A rotamer library to enable modeling and design of peptoid foldamers

Journal of the American Chemical Society

Volumn 136, Issue 24, 2014, Pages 8772-8782

  Renfrew, P Douglas ^a   Craven, Timothy W ^a   Butterfoss, Glenn L ^c   Kirshenbaum, Kent ^a   Bonneau, Richard ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; AMPHIPHILES; BIOMIMETICS; CHAINS; OLIGOMERS; PROTEINS; QUANTUM THEORY;

ACCURATE PREDICTION; COMPUTATIONAL APPROACH; CONFORMATIONAL STATE; ENERGETIC PARAMETERS; ROTATIONAL ISOMERISMS; SECONDARY STRUCTURES; STRUCTURE PREDICTION; TERTIARY STRUCTURES;

STRUCTURAL DESIGN;

OLIGOMER; PEPTOID; PEPTIDE LIBRARY;

ARTICLE; BIOMIMETICS; CHEMICAL STRUCTURE; CONFORMATIONAL TRANSITION; ISOMERISM; MOLECULAR MECHANICS; PROTEIN TERTIARY STRUCTURE; CHEMISTRY; PEPTIDE LIBRARY; PROTEIN FOLDING; QUANTUM THEORY;

MODELS, MOLECULAR; MOLECULAR STRUCTURE; PEPTIDE LIBRARY; PEPTOIDS; PROTEIN FOLDING; QUANTUM THEORY;

EID: 84902682675     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja503776z     Document Type: Article

References (55)

1. Koga, N.; Tatsumi-Koga, R.; Liu, G.; Xiao, R.; Acton, T. B.; Montelione, G. T.; Baker, D. Nature 2012, 491, 222-227
2. Bida, J.; Das, R. Curr. Opin. Struct. Biol. 2012, 22, 457-466
3. King, N. P.; Sheffler, W.; Sawaya, M. R.; Vollmar, B. S.; Sumida, J. P.; Andr, I.; Gonen, T.; Yeates, T. O.; Baker, D. Science 2012, 336, 1171-1174
4. Gellman, S. H. Acc. Chem. Res. 1998, 31, 173-180
5. Dunbrack, R. L., Jr. Curr. Opin. Struct. Biol. 2002, 12, 431-440
6. Petersson, E. J.; Schepartz, A. J. Am. Chem. Soc. 2008, 130, 821-823
7. Cao, J.; Kline, M.; Chen, Z.; Luan, B.; Lv, M.; Zhang, W.; Lian, C.; Wang, Q.; Huang, Q.; Wei, X.; Deng, J.; Zhu, J.; Gong, B. Chem. Commun. 2012, 48, 11112-11114
8. Tosovska, P.; Arora, P. S. Org. Lett. 2010, 12, 1588-1591
9. Lee, B.-C.; Chu, T. K.; Dill, K. A.; Zuckermann, R. N. J. Am. Chem. Soc. 2008, 130, 8847-8855
10. Kwon, I.; Wang, P.; Tirrell, D. A. J. Am. Chem. Soc. 2006, 128, 11778-11783
11. Reinert, Z. E.; Lengyel, G. A.; Horne, W. S. J. Am. Chem. Soc. 2013, 135, 12528-12531
12. Huang, M. L.; Ehre, D.; Jiang, Q.; Hu, C.; Kirshenbaum, K.; Ward, M. D. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 19922-19927
13. Maayan, G.; Ward, M. D.; Kirshenbaum, K. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 13679-13684
14. Raveendra, B.; Wu, H.; Baccala, R.; Reddy, M.; Schilke, J.; Bennett, J.; Theofilopoulos, A.; Kodadek, T. Chem. Biol. 2013, 20, 351-359
15. Utku, Y.; Dehan, E.; Ouerfelli, O.; Piano, F.; Zuckermann, R. N.; Pagano, M.; Kirshenbaum, K. Mol. BioSyst. 2006, 2, 312-317
16. Zuckermann, R. N.; Kerr, J. M.; Kent, S. B. H.; Moos, W. H. J. Am. Chem. Soc. 1992, 114, 10646-10647
17. Culf, A. S.; Ouellette, R. J. Molecules 2010, 15, 5282-5335
18. Crapster, J. A.; Guzei, I. A.; Blackwell, H. E. Angew. Chem., Int. Ed. 2013, 52, 5079-5084
19. Butterfoss, G. L.; Yoo, B.; Jaworski, J. N.; Chorny, I.; Dill, K. A.; Zuckermann, R. N.; Bonneau, R.; Kirshenbaum, K.; Voelz, V. A. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 14320-14325
20. Seo, J.; Barron, A. E.; Zuckermann, R. N. Org. Lett. 2010, 12, 492-495
21. Huang, M. L.; Shin, S. B. Y.; Benson, M. A.; Torres, V. J.; Kirshenbaum, K. ChemMedChem 2012, 7, 114-122
22. Chongsiriwatana, N. P.; Patch, J. A.; Czyzewski, A. M.; Dohm, M. T.; Ivankin, A.; Gidalevitz, D.; Zuckermann, R. N.; Barron, A. E. Proc. Natl. Acad. Sci. U S.A. 2008, 105, 2794-2799
23. Nguyen, J. T.; Porter, M.; Amoui, M.; Miller, W. T.; Zuckermann, R. N.; Lim, W. A. Chem. Biol. 2000, 7, 463-473
24. Nguyen, J. T.; Turck, C. W.; Cohen, F. E.; Zuckermann, R. N.; Lim, W. A. Science 1998, 282, 2088-2092
25. Shah, N. H.; Butterfoss, G. L.; Nguyen, K.; Yoo, B.; Bonneau, R.; Rabenstein, D. L.; Kirshenbaum, K. J. Am. Chem. Soc. 2008, 130, 16622-16632
26. Stringer, J. R.; Crapster, J. A.; Guzei, I. A.; Blackwell, H. E. J. Am. Chem. Soc. 2011, 133, 15559-15567
27. Huang, M. L.; Benson, M. A.; Shin, S. B. Y.; Torres, V. J.; Kirshenbaum, K. Eur. J. Org. Chem. 2013, 2013, 3560-3566
28. Naffin, J. L.; Han, Y.; Olivos, H. J.; Reddy, M.; Sun, T.; Kodadek, T. Chem. Biol. 2003, 10, 251-259
29. Nam, K. T.; Shelby, S. A.; Choi, P. H.; Marciel, A. B.; Chen, R.; Tan, L.; Chu, T. K.; Mesch, R. A.; Lee, B.-C.; Connolly, M. D.; Kisielowski, C.; Zuckermann, R. N. Nat. Mater. 2010, 9, 454-460
30. Vollrath, S. B. L.; Hu, C.; Bräse, S.; Kirshenbaum, K. Chem. Commun. 2013, 49, 2317-2319
31. Levine, P. M.; Craven, T. W.; Bonneau, R.; Kirshenbaum, K. Org. Biomol. Chem. 2013, 11, 4142-4146
32. Dunbrack, R. L.; Cohen, F. E. Protein Sci. 1997, 6, 1661-1681
33. Shapovalov, M. V.; Dunbrack, R. L. Structure 2011, 19, 844-858
34. Renfrew, P. D.; Choi, E. J.; Bonneau, R.; Kuhlman, B. PLoS One 2012, 7, e32637
35. Gfeller, D.; Michielin, O.; Zoete, V. J. Comput. Chem. 2012, 33, 1525-1535
36. Shandler, S. J.; Shapovalov, M. V.; Dunbrack, J.; DeGrado, W. F. J. Am. Chem. Soc. 2010, 132, 7312-7320
37. Leaver-Fay, A.; An Object-Oriented Software Suite for the Simulation and Design of Macromolecules. In Methods in Enzymology; Johnson, M. L.; Brand, L., Eds.; Computer Methods, Part C; Academic Press: New York, 2011; Vol. 487; pp 545-574.
38. Leh, J.; Kirshenbaum, K. Peptoid Data Bank; http://www.nyu.edu/projects/ kirshenbaum/Peptoid-Databank.html, 2012.
39. Huang, K.; Wu, C. W.; Sanborn, T. J.; Patch, J. A.; Kirshenbaum, K.; Zuckermann, R. N.; Barron, A. E.; Radhakrishnan, I. J. Am. Chem. Soc. 2006, 128, 1733-1738
40. Drew, K. PLoS One 2013, 8, e67051
41. Butterfoss, G. L.; Renfrew, P. D.; Kuhlman, B.; Kirshenbaum, K.; Bonneau, R. J. Am. Chem. Soc. 2009, 131, 16798-16807
42. As agreed upon at the 8th Peptoid Summit, August 2012.
43. Lovell, S. C.; Word, J. M.; Richardson, J. S.; Richardson, D. C. Proteins: Struct., Funct., Bioinf. 2000, 40, 389-408
44. Jordan, P. A.; Paul, B.; Butterfoss, G. L.; Renfrew, P. D.; Bonneau, R.; Kirshenbaum, K. Peptide Sci. 2011, 96, 617-626
45. Frisch, M. J. GAUSSIAN 09, Revision A.1; Gaussian Inc.: Wallingford, CT, 2009.
46. Kuhlman, B.; Baker, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 10383-10388
47. Armand, P.; Kirshenbaum, K.; Falicov, A.; Dunbrack, R. L., Jr.; Dill, K. A.; Zuckermann, R. N.; Cohen, F. E. Folding Des. 1997, 2, 369-375
48. Laursen, J. S.; Engel-Andreasen, J.; Fristrup, P.; Harris, P.; Olsen, C. A. J. Am. Chem. Soc. 2013, 135, 2835-2844
49. Winkler, F.; Dunitz, J. J. Mol. Biol. 1971, 59, 169-182
50. Paul, B.; Butterfoss, G. L.; Boswell, M. G.; Renfrew, P. D.; Yeung, F. G.; Shah, N. H.; Wolf, C.; Bonneau, R.; Kirshenbaum, K. J. Am. Chem. Soc. 2011, 133, 10910-10919
51. Dunbrack, R. L.; Karplus, M. Nat. Struct. Mol. Biol. 1994, 1, 334-340
52. Richardson, J. S.; Richardson, D. C. Biopolymers 2013, 99, 170-182
53. Leaver-Fay, A. In Methods in Enzymology; A. E. Keating, Ed.; Methods in Protein Design; Academic Press: New York, 2013; Vol. 523; pp 109-143.
54. Krivov, G. G.; Shapovalov, M. V.; Dunbrack, R. L. Proteins: Struct., Funct., Bioinf. 2009, 77, 778-795
55. Butterfoss, G. L.; Drew, K.; Renfrew, P. D.; Kirshenbaum, K.; Bonneau, R. Conformational Preferences of Peptide-Peptoid Hybrid Oligomers. Pept. Sci. 2014, accepted.