Molecular simulations of peptides: A useful tool for the development of new drugs and for the study of molecular recognition

Methods in Molecular Biology

Volumn 570, Issue , 2009, Pages 77-153

  Meli, Massimiliano ^a   Colombo, Giorgio ^a  

^a CNR   (Italy)

Author keywords

Drug design; molecular recognition; peptides; self organization

Indexed keywords

ANTINEOPLASTIC AGENT; PEPTIDE;

ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; HUMAN; METABOLISM; MOLECULAR DYNAMICS; MONTE CARLO METHOD; NEOPLASM; PHYSIOLOGY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; REVIEW; STRUCTURE ACTIVITY RELATION; SYNTHESIS;

ANIMALS; ANTINEOPLASTIC AGENTS; DRUG DESIGN; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MONTE CARLO METHOD; NEOPLASMS; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 73949154012     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-394-7_4     Document Type: Article

References (135)

1. Eisenberg, D.; Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Sambashivan, S.; Ivanova, M. I.; Madsen, A. O.; Riekel, C. (2006) The Structural Biology of Protein Aggregation Diseases: Fundamental Questions and Some Answers. Acc. Chem. Res 39, 568-575.
2. Plescia, J.; Salz, W.; Xia, F.; Pennati, M.; Zaffaroni, N.; Daidone, M. G.; Meli, M.; Dohi, T.; Fortugno, P.; Nefedova, Y.; Gabrilovich, D. I.; Colombo, G.; Altieri, D. C. (2005) Rational design of Shepherdin, a novel anticancer agent. Cancer Cell 7, 457-467.
3. Fortugno, P.; Beltrami, E.; Plescia, J.; Fontana, J.; Pradhan, D.; Marchisio, P. C.; Sessa, W. C.; Altieri, D. C. (2003) Regulation of survivin function by Hsp90. Proc. Natl. Acad. Sci. USA 100, 13791-13796.
4. Zaffaroni, N.; Daidone, M. G. (2002) Survivin expression and resistance to anticancer treatments: Perspectives for new therapeutic interventions. Drug Resist. Updat. 5, 65-72
5. Verdecia, M. A., Huang, H., Dutil, E., Kaiser, D. A., Hunter, T., and Noel, J. P. (2000) Structure of the human anti-apoptotic protein survivin reveals a dimeric arrangement. Nat. Struct. Biol. 7, 602-608.
6. Lindahl, E.; Hess, B.; van-der-Spoel, D. (2001) Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7, 306-317.
7. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. (1998) Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function. J. Comp. Chem. 19, 1639-1662.
8. Gyurkocza, B.; Plescia, J.; Raskett, G. M.; Garlick, D. S.; Lowry, P. A.; Carter, B. Z.; Andreeff, M.; Meli, M.; Colombo, G.; Altieri, D. C. (2006) Antileukemic activity of Shepherdin and molecular diversity of hsp90 inhibitors. J. Natl. Cancer Inst. 98, 1068-1077.
9. Meli, M.; Pennati, M.; Curto, M.; Daidone, M. G.; Plescia, J.; Toba, S.; Altieri, D. C.;Colombo, G. (2006) Small-Molecule targeting of HSP90 chaperone function: Rational identification of a new anti-cancer lead. J. Med. Chem. 49, 7721-30.
10. Accounts of Chemical Research (2006) 39, Special issue on aggregation.
11. de-la-Paz, M. L.; de-Mori, G. M. S.; Serrano, L.; Colombo, G. (2005) Sequence dependence of amyloid fibril formation: Insights from molecular dynamics simulations. J. Mol. Biol. 349, 583-596.
12. De Mori, G. M. S.; Micheletti, C.; Colombo, G. (2004) All-atom folding simulations of the villin headpiece from stochastically selected coarse-grained structures. J. Phys. Chem. B 108, 12267-12270.
13. Meli, M.; Morra, G.; Colombo, G. (2008) Investigating the mechanism of peptide aggregation: Insights from mixed monte carlo-molecular dynamics simulations. Biophys. J. 94, 4414-26.
14. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; Gunsteren, W. F. v.; Mark, A. E. (1999) Peptide folding: When simulation meets experiment. Angew. Chemie Intl. Ed. 38, 236-240.
15. Kabsch, W.; Sander, C. (1983) Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers 22, 2576-2637.
16. van Gunsteren, W. F.; Daura, X.; Mark, A. E. (1998) GROMOS Force Field. Encyclopedia Comput. Chem. 2, 1211-1216.
17. van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H.; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. (1996) Biomolecular Simulation: The GROMOS96 Manual and User Guide. In vdf Hochschulverlag, ETH Zurich: Switzerland.
18. Darden, T.; York, D.; Pedersen, L. (1993) Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
19. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. (1995) A smooth particle mesh Ewald potential. J. Chem. Phys.103, 8577-8592.
20. Unger, R.; Moult, J. (1993) Genetic algorithm for protein folding simulation. J. Mol. Biol. 231, 75-81.
21. Rensburg, E. J. v.; Orlandini, E.; Whittington, S. (1996) Monte-Carlo study of the interacting self-avoiding walk in three dimension. J. Stat. Phys.82, 155-181.
22. Lee, J.; Scheraga, H.; Rackovsky, S. (1997) New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. 18, 1222-1232.
23. Irbäck, A.; Potthast, F. (1995) Studies of an off-lattice model for protein folding: Sequence dependence and improved sampling at finite temperature. J. Chem. Phys.103, 10298-10305.
24. Hansmann, U.; Okamoto, Y. (1999) New Monte Carlo algorithms for protein folding. Curr. Opin. Struct. Biol. 9, 177-183.
25. Scheraga, H.; Hao, M. (1999) Entropy sampling Monte Carlo for polypeptides and proteins. Adv. Chem. Phys. 105, 243-272.
26. Arkin, H.; Yarkin, F.; Celik, T.; Berg, B.; Meirovitch, H. (2002) Multicanonical simulations of some peptides. Comp. Phys. Comm. 147, 600-603.
27. Garcia, A.; Onuchic, J. (2003) Folding a protein in a computer: An atomic description of the folding/unfolding of protein. Proc Natl Acad Sci USA 100, 13898-13903.
28. Kolinski, A.; Godzik, A.; Skolnick, J. (1998) Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, b, and a, b proteins. J. Chem. Phys. 108, 2608-2617.
29. Micheletti, C.; Banavar, J. R.; Maritan, A.; Seno, F. (1999) Protein structures and optimal folding from a geometrical variational principle. Phys. Rev. Lett. 82, 3372-3375.
30. Baker, D. (2000) A surprising simplicity to protein folding. Nature 405, 39-42.
31. Clementi, C.; Nymeyer, H.; Onuchic, J. N. (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and en-route intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298, 937-953.
32. Klimov, D. K.; Thirumalai, D. (2000) Native topology determines force-induced unfolding pathways in globular proteins. J. Chem. Phys. 113, 8319-8328.
33. Cieplak, M.; Hoang, T. X. (2000) Scaling of folding properties in go models of proteins. J. Biol. Phys. 26, 273-294.
34. Hao, H. M.; Scheraga, H. A. (1997) On foldable protein-like models: A statisticalmechanical study with Monte Carlo simulations. Physica A 244, 124-145.
35. Tiana, G.; Broglia, R. A. (2001) Statistical Analysis of Native Contact Formation in the Folding of Designed Model Proteins. J. Chem. Phys. 114, 2503.
36. Lazaridis, T.; Karplus, M. (1997) New view of protein folding reconciled with the old through multiple unfolding trajectories. Science 278, 1928-1931.
37. Bahar, I.; Erman, B.; Jernigan, R. L.; Atilgan, A. R.; Covell, D. G. (1999) Collective Motions in HIV-1 Reverse Transcriptase: Examination of Flexibility and Enzyme Function. J. Mol. Biol. 285, 1023-1037.
38. Hoang, T. X.; Cieplak, M. (2000) Molecular dynamics of folding of secondary structures in go-type models of proteins. J. Chem. Phys. 112, 6851-6862.
39. Favrin, G.; Irback, A.; Wallin, S. (2002) Folding of a small helical protein using hydrogen bonds and hydrophobicity forces. Proteins 47, 99-105.
40. Vieth, M.; Kolinski, A.; Brooks, C.; Skolnick, J. (1994) Prediction of the folding pathways and structure of the gcn4 leucine zipper. J. Mol. Biol. 237, 361-367.
41. Liwo, A.; Pincus, M.; Wawak, R.; Rackowsky, S.; Scheraga, H. (1993) Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide. Protein Sci. 2, 1715-1731.
42. Park, B.; Levitt, M. (1996) Energy functions that discriminate x-ray and near-native folds from well-constructed decoys. Proteins 258, 367-392.
43. Kolinski, A.; Galazka, W.; Skolnick, J. (1993) A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins. J. Chem. Phys. 98(9), 7420-7433.
44. Kolinsky, A.; Skolnick, J. (1994) Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 18, 338-352.
45. Correa, P. (1990) The building of protein structures from a-carbon coordinates. Proteins 7, 366-377.
46. Rey, A.; Skolnick, J. (1991) Efficient algorithm for the reconstruction of a protein backbone from the a-carbon coordinates. J. Comput. Chem. 13, 443-456.
47. Holm, L.; Sander, C. (1991) Database algorithm for generating protein backbone and side-chain coordinates from a c trace, application to model building and detection of coordinate errors. J. Mol. Biol. 218, 183-194.
48. Bower, M.; Cohen, F.; Dunbrak, R. (1997) Prediction of protein side-chain rotamers from a backbone-dependent rotamer library. J. Mol. Biol. 267, 1268-1282.
49. Kazmierkiewicz, R.; Liwo, A.; Scheraga, H. (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys. Chem. 100, 261-280.
50. Kabsch, W. (1978) A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 34, 828-829.
51. de-Mori, G. M. S.; Colombo, G.; Micheletti, C. (2005) Study of the villin headpiece folding dynamics by combining coarsegrained Monte Carlo evolution and allatom molecular dynamics. Proteins-struct. funct. bioinform. 58, 459 471.
52. Hobohm, U.; Scharf, M.; Schneider, R.; Sander, C. (1992) Selection of a representative set of structures from the brookhaven protein data bank. Protein Sci. 1, 409-417.
53. Hobohm, U.; Sander, C. (1992) Enlarged representative set of protein structures. Protein Sci. 2, 522.
54. Hengartner, M. O. (2000) The biochemistry of apoptosis. Nature 107, 770-776.
55. Whitesell, L.; Lindquist, S. (2005) Hsp90 and the chaperoning of cancer. Nat. Rev. Cancer 5, 761-772.
56. Takayama, S.; Reed, J. C.; Homma, S. (2003) Heat-shock proteins as regulators of apoptosis. Oncogene 22, 9041-9047.
57. Dymock, B. W.; Drysdale, M. J.; McDonald, E.; Workman, P. (2004) Inhibitors of HSP90 and other chaperones for the treatment of cancer. Expert. Opin. Ther. Patents 14, 837-847.
58. Morimoto, R. I.; Santoro, M. G. (1998) Stress-inducible responses and heat shock proteins: New pharmacologic targets for cytoprotection. Nat. Biotechnol. 16, 833-838.
59. Whitesell, L.; Lindquist, S. (2005) Hsp90 and the chaperoning of cancer. Nat. Rev. Cancer 5, 761-772.
60. Young, J. C.; Moarefi, I.; Hartl, F. U. (2001) Hsp90: A specialized but essential protein-folding tool. J. Cell. Biol. 154, 267-273.
61. Morishima, Y.; Murphy, P. J.; Li, D. P.; Sanchez, E. R.; Pratt, W. B. (2000) Stepwise assembly of a glucocorticoid receptor hsp90 heterocomplex resolves two sequential ATP-dependent events involving first hsp70 and then hsp90 in opening of the steroid binding pocket. J. Biol. Chem. 275, 18054-18060.
62. Marcu, M. G.; Chadli, A.; Bouhouche, I.; Catelli, M.; Neckers, L. M. (2000) The heat shock protein 90 antagonist novobiocin interacts with a previously unrecognized ATP-binding domain in the carboxyl terminus of the chaperone. J. Biol. Chem. 275, 37181-37186.
63. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684.
64. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. (1987) The missing term in effective pair potentials. J. Phys. Chem. 91, 6269-6271.
65. Hess, B.; Bekker, H.; Fraaije, J. G. E. M.; Berendsen, H. J. C. (1997) A linear constraint solver for molecular simulations. J. Comp. Chem. 18, 1463-1472.
66. Miyamoto, S.; Kollman, P. A. (1992) SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comp. Chem. 13, 952-962.
67. Spoel, D. v. d.; Lindahl, E.; Hess, B.; Buuren, A. R. v.; Apol, E.; Meulenhoff, P. J.; Tieleman, D. P.; Sijbers, A. L. T. M.; Feenstra, K. A.; Drunen, R. v.; Berendsen, H. J. C. (2004) Gromacs User Manual version 3.2. www.gromacs.org.
68. Daura, X.; Antes, I.; van Gunsteren, W. F.; Thiel, W.; Mark, A. E. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins: Struct. Funct. Genet. 36, 542-555.
69. Guex, N.; Peitsch, M. C. (1997) SWISSMODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18, 2714-2723.
70. Stebbins, C. E.; Russo, A. A.; Schneider, C.; Rosen, N.; Hartl, F. U.; Pavletich, N. P. (1997) Crystal Structure of Hsp90-Geldanamycin complex: Targeting of a protein chaperone by an antitumor agent. Cell 89, 239-250.
71. Solmajer, T.; Mehler, E. L. (1991) Electrostatic Screening in Molecular Dynamics simulations. Protein Eng. 4, 911.
72. Hetenyi, C.; van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Prot. Sci. 11, 1729-1737.
73. Lee, Y. S.; Marcu, M. G.; Neckers, L. (2004) Quantum chemical calculations and mutational analysis suggest heat shock protein 90 catalyzes trans-cis isomerization of geldanamycin. Chem. Biol. 11, 991-998.
74. Roe, S. M.; Ali, M. M.; Meyer, P.; Vaughan, C. K.; Panaretou, B.; Piper, P. W.; Prodromou, C.; Pearl, L. H. (2004) The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37). Cell 116, 87-98.
75. Altieri, D. C. (2003) Validating Survivin as a Cancer Therapeutic Target. Nat. Rev. Cancer 3, 46-54.
76. Isaacs, J. S.; Xu, W.; Neckers, L. (2003) Heat shock protein 90 as a molecular target for cancer therapeutics. Cancer Cell 3, 213-217.
77. Neckers, L.; Ivy, S. P. (2003) Heat Shock Protein 90. Curr. Op. Oncol. 15, 419-424.
78. Chen, Y. N.; Sharma, S. K.; Ramsey, T. M.; Jiang, L.; Martin, M. S.; Baker, K.; P. D. Adams; Bair, K. W. (1999) Selective killing of transformed cells by cyclin/cyclin-dependent kinase 2 antagonists. Proc. Natl. Acad. Sci. USA 96, 4325-4329.
79. Sawada, M.; Hayes, P.; Matsuyama, S. (2003) Cytoprotective membrane-permeable peptides designed from the Bax-binding domain of Ku70. Nat. Cell Biol. 5, 352-357.
80. Swanton, C. (2004) Cell-cycle targeted therapies. Lancet Oncol. 5, 27-36.
81. Vogelstein, B.; Lane, D.; Levine, A. J. (2000) Surfing the p53 network. Nature 408, 307-310.
82. Johnstone, R. W.; Ruefli, A. A.; Lowe, S. W. (2002) Apoptosis: A link between cancer genetics and chemotherapy. Cell 108, 153-164.
83. Vassilev, L. T.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C. (2004) In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303, 844-848.
84. Sausville, E. A.; Tomaszewski, J. E.; Ivy, P. (2003) Clinical development of 17-allylamino, 17-demethoxygeldanamycin. Curr. Cancer Drug Targets 3, 377-383.
85. Beere, H. M. (2004) "The stress of dying": The role of heat shock proteins in the regulation of apoptosis. J. Cell Sci. 117, 2641-2651.
86. Kamal, A.; Boehm, M. F.; Borrows, F. J. (2004) Therapeutic and diagnostic implications of Hsp90 activation. Trends Mol. Med. 10, 283-290
87. Guillemard, V.; Saragovi, H. U. (2004) Novel approaches for targeted cancer therapy. Curr.CancerDrug Targets 4, 313-326.
88. Muchmore, S. W.; Chen, J.; Jakob, C.; Zakula, D.; Matayoshi, E. D.; Wu, W.; Zhang, H.; Li, F.; Ng, S. C.; Altieri, D. C. (2000) Crystal structure and mutagenic analysis of the inhibitor-of-apoptosis protein survivin. Mol. Cell 6, 173-182.
89. Li, A.; Daggett, V. (1998) Molecular Dynamics Simulation of the Unfolding of Barnase: Characterization of the Major Intermediate. J. Mol. Biol. 275, 677-694.
90. Vogelstein, B.; Kinzler, K. W. (2004) Cancer genes and the pathways they control. Nat. Med. 10, 789-799.
91. O'Dwyer, M. E.; Druker, B. J. (2000) Status of Bcr-Abl tyrosine kinase inhibitors in chronic myelogenous leukemia. Curr. Op. Oncol. 12, 594-597.
92. O'Dwyer, M. E.; Druker, B. J. (2000) STI571: An inhibitor of the BCR-ABL tyrosine kinase for the treatment of chronic myelogenous leukemia. Lancet Oncol. 1, 207-211.
93. Paez, J. G.; Janne, P. A.; Lee, J. C.; Tracy, S.; Greulich, H.; Gabriel, S.; Herman, P.; Kaye, F. J.; Lindeman, N.; Boggon, T. J.; Naoki, K.; Sasaki, H.; Fujii, Y.; Eck, M. J.; Sellers, W. R.; Johnson, B. E.; Meyerson, M. (2004) EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy Science 304, 1497-1500.
94. Workman, P. (2003) Overview: Translating Hsp90 Biology into Hsp90 Drugs. Curr. Cancer. Drug. Targets 3, 297-300.
95. Mehler, E. L.; Solmajer, T. (1991) Electrostatic effects in proteins. Comparison of dielectric and charge models. Prot. Eng. 4, 903-910.
96. Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F. v.; Mark, A. E. (1998) Reversible Peptide Folding in Solution by Molecular Dynamics Simulation. J. Mol. Biol. 280, 925-932.
97. Catalyst (2005) Accelrys, San Diego CA, USA.
98. Ferris, J. P.;Devadas, B.;Huang,C.H.; Ren, W. Y. (1985) Nucleosides fromcarbohydrate adducts of diaminomaleonitrile. A novel synchapter of 5-amino-1-(beta-D-ribofuranosyl) imidazole-4-carboxamide and 5-amino-1-(beta-D-ribopyranosyl)imidazole-4-carboxamide. J. Org. Chem. 50, 747-754.
99. Folini, M.; Brambilla, C.; Villa, R.; Gandellini, P.; Vignati, S.; Paduano, F.; Daidone, M. G.; Zaffaroni, N. (2005) Antisense oligonucleotide- mediated inhibition of hTERT, but not hTERC, induces rapid cell growth decline and apoptosis in the absence of telomere shortening in human prostate cancer cells Eur. J. Cancer 41, 624-634
100. Vilenchik, M.; Solit, D.; Basso, A.; Huezo, H.; Lucas, B.; He, H.; Rosen, N.; Spampinato, C.; Modrich, P.; Chiosis, G. (2004) Targeting wide-range oncogenic transformation via PU24FCL, a specific inhibitor of Tumor Hsp90. Chem. Biol. 11, 787-797.
101. Chiosis, G.; Lucas, B.; Shtil, A.; Huezo, H.; Rosen, N. (2002) Development of a purinescaffold novel class of Hsp90 Binders that inhibit the proliferation of cancer cells and induce the degradation of Her2 tyrosine kinase. Bioorg. Med. Chem. 10, 3555-3564.
102. Dymock, B. W.; Barril, X.; Brough, P. A.; Cansfield, J. E.; Massey, A.; McDonald, E.; Hubbard, R. E.; Surgenor, A.; Roughley, S. D.; Webb, P.; Workman, P.; Wright, L.; Drysdale, M. J. (2005) Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design. J. Med. Chem. 48, 4212-4215.
103. Wright, L.; Barril, X.; Dymock, B. W.; Sheridan, L.; Surgenor, A.; Beswick, M.; Drysdale, M. J.; Collier, A.; Massey, A.; Davies, N.; Fink, A.; Fromont, C.; Aherne, W.; Boxall, K.; Sharp, S.; Workman, P.; Hubbard, R. E. (2004) Structure-Activity relationships in purine-based inhibitor binding to Hsp90 Isoforms. Chem. Biol. 11, 775-785.
104. Holt, S. E.; Aisner, D. L.; Baur, J.; Tesmer, V. M.; Dy, M.; Ouellette, M.; Trager, J. B.; Morin, G. B.; Toft, D. O.; Shay, J. W.; Wright, W. E.; White, M. A. (1999) Functional requirement of p23 and Hsp90 in telomerase complexes Genes & Devel. 13, 817-826.
105. Janin, Y. L. (2005) Heat Shock Protein 90 inhibitors. A text book example of medicinal chemistry? J. Med. Chem. 48, 7503-7512.
106. Sausville, E. A. (2004) Geldanamycin Analogs. J. Chemother. 16(S4), 68-69.
107. Giri, S.; Nath, N.; Smith, B.; Viollet, B.; Singh, A. K.; Singh, I. (2004) 5-aminoimidazole-4-carboxamide-1-beta-4-ribofuranoside inhibits proinflammatory response in glial cells: A possible role of AMP-activated protein kinase. J. Neurosci. 24, 479-487.
108. Nath, N.; Giri, S.; Prasad, R.; Salem, M. L.; Singh, A. K.; Singh, I., (2005) 5-Aminoimidazole-4-carboxamide ribonucleoside: A novel immunomodulator with therapeutic efficacy in experimental autoimmune encephalomyelitis J. Immunol. 175, 566-574.
109. Rattan, R.; Giri, S.; Singh, A. K.; Singh, I. (2005) 5-Aminoimidazole-4- carboxamide-1-beta-D-ribofuranoside inhibits cancer cell proliferation in vitro and in vivo via AMP-activated Protein Kinase. J. Biol. Chem. 280, 39582-39593.
110. Paduano, F.; Villa, R.; Pennati, M.; Folini, M.; Binda, M.; Daidone, M. G.; Zaffaroni, N. (2006) Silencing of survivin gene by small interfering RNAs produces supraadditive growth suppression in combination with 17-allylamino-17-demethoxygeldanamycin in human prostate cancer cells. Mol. Cancer Ther. 5, 179-186.
111. Rutledge, G.; Behnke, E.; Liang, Y. X.; You, S. W.; Tay, D. K. C.; Zhang, S.; So, K. F.; Schneider, G. E. (2006) Nano neuro knitting: Peptide nanofiber scaffold for brain repair and axon regeneration with functional return of vision. PNAS 103, 5054-5059.
112. Daidone, I.; Amadei, A.; Di Nola, A. (2005) Thermodynamic and kinetic characterization of a β-hairpin peptide in solution: An extended phase space sampling by molecular dynamics simulations in explicit water. Proteins 59, 510-518.
113. Ma, B.; Nussinov, R. (2002) Molecular dynamics simulation of alanine beta-sheet oligomers: Insight into amyloid formation. Protein Sci. 11, 2335-2350.
114. Urbanc, B.; Ding, C. L.; Sammond, D.; Khare, S. (2004) Molecular dynamics simulation of amyloid beta dimer formation. Biophys. J. 87, 2310.
115. Dokholyan, N. V. (2006) Studies of folding and misfolding using simplified models. Curr. Opin. Struct. Biol.16, 79-85.
116. Flock, D.; Daidone, I.; Di Nola, A. (2004) A Molecular Dynamics study of acylphosphatase in aggregation promoting conditions: The influence of TFE/water solvent. Biopolymers 75, 491-496.
117. Wei, G.; Shea, J. E. (2006) Effects of solvent on the structure of the Alzheimer amyloidbeta( 25-35) peptide. 91, 1638-1647.
118. Cuniasse, P.; Raynal, I.; Yiotakis, A.; Dive, V. (1997) Accounting for ConformationalVariability in NMR Structure of Cyclopeptides: Ensemble Averaging of Interproton Distance and Coupling Constant Restraints. J. Am. Chem. Soc. 19, 5239-5248.
119. Favrin, G.; Irbäck, A.; Mohanty, S. (2004) Oligomerization of Amyloid Aβ16-22 Peptides Using Hydrogen Bonds and Hydrophobicity Forces. Biophys. J.87, 3657-3664.
120. Burkoth, T. S.; Benzinger, T. L. S.; Jones, D. N. M.; Hallenga, K.; Meredith, S. C.; Lynn, D. G. (1998) C-Terminal PEG Blocks the Irreversible Step in-Amyloid(10-35) Fibrillogenesis. J. Am. Chem. Soc. 120, 7655-7656.
121. Burkoth, T. S.; Benzinger, T. L. S.; Urban, V.; Lynn, D. G.; Meredith, S. C.; Thiyagarajan, P. (1999) Self-Assembly of A(10-35)-PEG Block Copolymer Fibrils. J. Am. Chem. Soc. 121, 7429-7430.
122. Zheng, J.; Tsai, M. B.; Nussinov, R. (2006) Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys. J. 91, 824-833.
123. Walsh, D. M.; Klyubin, I.; Fadeeva, J. V.; Cullen, W. K.; Anwyl, R.; Wolfe, M. S.; Rowan, R. J.; Selkoe, D. J. (2002) Naturally secreted oligomers of amyloid beta protein potently inhibit hippocampal long-term potentiation in vivo. Nature 416, 535-539.
124. Bucciantini, M.; Giannoni, E.; Chiti, F.; Baroni, F.; Formigli, L.; Zurdo, J.; Taddei, N.; Ramponi, G.; Dobson, C. M.; Stefani, M. (2002) Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416, 507-511.
125. Kayed, R.; Head, E.; Thompson, J. L.; McIntire, T. M.; Milton, S. C.; Cotman, C. W.; Glabe, C. G. (2003) Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis. Science 300, 486-489.
126. Mousseau, N.; Derreumaux, P. (2005) Exploring the Early Steps of Amyloid Peptide Aggregation by Computers. Acc. Chem. Res. 38, 885-891.
127. Nilsson, M. R. (2004) Techniques to study amyloid fibril formation in vitro. Methods 34, 151-160.
128. Bitan, G.; Teplow, D. B. (2004) Rapid photochemical cross-linking-A new tool for studies of metastable, amyloidogenic protein assemblies. Acc. Chem. Res. 37, 357-364.
129. Nelson, R.; Sawaya, M. R.; Balbirnie, M.; Madsen, A. O.;Riekel, C.;Grothe, R.; Eisenberg, D. (2005) Structure of the cross-b spine of amyloid-like fibrils. Nature 435, 773-778.
130. Fersht, A. R. (2002) On the simulation of protein folding by short time scale molecular dynamics and distributed computing. PNAS 99, 14122-14125.
131. Derrick, J. P.; Wigley, D. B. (1992) Crystalstructure of a streptococal protein-G domain bound to an fab fragment. Nature 359, 752-754.
132. Gabius, H.-J. (1998) The How and Why of Protein-carbohydrate Interaction: A Primer to Theoretical Concept and a Guide to application in drug Design. Pharmaceutical Res. 15, 23-30.
133. Ban, T.; Yamaguchi, K.; Goto, Y. (2006) Direct Observation of Amyloid Fibril Growth, Propagation, and Adaptation. Acc. Chem. Res. 39, 663-670.
134. Patino, M. M.; Liu, J. J.; Glover, J. R.; Lindquist, S. (1996) Support for the prion hypochapter for inheritance of a phenotypic trait in yeast. Science 273, 622-626.
135. Serio, T. R. (2000) Nucleated conformational conversion and the replication of conformational information by a prion determinant. Science 289, 1317-1321.