello VP (2006) Rational design of a reversible pH-responsive switch for peptide self-assembly. J Am Chem Soc 128: 6770-6771.
37. Dublin SN, Conticello VP (2008) Design of a selective metal ion switch for self-assembly of peptide-based fibrils. J Am Chem Soc 130: 49-51.
38. Dublin S, Zimenkov Y, Conticello VP (2009) Engineering responsive mechanisms to control the assembly of peptide-based nanostructures. Biochem Soc Trans 37: 653-659.
39. Lee DH, Severin K, Yokobayashi Y, Ghadiri MR (1997) Emergence of symbiosis in peptide self-replication through a hypercyclic network. Nature 390: 591-594.
40. Severin K, Lee DH, Kennan AJ, Ghadiri MR (1997) A synthetic peptide ligase. Nature 389: 706-709.
41. Yao S, Ghosh I, Zutshi R, Chmielewski J (1998) Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature 396: 447-450.
42. Ashkenasy G, Ghadiri MR (2004) Boolean logic functions of a synthetic peptide network. J Am Chem Soc 126: 11140-11141.
43. Ashkenasy G, Jagasia R, Yadav M, Ghadiri MR (2004) Design of a directed molecular network. Proc Natl Acad Sci USA 101: 10872-10877.
44. Ryadnov MG, Woolfson DN (2007) Self-assembled templates for polypeptide synthesis. J Am Chem Soc 129: 14074-14081.
45. Ura Y, Beierle JM, Leman LJ, Orgel LE, Ghadiri MR (2009) Self-assembling sequence-adaptive peptide nucleic acids. Science 325: 73-77.
46. Walker LC, LeVine H, Mattson MP, Jucker M (2006) Inducible proteopathies. Trends Neurosci 29: 438-443.
47. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM. Designing conditions for in vitro formation of amyloid protofilaments and fibrils; 1998 Nov 08-09; Irvine, CA. Proc Natl Acad Sci USA pp. 3590-3594.
48. Guijarro JI, Sunde M, Jones JA, Campbell ID, Dobson CM (1998) Amyloid fibril formation by an SH3 domain. Proc Natl Acad Sci USA 95: 4224- 4228.
49. Dobson CM (1999) Protein misfolding, evolution and disease. Trends Biochem Sci 24: 329-332.
50. Dong J, Lu K, Lakdawala AS, Mehta AK, Lynn DG (2006) Controlling amyloid growth in multiple dimensions. Amyloid 13: 206-215.
51. Tessier PM, Lindquist S (2009) Unraveling infectious structures, strain variants and species barriers for the yeast prion PSI+. Nat Struct Mol Biol 16: 598-605.
52. Iconomidou VA, Hamodrakas SJ (2008) Natural protective amyloids. Curr Protein Pept Sci 9: 291-309.
53. Barlow DE, Dickinson GH, Orihuela B, Kulp JL, Rittschof D, Wahl KJ (2010) Characterization of the adhesive plaque of the Barnacle Balanus amphitrite: amyloid-like nanofibrils are a major component. Langmuir 26: 6549-6556.
54. Hammer ND, Schmidt JC, Chapman MR (2007) The curli nucleator protein, CsgB, contains an amyloidogenic domain that directs CsgA polymerization. Proc Natl Acad Sci USA 104: 12494-12499.
55. Romero D, Aguilar C, Losick R, Kolter R (2010) Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci USA 107: 2230-2234.
56. Fowler DM, Koulov AV, Alory-Jost C, Marks MS, Balch WE, Kelly JW (2006) Functional amyloid formation within mammalian tissue. PLoS Biol 4: e6.
57. Fowler DM, Koulov AV, Balch WE, Kelly JW (2007) Functional amyloid - from bacteria to humans. Trends Biochem Sci 32: 217-224.
58. Vauthey S, Santoso S, Gong H, Watson N, Zhang S (2002) Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc Natl Acad Sci USA 99: 5355-5360.
59. Tjernberg LO, Naslund J, Lindqvist F, Johansson J, Karlstrom AR, Thyberg J, Terenius L, Nordstedt C (1996) Arrest of β-amyloid fibril formation by a pentapeptide ligand. J Biol Chem 271: 8545-8548.
60. Benzinger TLS, Gregory DM, Burkoth TS, Miller-Auer H, Lynn DG, Botto RE, Meredith SC (1998) Propagating structure of Alzheimer's β -amyloid(10-35) is parallel β-sheet with residues in exact register. Proc Natl Acad Sci USA 95: 13407-13412.
61. Balbach JJ, Ishii Y, Antzutkin ON, Leapman RD, Rizzo NW, Dyda F, Reed J, Tycko R (2000) Amyloid fibril formation by Aβ16-22, a sevenresidue fragment of the Alzheimer's β-amyloid peptide, and structural characterization by solid state NMR. Biochemistry 39: 13748-13759.
62. Park J, Kahng B, Hwang W (2009) Thermodynamic selection of steric zipper patterns in the amyloid cross-β spine. PLoS Comput Biol 5: e1000492.
63. Wallace JA, Shen JK (2010) Probing the strand orientation and registry alignment in the propagation of amyloid fibrils. Biochemistry 49: 5290-5298.
64. Williams AD, Portelius E, Kheterpal I, Guo JT, Cook KD, Xu Y, Wetzel R (2004) Mapping Aβ amyloid fibril secondary structure using scanning proline mutagenesis. J Mol Biol 335: 833-842.
65. Klimov DK, Thirumalai D (2003) Dissecting the assembly of Aβ(16-22) amyloid peptides into antiparallel β sheets. Structure 11: 295-307.
66. Hamley IW (2007) Peptide fibrillization. Angew Chem-Int Edit 46: 8128-8147.
67. Liang Y, Lynn DG, Berland KM (2010) Direct observation of nucleation and growth in amyloid self-assembly. J Am Chem Soc 132: 6306-6308.
68. Liang Y, Pingali SV, Jogalekar AS, Snyder JP, Thiyagarajan P, Lynn DG (2008) Cross-strand pairing and amyloid assembly. Biochemistry 47: 10018-10026.
69. Petkova AT, Yau WM, Tycko R (2006) Experimental constraints on quaternary structure in Alzheimer's β-amyloid fibrils. Biochemistry 45: 498-512.
70. Tycko R, Sciarretta KL, Orgel JPRO, Meredith SC (2009) Evidence for novel-sheet structures in Iowa-mutant-amyloid fibrils. Biochemistry 48: 6072-6084.
71. Ni R, Childers WS, Mehta AK, Lynn DG (2012) Glutamine regulation of cross-β architecture. J Am Chem Soc, submitted.
72. Mantyh PW, Ghilardi JR, Rogers S, Demaster E, Allen CJ, Stimson ER, Maggio JE (1993) Aluminum, iron, and zinc ions promote aggregation of physiological concentrations of β-amyloid peptide. J Neurochem 61: 1171-1174.
73. Bush AI, Pettingell WH, Multhaup G, Paradis MD, Vonsattel JP, Gusella JF, Beyreuther K, Masters CL, Tanzi RE (1994) Rapid induction of Alzheimer Aβ amyloid formation by zinc. Science 265: 1464-1467.
74. Allsop D, Mayes J, Moore S, Masad A, Tabner BJ (2008) Metal-dependent generation of reactive oxygen species from amyloid proteins implicated in neurodegenerative disease. Biochem Soc Trans 36: 1293-1298.
75. Zhu X, Su B, Wang X, Smith MA, Perry G (2007) Causes of oxidative stress in Alzheimer disease. Cell Mol Life Sci 64: 2202-2210.
76. Allan Butterfield D (2002) Amyloid β-peptide (1-42)-induced oxidative stress and neurotoxicity: implications for neurodegeneration in Alzheimer's disease brain. A review. Free Radic Res 36: 1307-1313.
77. Bush AI (2003) The metallobiology of Alzheimer's disease. Trends Neurosci 26: 207-214.
78. Bush AI, Masters CL, Tanzi RE (2003) Copper, β-amyloid, and Alzheimer's disease: tapping a sensitive connection. Proc Natl Acad Sci USA 100: 11193-11194.
79. Adlard PA, Bush AI (2006) Metals and Alzheimer's disease. J Alzheimer's Dis 10: 145-163.
80. Molina-Holgado F, Hider RC, Gaeta A, Williams R, Francis P (2007) Metals ions and neurodegeneration. Biometals 20: 639-654.
81. Dong J, Canfield JM, Mehta AK, Shokes JE, Tian B, Childers WS, Simmons JA, Mao Z, Scott RA, Warncke K, Lynn DG (2007) Engineering metal ion coordination to regulate amyloid fibril assembly and toxicity. Proc Natl Acad Sci USA 104: 13313-13318.
82. Hernández-Guzmán J, Sun L, Mehta AK, Dong J, Lynn DG, Warncke K, Structure of equatorial bis-imidazole coordination of Cu(II) in model and amyloid-β peptide complexes revealed by electron spin-echo envelope modulation spectroscopy. submitted.
83. Sikorski P, Atkins ED, Serpell LC (2003) Structure and texture of fibrous crystals formed by Alzheimer's Aβ(11-25) peptide fragment. Structure 11: 915-926.
84. Petkova AT, Buntkowsky G, Dyda F, Leapman RD, Yau WM, Tycko R (2004) Solid state NMR reveals a pH-dependent antiparallel β-sheet registry in fibrils formed by a β-amyloid peptide. J Mol Biol 335: 247- 260.
85. Nelson R, Sawaya MR, Balbirnie M, Madsen AO, Riekel C, Grothe R, Eisenberg D (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435: 773-778.
86. Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJW, McFarlane HT, Madsen AO, Riekel C, Eisenberg D (2007) Atomic structures of amyloid cross-β spines reveal varied steric zippers. Nature 447: 453-457.
87. Negureanu L, Baumketner A (2009) Microscopic factors that control β-sheet registry in amyloid fibrils formed by fragment 11-25 of amyloid β peptide: insights from computer simulations. J Mol Biol 389: 921-937.
88. Dong J, Shokes JE, Scott RA, Lynn DG (2006) Modulating amyloid selfassembly and fibril morphology with Zn(II). J Am Chem Soc 128: 3540- 3542.
89. Liu P, Ni R, Mehta AK, Childers WS, Lakdawala A, Pingali SV, Thiyagarajan P, Lynn DG (2008) Nucleobase-directed amyloid nanotube assembly. J Am Chem Soc 130: 16867-16869.
90. Han XG, Leroy JL, Gueron M (1998) An intramolecular i-motif: the solution structure and base-pair opening kinetics of d(5mCCT(3) CCT(3)ACCT(3)CC). J Mol Biol 278: 949-965.
91. Nonin-Lecomte S, Leroy JL (2001) Structure of a C-rich strand fragment of the human centromeric satellite III: a pH-dependent intercalation topology. J Mol Biol 309: 491-506.
92. Childers WS, Mehta AK, Lu K, Lynn DG (2009) Templating molecular arrays in amyloid's cross-β grooves. J Am Chem Soc 131: 10165- 10172.
93. Divry PFM (1927) Omptes rendus des seances de la societie de biologie et de ses filiales 97: 1808.
94. Puchtler H, Sweat F, Levine M (1962) On binding of Congo red by amyloid. J Histochem Cytochem 10: 355.
95. Frid PA, SV, Popovic, N (2007) Brain Res Rev 53: 135.
96. Kasha M (1959) Relation between exciton bands and conduction bands in molecular lamellar systems. Rev Modern Phys 31: 162.
97. Harada NN, Nakanishi K (1983) Circular dichroic spectroscopy - exciton coupling in organic stereochemistry. Mill Valley, CA: University Science Books.
98. Jelley EE (1936) Spectral absorption and fluorescence of dyes in the molecular state. Nature 138: 1009-1010.
99. Scheibe G, Rivas A (1936) A new method in quantitive emission spectral analysis adaptable also as a micro method. Angew Chem 49: 0443-0446.
100. Jin LW, Claborn KA, Kurimoto M, Geday MA, Maezawa I, Sohraby F, Estrada M, Kaminksy W, Kahr B (2003) Imaging linear birefringence and dichroism in cerebral amyloid pathologies. Proc Natl Acad Sci USA 100: 15294-15298.
101. Liang Y, Guo P, Pingali SV, Pabit S, Thiyagarajan P, Berland KM, Lynn DG (2008) Light harvesting antenna on an amyloid scaffold. Chem Commun 48: 6522-6524.
102. Morgan DM, Dong J, Jacob J, Lu K, Apkarian RP, Thiyagarajan P, Lynn DG (2002) Metal switch for amyloid formation: insight into the structure of the nucleus. J Am Chem Soc 124: 12644-12645.
103. Zhang SG, Holmes T, Lockshin C, Rich A (1993) Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane. Proc Natl Acad Sci USA 90: 3334-3338.
104. Vauthey S, Santoso S, Gong HY, Watson N, Zhang SG (2002) Molecular self-assembly of surfactant-like peptides to form nanotubes and nanovesicles. Proc Natl Acad Sci USA 99: 5355-5360.
105. Santoso S, Hwang W, Hartman H, Zhang SG (2002) Self-assembly of surfactant-like peptides with variable glycine tails to form nanotubes and nanovesicles. Nano Lett 2: 687-691.
106. Lu K, Conticello VP, Lynn DG (2004) Templating colloidal metal nanoparticle assemblies: use of the Aβ amyloid peptide nanotube. In: Conticello VP, Chilkoti A, Atkins E, Lynn DG, editors. Mater Res Soc Synp Proc 826E. Warrendale, PA, V1.6.
107. Lu K, Guo L, Mehta AK, Childers WS, Dublin SN, Skanthakumar S, Conticello VP, Thiyagarajan P, Apkarian RP, Lynn DG (2007) Macroscale assembly of peptide nanotubes. Chem Commun (Camb) 26: 2729- 2731.
108. Tavares FW, Bratko D, Striolo A, Blanch HW, Prausnitz JM (2004) Phase behavior of aqueous solutions containing dipolar proteins from second-order perturbation theory. J Chem Phys 120: 9859-9869.
109. Bacquet RJ, Rossky PJ (1988) Ionic distributions and competitive association in DNA mixed salt-solutions. J Phys Chem 92: 3604-3612.
110. Matsumoto K, Vaughn M, Bruce BD, Koutsopoulos S, Zhang S (2009) Designer peptide surfactants stabilize functional photosystem-I membrane complex in aqueous solution for extended time. J Phys Chem B 113: 75-83.
111. Giraldo R (2010) Amyloid assemblies: protein legos at a crossroads in bottom-up synthetic biology. Chembiochem 11: 2347-2357.
112. Lehn JM (2002) Toward complex matter: supramolecular chemistry and self-organization. Proc Natl Acad Sci USA 99: 4763-4768.
113. Gasparini G, Dal Molin M, Prins LJ (2010) Dynamic approaches towards catalyst discovery. Eur J Org Chem 2010: 2429-2440.
114. Hammarstrom P, Ali MM, Mishra R, Salagic B, Svensson S, Tengvall P, Lundstrom I (2011) An auto-catalytic surface for conformational replication of amyloid fibrils-genesis of an amyloid world? Orig Life Evol Biosph. 41: 373-383
115. Yang AS, Honig B (1995) Free-energy determinants of secondary structure formation. 2. Antiparallel β-sheets. J Mol Biol 252: 366-376.
116. Smith CK, Regan L (1995) Guidelines for protein design-the energetics of β-sheet side-chain interactions. Science 270: 980-982.
117. Kiehna SE, Waters ML (2003) Sequence dependence of β-hairpin structure: comparison of a salt bridge and an aromatic interaction. Protein Sci 12: 2657-2667.
118. Nowick JS (2008) Exploring β-sheet structure and interactions with chemical model systems. Acc Chem Res 41: 1319-1330.
119. Searle MS, Ciani B (2004) Design of β-sheet systems for understanding the thermodynamics and kinetics of protein folding. Curr Opin Struct Biol 14: 458-464.
120. Wu L, McElheny D, Takekiyo T, Keiderling TA (2010) Geometry and efficacy of cross-strand Trp/Trp, Trp/Tyr, and Tyr/Tyr aromatic interaction in a β-hairpin peptide. Biochem 49: 4705-4714.
121. Biancalana M, Makabe K, Koide A, Koide S (2008) Aromatic crossstrand ladders control the structure and stability of β-rich peptide self-assembly mimics. J Mol Biol 383: 205-213.
122. Makabe K, Yan S, Tereshko V, Gawlak G, Koide S (2007) β-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of β-strand pairing. J Am Chem Soc 129: 14661-14669.
123. Merkel JS, Regan L (1998) Aromatic rescue of glycine in β sheets. Fold Des 3: 449-455.
124. Merkel JS, Sturtevant JM, Regan L (1999) Sidechain interactions in parallel β sheets: the energetics of cross-strand pairings. Struct Fold Des 7: 1333-1343.
125. Takahashi Y, Mihara H (2004) Construction of a chemically and conformationally self-replicating system of amyloid-like fibrils. Bioorg Med Chem 12: 693-699.
126. Rubinov B, Wagner N, Rapaport H, Ashkenasy G (2009) Self-replicating amphiphilic β-sheet peptides. Angew Chem Int Ed Engl 48: 6683- 6686.
127. Rubinov B, Wagner N, Matmor M, Regev O, Ashkenasy N, Ashkenasy G (2012) Transient fibril structures facilitating nonenzymatic selfreplication. ACS nano, Article ASAP.