Molecular basis for nanoscopic membrane curvature generation from quantum mechanical models and synthetic transporter sequences

Journal of the American Chemical Society

Volumn 134, Issue 46, 2012, Pages 19207-19216

  Schmidt, Nathan W ^a   Lis, Michael ^c   Zhao, Kun ^a   Lai, Ghee Hwee ^a   Alexandrova, Anastassia N ^b   Tew, Gregory N ^c   Wong, Gerard C L ^a  

^a Engineering IV   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTI-MICROBIAL ACTIVITY; BUTYL GROUP; CATIONIC AMINO ACIDS; CLOSE PACKING; FACE TO FACE; GAUSSIANS; GEOMETRIC CONSTRAINT; GRAM POSITIVE; GUANIDINIUM; H-BONDING INTERACTION; HYDROPHOBIC GROUPS; LIPID COMPOSITION; MEMBRANE ACTIVITY; MEMBRANE CURVATURE; MINIMUM MODELS; MOLECULAR BASIS; MOLECULAR DESIGN; NANO SCALE; PHOSPHATE GROUP; POLYPEPTIDE BACKBONES; QUANTUM MECHANICAL; QUANTUM MECHANICAL MODEL; RED BLOOD CELL;

AMINO ACIDS; HYDROPHOBICITY; PEPTIDES; PHOSPHATES; PHOSPHOLIPIDS; POLYMERS; QUANTUM THEORY;

MEMBRANES;

ARGININE; GUANIDINE; LYSINE; PHENYL GROUP; PHOSPHATE; PHOSPHOLIPID; POLYMER; POLYPEPTIDE ANTIBIOTIC AGENT;

ANTIMICROBIAL ACTIVITY; ARTICLE; CALCULATION; ERYTHROCYTE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR BIOLOGY; NONHUMAN; QUANTUM MECHANICS;

MEMBRANES, ARTIFICIAL; MODELS, MOLECULAR; QUANTUM THEORY; SCATTERING, RADIATION;

EID: 84869386745     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja308459j     Document Type: Article

References (77)

1. Vivès, E.; Brodin, P.; Lebleu, B. J. Biol. Chem. 1997, 272, 16010-17
2. Futaki, S.; Suzuki, T.; Ohashi, W.; Yagami, T.; Tanaka, S.; Ueda, K.; Sugiura, Y. J. Biol. Chem. 2001, 276, 5836-40
3. El-Sayed, A.; Futaki, S.; Harashima, H. AAPS J. 2009, 11, 13-22
4. Wender, P. A.; Galliher, W. C.; Goun, E. A.; Jones, L. R.; Pillow, T. H. Adv. Drug Delivery Rev. 2008, 60, 452-72
5. Torchilin, V. P.; Rammohan, R.; Weissig, V.; Levchenko, T. S. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 8786-91
6. Lewin, M.; Carlesso, N.; Tung, C.-H.; Tang, X.-W.; Cory, D.; Scadden, D. T.; Weissleder, R. Nat. Biotechnol. 2000, 18, 410-14
7. Ganz, T. Nat. Rev. Immunol. 2003, 3, 710-20
8. Lehrer, R. I. Nat. Rev. Microbiol. 2004, 2, 727-38
9. Selsted, M. E.; Ouellette, A. J. Nat. Immunol. 2005, 6, 551-57
10. Wender, P. A.; Mitchell, D. J.; Pattabiraman, K.; Pelkey, E. T.; Steinman, L.; Rothbard, J. B. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 13003-08
11. Mitchell, D. J.; Steinman, L.; Kim, D. T.; Fathman, C. G.; Rothbard, J. B. J. Pept. Res. 2000, 56, 318-25
12. Rothbard, J. B.; Kreider, E.; VanDeusen, C. L.; Wright, L.; Wylie, B. L.; Wender, P. A. J. Med. Chem. 2002, 45, 3612-18
13. Cooley, C. B.; Trantow, B. M.; Nederberg, F.; Kiesewetter, M. K.; Hedrick, J. L.; Waymouth, R. M.; Wender, P. A. J. Am. Chem. Soc. 2009, 131, 16401-03
14. Hennig, A.; Gabriel, G. J.; Tew, G. N.; Matile, S. J. Am. Chem. Soc. 2008, 130, 10338-44
15. Kolonko, E. M.; Kiessling, L. L. J. Am. Chem. Soc. 2008, 130, 5626-27
16. Som, A.; Reuter, A.; Tew, G. N. Angew. Chem., Int. Ed. 2012, 51, 980-83
17. Som, A.; Tezgel, A. O.; Gabriel, G. J.; Tew, G. N. Angew. Chem., Int. Ed. 2011, 50, 6147-50
18. Tezgel, A. O. z. l.; Telfer, J. C.; Tew, G. N. Biomacromolecules 2011, 12, 3078-83
19. Wender, P. A.; Rothbard, J. B.; Jessop, T. C.; Kreider, E. L.; Wylie, B. L. J. Am. Chem. Soc. 2002, 124, 13382-83
20. Wender, P. A.; Kreider, E.; Pelkey, E. T.; Rothbard, J.; VanDeusen, C. L. Org. Lett. 2005, 7, 4815-18
21. Elson-Schwab, L.; Garner, O. B.; Schuksz, M.; Crawford, B. E.; Esko, J. D.; Tor, Y. J. Biol. Chem. 2007, 282, 13585-91
22. Rothbard, J. B.; Jessop, T. C.; Wender, P. A. Adv. Drug Delivery Rev. 2005, 57, 495-504
23. Rothbard, J. B.; Jessop, T. C.; Lewis, R. S.; Murray, B. A.; Wender, P. A. J. Am. Chem. Soc. 2004, 126, 9506-07
24. Drin, G.; Déméné, H.; Temsamani, J.; Brasseur, R. Biochemistry 2001, 40, 1824-34
25. Iwasa, A.; Akita, H.; Khalil, I.; Kogure, K.; Futaki, S.; Harashima, H. Biochim. Biophys. Acta, Biomembr. 2006, 1758, 713-20
26. Maiolo, J. R.; Ferrer, M.; Ottinger, E. A. Biochim. Biophys. Acta, Biomembr. 2005, 1712, 161-72
27. Persson, D.; Thorén, P. E. G.; Herner, M.; Lincoln, P.; Nordén, B. Biochemistry 2002, 42, 421-29
28. Ter-Avetisyan, G.; Tünnemann, G.; Nowak, D.; Nitschke, M.; Herrmann, A.; Drab, M.; Cardoso, M. C. J. Biol. Chem. 2009, 284, 3370-78
29. Thorén, P. E. G.; Persson, D.; Lincoln, P.; Nordén, B. Biophys. Chem. 2005, 114, 169-79
30. Drin, G.; Cottin, S.; Blanc, E.; Rees, A. R.; Temsamani, J. J. Biol. Chem. 2003, 278, 31192-201
31. Nakase, I.; Niwa, M.; Takeuchi, T.; Sonomura, K.; Kawabata, N.; Koike, Y.; Takehashi, M.; Tanaka, S.; Ueda, K.; Simpson, J. C.; Jones, A. T.; Sugiura, Y.; Futaki, S. Mol. Ther. 2004, 10, 1011-22
32. Richard, J. P.; Melikov, K.; Brooks, H.; Prevot, P.; Lebleu, B.; Chernomordik, L. V. J. Biol. Chem. 2005, 280, 15300-06
33. Richard, J. P.; Melikov, K.; Vives, E.; Ramos, C.; Verbeure, B.; Gait, M. J.; Chernomordik, L. V.; Lebleu, B. J. Biol. Chem. 2003, 278, 585-90
34. Wadia, J. S.; Stan, R. V.; Dowdy, S. F. Nat. Med. 2004, 10, 310-15
35. Ziegler, A. Adv. Drug Delivery Rev. 2008, 60, 580-97
36. Gump, J. M.; Dowdy, S. F. Trends Mol. Med. 2007, 13, 443-48
37. Guterstam, P.; Madani, F.; Hirose, H.; Takeuchi, T.; Futaki, S.; El Andaloussi, S.; Gräslund, A.; Langel, Ü. Biochim. Biophys. Acta, Biomembr. 2009, 1788, 2509-17
38. Heitz, F.; Morris, M. C.; Divita, G. Br. J. Pharmacol. 2009, 157, 195-206
39. Mishra, A.; Lai, G. H.; Schmidt, N. W.; Sun, V. Z.; Rodriguez, A. R.; Tong, R.; Tang, L.; Cheng, J.; Deming, T. J.; Kamei, D. T.; Wong, G. C. L. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 16883-88
40. Schmidt, N. W.; Mishra, A.; Lai, G. H.; Davis, M.; Sanders, L. K.; Tran, D.; Garcia, A.; Tai, K. P.; McCray, P. B.; Ouellette, A. J.; Selsted, M. E.; Wong, G. C. L. J. Am. Chem. Soc. 2011, 133, 6720-27
41. Schmidt, N.; Mishra, A.; Lai, G. H.; Wong, G. C. L. FEBS Lett. 2010, 584, 1806-13
42. Schug, K. A.; Lindner, W. Chem. Rev. 2004, 105, 67-114
43. Conner, S. D.; Schmid, S. L. Nature 2003, 422, 37-44
44. Braun, A. R.; Sevcsik, E.; Chin, P.; Rhoades, E.; Tristram-Nagle, S.; Sachs, J. N. J. Am. Chem. Soc. 2012, 134, 2613-20
45. Pednekar, D.; Tendulkar, A.; Durani, S. Proteins: Struct., Funct., Bioinform. 2009, 74, 155-63
46. Papoian, G. A.; Ulander, J.; Eastwood, M. P.; Luthey-Schulten, Z.; Wolynes, P. G. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352-57
47. Yuzlenko, O.; Lazaridis, T. J. Phys. Chem. B 2011, 115, 13674-84
48. McMahon, H. T.; Gallop, J. L. Nature 2005, 438, 590-96
49. Matsuzaki, K.; Sugishita, K.-i.; Ishibe, N.; Ueha, M.; Nakata, S.; Miyajima, K.; Epand, R. M. Biochemistry 1998, 37, 11856-63
50. Parr, R. G.; Yang, W. Density-functional theory of atoms and molecules; Oxford Univ. Press: Oxford, 1989.
51. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-52
52. Perdew, J. P.; Chevary, J. A.; Vosko, S. H.; Jackson, K. A.; Pederson, M. R.; Singh, D. J.; Fiolhais, C. Phys. Rev. B 1992, 46, 6671-87
53. Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P. V. R. J. Comput. Chem. 1983, 4, 294-301
54. Frisch, M. J.; Pople, J., A; Binkley, S., J J. Chem. Phys. 1984, 80, 3265-69
55. Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1988, 153, 503-06
56. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 275-80
57. Frisch, M. J.; Head-Gordon, M.; Pople, J. A. Chem. Phys. Lett. 1990, 166, 281-89
58. Tubert-Brohman, I.; Guimarães, C. R. W.; Repasky, M. P.; Jorgensen, W. L. J. Comput. Chem. 2004, 25, 138-50
59. Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. J. Comput. Chem. 2002, 23, 1601-22
60. Jorgensen, W. L.; Ulmschneider, J. P.; Tirado-Rives, J. J. Phys. Chem. B 2004, 108, 16264-70
61. Frisch, M. J.; Gaussian 09, Revision A.1; Gaussian, Inc.: Wallingford, CT, 2009.
62. Jorgensen, W. L.; Tirado-Rives, J. J. Comput. Chem. 2005, 26, 1689-700
63. Gabriel, G. J.; Madkour, A. E.; Dabkowski, J. M.; Nelson, C. F.; Nüsslein, K.; Tew, G. N. Biomacromolecules 2008, 9, 2980-83
64. usaxs.xor.aps.anl.gov/staff/ilavsky/nika.html.
65. www.esrf.eu/computing/scientific/FIT2D/.
66. Harper, P. E.; Mannock, D. A.; Lewis, R. N. A. H.; McElhaney, R. N.; Gruner, S. M. Biophys. J. 2001, 81, 2693-706
67. Tristram-Nagle, S.; Petrache, H. I.; Nagle, J. F. Biophys. J. 1998, 75, 917-25
68. Homchaudhuri, L.; Swaminathan, R. Bull. Chem. Soc. Jpn. 2004, 77, 765-69
69. Vondráşek, J. í.; Mason, P. E.; Heyda, J.; Collins, K. D.; Jungwirth, P. J. Phys. Chem. B 2009, 113, 9041-45
70. No, K. T.; Nam, K.-Y.; Scheraga, H. A. J. Am. Chem. Soc. 1997, 119, 12917-22
71. Mishra, A.; Gordon, V.; Yang, L.; Coridan, R.; Wong, G. Angew. Chem., Int. Ed. 2008, 47, 2986-89
72. Harper, P. E.; Gruner, S. M. Eur. Phys. J. E: Soft Matter Biol. Phys. 2000, 2, 217-28
73. Yeaman, M. R.; Yount, N. Y. Pharmacol. Rev. 2003, 55, 27-55
74. Tew, G. N.; Scott, R. W.; Klein, M. L.; DeGrado, W. F. Acc. Chem. Res. 2009, 43, 30-39
75. Tossi, A.; Sandri, L.; Giangaspero, A. Pept. Sci. 2000, 55, 4-30
76. Fischer, D.; Li, Y.; Ahlemeyer, B.; Krieglstein, J.; Kissel, T. Biomaterials 2003, 24, 1121-31
77. Epand, R. F.; Mowery, B. P.; Lee, S. E.; Stahl, S. S.; Lehrer, R. I.; Gellman, S. H.; Epand, R. M. J. Mol. Biol. 2008, 379, 38-50