Self-assembly of cyclo-diphenylalanine peptides in vacuum

Journal of Physical Chemistry B

Volumn 118, Issue 24, 2014, Pages 6644-6652

  Jeon, Joohyun ^a   Shell, M Scott ^a  

^a University of California   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAINS; HYDROGEN BONDS; HYDROPHILICITY; HYDROPHOBICITY; LADDERS; MOLECULAR DYNAMICS; PEPTIDES; SELF ASSEMBLY; VACUUM; VAN DER WAALS FORCES; VAPORS;

DRIVING FORCES; HYDROPHILIC SURFACES; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; REPLICA EXCHANGE; STRUCTURAL ASSOCIATIONS; VAN DER WAALS INTERACTIONS;

BIOINFORMATICS;

DIPHENYLALANINE; NANOMATERIAL; PEPTIDE; PHENYLALANINE;

ANALOGS AND DERIVATIVES; CHEMICAL PHENOMENA; CHEMISTRY; HYDROGEN BOND; MOLECULAR DYNAMICS; STATIC ELECTRICITY; THERMODYNAMICS; VACUUM;

HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR DYNAMICS SIMULATION; NANOSTRUCTURES; PEPTIDES; PHENYLALANINE; STATIC ELECTRICITY; THERMODYNAMICS; VACUUM;

EID: 84902969637     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp501503x     Document Type: Article

References (42)

1. Yan, X.; Zhu, P.; Li, J. Self-Assembly and Application of Diphenylalanine-Based Nanostructures Chem. Soc. Rev. 2010, 39, 1877-1890
2. Rosenman, G.; Beker, P.; Koren, I.; Yevnin, M.; Bank-Srour, B.; Mishina, E.; Semin, S. Bioinspired Peptide Nanotubes: Deposition Technology, Basic Physics and Nanotechnology Applications J. Pept. Sci. 2011, 17, 75-87
3. Reches, M.; Gazit, E. Casting Metal Nanowires within Discrete Self-Assembled Peptide Nanotubes Science 2003, 300, 625-627
4. Kol, N.; Adler-Abramovich, L.; Barlam, D.; Shneck, R. Z.; Gazit, E.; Rousso, I. Self-Assembled Peptide Nanotubes Are Uniquely Rigid Bioinspired Supramolecular Structures Nano Lett. 2005, 5, 1343-1346
5. Sedman, V. L.; Adler-Abramovich, L.; Allen, S.; Gazit, E.; Tendler, S. J. B. Direct Observation of the Release of Phenylalanine from Diphenylalanine Nanotubes J. Am. Chem. Soc. 2006, 128, 6903-6908
6. Adler-Abramovich, L.; Reches, M.; Sedman, V. L.; Allen, S.; Tendler, S. J. B.; Gazit, E. Thermal and Chemical Stability of Diphenylalanine Peptide Nanotubes: Implications for Nanotechnological Applications Langmuir 2006, 22, 1313-1320
7. Amdursky, N.; Beker, P.; Koren, I.; Bank-Srour, B.; Mishina, E.; Semin, S.; Rasing, T.; Rosenberg, Y.; Barkay, Z.; Gazit, E. Structural Transition in Peptide Nanotubes Biomacromolecules 2011, 12, 1349-1354
8. Govindaraju, T.; Pandeeswar, M.; Jayaramulu, K.; Jaipuria, G.; Atreya, H. S. Spontaneous Self-Assembly of Designed Cyclic Dipeptide (Phg-Phg) into Two-Dimensional Nano- and Mesosheets Supramol. Chem. 2011, 23, 487-492
9. Mahler, A.; Reches, M.; Rechter, M.; Cohen, S.; Gazit, E. Rigid, Self-Assembled Hydrogel Composed of a Modified Aromatic Dipeptide Adv. Mater. 2006, 18, 1365-1370
10. Silva, R. F.; Araújo, D. R.; Silva, E. R.; Ando, R. A.; Alves, W. A. L-Diphenylalanine Microtubes as a Potential Drug-Delivery System: Characterization, Release Kinetics, and Cytotoxicity Langmuir 2013, 29, 10205-10212
11. Yemini, M.; Reches, M.; Gazit, E.; Rishpon, J. Peptide Nanotube-Modified Electrodes for Enzyme-Biosensor Applications Anal. Chem. 2005, 77, 5155-5159
12. Adler-Abramovich, L.; Aronov, D.; Beker, P.; Yevnin, M.; Stempler, S.; Buzhansky, L.; Rosenman, G.; Gazit, E. Self-Assembled Arrays of Peptide Nanotubes by Vapour Deposition Nat. Nanotechnol. 2009, 4, 849-854
13. Beker, P.; Rosenman, G. Bioinspired Nanostructural Peptide Materials for Supercapacitor Electrodes J. Mater. Res. 2010, 25, 1661-1666
14. Bank-Srour, B.; Becker, P.; Krasovitsky, L.; Gladkikh, A.; Rosenberg, Y.; Barkay, Z.; Rosenman, G. Physical Vapor Deposition of Peptide Nanostructures Polym. J. 2013, 45, 494-503
15. Gorbitz, C. H. The Structure of Nanotubes Formed by Diphenylalanine, the Core Recognition Motif of Alzheimer's beta-Amyloid Polypeptide Chem. Commun. 2006, 2332
16. Beker, P.; Koren, I.; Amdursky, N.; Gazit, E.; Rosenman, G. Bioinspired Peptide Nanotubes as Supercapacitor Electrodes J. Mater. Sci. 2010, 45, 6374-6378
17. Lee, J. S.; Ryu, J.; Park, C. B. Bio-Inspired Fabrication of Superhydrophobic Surfaces through Peptide Self-Assembly Soft Matter 2009, 5, 2717-2720
18. Gdaniec, M.; Liberek, B. Structure of Cyclo(- l -Phenylalanyl- l -Phenylalanyl-) Acta Crystallogr. C 1986, 42, 1343-1345
19. Lee, J. S.; Yoon, I.; Kim, J.; Ihee, H.; Kim, B.; Park, C. B. Self-Assembly of Semiconducting Photoluminescent Peptide Nanowires in the Vapor Phase Angew. Chem., Int. Ed. 2011, 50, 1164-1167
20. Sinnokrot, M. O.; Sherrill, C. D. High-Accuracy Quantum Mechanical Studies of π-π Interactions in Benzene Dimers J. Phys. Chem. A 2006, 110, 10656-10668
21. Govindaraju, T. Spontaneous Self-Assembly of Aromatic Cyclic Dipeptide into Fibre Bundles with High Thermal Stability and Propensity for Gelation Supramol. Chem. 2011, 23, 759-767
22. Joshi, K. B.; Verma, S. Participation of Aromatic Side Chains in Diketopiperazine Ensembles Tetrahedron Lett. 2008, 49, 4231-4234
23. Song, Y.; Challa, S. R.; Medforth, C. J.; Qiu, Y.; Watt, R. K.; Pena, D.; Miller, J. E.; Swol, F.; van Shelnutt, J. A. Synthesis of Peptide-Nanotube Platinum-Nanoparticle Composites Chem. Commun. 2004, 1044
24. Guo, C.; Luo, Y.; Zhou, R.; Wei, G. Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes ACS Nano 2012, 6, 3907-3918
25. Guo, C.; Luo, Y.; Zhou, R.; Wei, G. Triphenylalanine Peptides Self-Assemble into Nanospheres and Nanorods That Are Different from the Nanovesicles and Nanotubes Formed by Diphenylalanine Peptides Nanoscale 2014, 6, 2800
26. Tamamis, P.; Adler-Abramovich, L.; Reches, M.; Marshall, K.; Sikorski, P.; Serpell, L.; Gazit, E.; Archontis, G. Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations Biophys. J. 2009, 96, 5020-5029
27. Dalgicdir, C.; Sensoy, O.; Peter, C.; Sayar, M. A Transferable Coarse-Grained Model for Diphenylalanine: How To Represent an Environment Driven Conformational Transition J. Chem. Phys. 2013, 139, 234115
28. Jeon, J.; Mills, C. E.; Shell, M. S. Molecular Insights into Diphenylalanine Nanotube Assembly: All-Atom Simulations of Oligomerization J. Phys. Chem. B 2013, 117, 3935-3943
29. Sugita, Y.; Okamoto, Y. Replica-Exchange Molecular Dynamics Method for Protein Folding Chem. Phys. Lett. 1999, 314, 141-151
30. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174
31. Case, D. A.; Darden, T. A.; Cheatham, III, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; AMBER 12, 2012.
32. Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a Package of Computer Programs for Applying Molecular Mechanics, Normal Mode Analysis, Molecular Dynamics and Free Energy Calculations to Simulate the Structural and Energetic Properties of Molecules Comput. Phys. Commun. 1995, 91, 1-41
33. Lloyd, S. Least Squares Quantization in PCM IEEE Trans. Inf. Theory 1982, 28, 129-137
34. Dill, K. A.; Ozkan, S. B.; Shell, M. S.; Weikl, T. R. The Protein Folding Problem Annu. Rev. Biophys. 2008, 37, 289-316
35. Gee, J.; Shell, M. S. Two-Dimensional Replica Exchange Approach for Peptide-Peptide Interactions J. Chem. Phys. 2011, 134, 064112
36. Ferrenberg, A. M.; Swendsen, R. H. Optimized Monte Carlo Data Analysis Phys. Rev. Lett. 1989, 63, 1195-1198
37. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. THE Weighted Histogram Analysis Method for Free Energy Calculations on Biomolecules. I. The Method J. Comput. Chem. 1992, 13, 1011-1021
38. Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. Multidimensional Free Energy Calculations Using the Weighted Histogram Analysis Method J. Comput. Chem. 1995, 16, 1339-1350
39. Baker, E. N.; Hubbard, R. E. Hydrogen Bonding in Globular Proteins Prog. Biophys. Mol. Biol. 1984, 44, 97-179
40. Jaworska, M.; Jeziorna, A.; Drabik, E.; Potrzebowski, M. J. Solid State NMR Study of Thermal Processes in Nanoassemblies Formed by Dipeptides J. Phys. Chem. C 2012, 116, 12330-12338
41. Ben-Tal, N.; Sitkoff, D.; Topol, I. A.; Yang, A.-S.; Burt, S. K.; Honig, B. Free Energy of Amide Hydrogen Bond Formation in Vacuum, in Water, and in Liquid Alkane Solution J. Phys. Chem. B 1997, 101, 450-457
42. Gervasio, F. L.; Chelli, R.; Procacci, P.; Schettino, V. The Nature of Intermolecular Interactions between Aromatic Amino Acid Residues Proteins Struct. Funct. Bioinf. 2002, 48, 117-125