How cations change peptide structure

Chemistry - A European Journal

Volumn 19, Issue 34, 2013, Pages 11224-11234

  Baldauf, Carsten ^a   Pagel, Kevin ^a   Warnke, Stephan ^a   Von Helden, Gert ^a   Koksch, Beate ^b   Blum, Volker ^a   Scheffler, Matthias ^a  

^a FRITZ HABER INSTITUT DER MAX PLANCK GESELLSCHAFT   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

density functional calculations; hydrogen bonds; IR spectroscopy; protein folding; protein structures

Indexed keywords

CONFORMATIONAL EFFECT; CONFORMATIONAL ENSEMBLE; DENSITY-FUNCTIONAL CALCULATIONS; GAS-PHASE INFRARED SPECTROSCOPY; HYDROGEN BONDING NETWORK; PROTEIN STRUCTURES; QUANTUM CHEMISTRY CALCULATIONS; SPECIFIC INTERACTION;

CONFORMATIONS; HYDROGEN BONDS; INFRARED SPECTROSCOPY; LITHIUM; POSITIVE IONS; PROTEIN FOLDING; QUANTUM CHEMISTRY; VAN DER WAALS FORCES;

PEPTIDES;

CATION; LITHIUM; PEPTIDE; SODIUM;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DENSITY-FUNCTIONAL CALCULATIONS; HYDROGEN BOND; HYDROGEN BONDS; INFRARED SPECTROPHOTOMETRY; INFRARED SPECTROSCOPY; PROTEIN FOLDING; PROTEIN STRUCTURES; PROTEIN TERTIARY STRUCTURE;

DENSITY-FUNCTIONAL CALCULATIONS; HYDROGEN BONDS; IR SPECTROSCOPY; PROTEIN FOLDING; PROTEIN STRUCTURES;

AMINO ACID SEQUENCE; CATIONS; HYDROGEN BONDING; LITHIUM; MODELS, MOLECULAR; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SODIUM; SPECTROPHOTOMETRY, INFRARED;

EID: 84882240711     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.201204554     Document Type: Article

References (72)

1. P. Pfeiffer, J. von Modelski, Hoppe-Seylers Z. Physiol. Chem. 1912, 81, 329-354.
2. P. Pfeiffer, Hoppe-Seylers Z. Physiol. Chem. 1924, 133, 22-61.
3. D. Seebach, H. Bossler, R. Flowers, E. Arnett, Helv. Chim. Acta 1994, 77, 291-305.
4. J. Kofron, P. Kuzmič, V. Kishore, E. Colõn-Bonilla, D. Rich, Biochemistry 1991, 30, 6127-6134.
5. H. Kessler, M. Gehrke, J. Lautz, M. Kock, D. Seebach, A. Thaler, Biochem Pharmacol. 1990, 40, 169-173.
6. M. Koeck, H. Kessler, D. Seebach, A. Thaler, J. Am. Chem. Soc. 1992, 114, 2676-2686.
7. E. Garand, M. Z. Kamrath, P. A. Jordan, A. B. Wolk, C. M. Leavitt, A. B. McCoy, S. J. Miller, M. A. Johnson, Science 2012, 335, 694-698.
8. D. Seebach, A. K. Beck, A. Studer, in Modern Synthetic Methods (Eds.:, B. Ernst, C Leumann,), Wiley-VCH, 1995; pp. 1-178.
9. G. Ramachandran, C. Ramakrishnan, V. Sasisekharan, J. Mol. Biol. 1963, 7, 95-99.
10. S. C. Lovell, I. W. Davis, W. B. Arendall, P. I. W. de Bakker, J. M. Word, M. G. Prisant, J. S. Richardson, D. C. Richardson, Proteins: Struct. Funct. Bioinf. 2003, 50, 437-450.
11. G. Fischer, Chem. Soc. Rev. 2000, 29, 119-127.
12. C. Dugave, L. Demange, Chem. Rev. 2003, 103, 2475-2532.
13. M. S. Weiss, A. Jabs, R. Hilgenfeld, Nat. Struct. Biol. 1998, 5, 676-676.
14. J. S. Richardson, Adv. Protein Chem. 1981, 34, 167-339.
15. For idealized backbone torsion angles for these turn types, see:, K. Möhle, M. Gußmann, H.-J. Hofmann, J. Comput. Chem. 1997, 18, 1415-1430.
16. C. M. Venkatachalam, Biopolymers 1968, 6, 1425-1436.
17. B. L. Sibanda, J. M. Thornton, Nature 1985, 316, 170-174.
18. E. G. Hutchinson, J. M. Thornton, Protein Sci. 1994, 3, 2207-2216.
19. C. Kunz, G. Jahreis, R. Günther, S. Berger, G. Fischer, H.-J. Hofmann, J. Pept. Sci. 2012, 18, 400-404.
20. A. Abo-Riziq, J. E. Bushnell, B. Crews, M. Callahan, L. Grace, M. S. de Vries, Chem. Phys. Lett. 2006, 431, 227-230.
21. J. Bakker, L. Aleese, G. Meijer, G. von Helden, Phys. Rev. Lett. 2003, 91, 203003.
22. I. Compagnon, J. Oomens, G. Meijer, G. von Helden, J. Am. Chem. Soc. 2006, 128, 3592-3597.
23. A. Kamariotis, O. V. Boyarkin, S. R. Mercier, R. D. Beck, M. F. Bush, E. R. Williams, T. R. Rizzo, J. Am. Chem. Soc. 2006, 128, 905-916.
24. A. Cimas, T. D. Vaden, T. S. J. A. de Boer, L. C. Snoek, M.-P. Gaigeot, J. Chem. Theory Comput. 2009, 5, 1068-1078.
25. W. H. James III, C. W. Müller, E. G. Buchanan, M. G. D. Nix, L. Guo, L. Roskop, M. S. Gordon, L. V. Slipchenko, S. H. Gellman, T. S. Zwier, J. Am. Chem. Soc. 2009, 131, 14243-14245.
26. W. H. James III, E. E. Baquero, S. H. Choi, S. H. Gellman, T. S. Zwier, J. Phys. Chem. A 2010, 114, 1581-1591.
27. M. Rossi, V. Blum, P. Kupser, G. von Helden, F. Bierau, K. Pagel, G. Meijer, M. Scheffler, J. Phys. Chem. Lett. 2010, 1, 3465-3470.
28. R. J. Plowright, E. Gloaguen, M. Mons, ChemPhysChem 2011, 12, 1889-1899.
29. S. Chutia, M. Rossi, V. Blum, J. Phys. Chem. B 2012, 116, 14788-14804.
30. M. Rossi, M. Scheffler, V. Blum, J. Phys. Chem. B 2013, 117, 5574-5584.
31. J. P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 1996, 77, 3865-3868.
32. A. Tkatchenko, M. Scheffler, Phys. Rev. Lett. 2009, 102, 073005.
33. W. Jorgensen, J. Ulmschneider, J. Tirado-Rives, J. Phys. Chem. B 2004, 108, 16264-16270.
34. J. Wang, P. Cieplak, P. Kollman, J. Comput. Chem. 2000, 21, 1049-1074.
35. R. Pappu, R. Hart, J. Ponder, J. Phys. Chem. B 1998, 102, 9725-9742.
36. B. Byun, I. Song, Y. Chung, K. Ryu, Y. Kang, J. Phys. Chem. B 2010, 114, 14077-14086.
37. Z. Wasserman, F. Salemme, Biopolymers 1990, 29, 1613-1631.
38. A. R. Fadel, D. Q. Jin, G. T. Montelione, R. M. Levy, J. Biomol. NMR 1995, 6, 221-226.
39. D. Oepts, A. van der Meer, P. van Amersfoort, Infrared Phys. Technol. 1995, 36, 297-308.
40. J. Valle, J. Eyler, J. Oomens, D. Moore, A. van der Meer, G. von Helden, G. Meijer, C. Hendrickson, A. Marshall, G. Blakney, Rev. Sci. Instrum. 2005, 76, 023103.
41. M.-P. Gaigeot, Phys. Chem. Chem. Phys. 2010, 12, 3336-3359.
42. J. Pendry, J. Phys. C: Solid State Phys 1980, 13, 937-944.
43. V. Blum, K. Heinz, Comput. Phys. Commun. 2001, 134, 392-425.
44. G. Grégoire, M. P. Gaigeot, D. C. Marinica, J. Lemaire, J. P. Schermann, C. Desfrancois, Phys. Chem. Chem. Phys. 2007, 9, 3082-3097.
45. S. Varma, S. B. Rempe, Biophys. Chem. 2006, 124, 192-199.
46. T. Ikeda, M. Boero, K. Terakura, J. Chem. Phys. 2007, 126, 034501.
47. D. Semrouni, O. P. Balaj, F. Calvo, C. F. Correia, C. Clavagura, G. Ohanessian, J. Am. Soc. Mass Spectrom. 2010, 21, 728-738.
48. O. P. Balaj, D. Semrouni, V. Steinmetz, E. Nicol, C. Clavaguéra, G. Ohanessian, Chem. Eur. J. 2012, 18, 4583-4592.
49. M. Kohtani, B. Kinnear, M. Jarrold, J. Am. Chem. Soc. 2000, 122, 12377-12378.
50. J. K. Martens, I. Compagnon, E. Nicol, T. B. McMahon, C. Clavaguéra, G. Ohanessian, J. Phys. Chem. Lett. 2012, 3, 3320-3324.
51. S. Y. Noskov, B. Roux, J. Mol. Biol. 2008, 377, 804-818.
52. F. N.-S. Hofmeister, Arch. Pharmakol. 1888, 25, 1-30.
53. P. H. von Hippel, K.-Y. Wong, J. Biol. Chem. 1965, 240, 3909-3923.
54. A. W. Omta, M. F. Kropman, S. Woutersen, H. J. Bakker, Science 2003, 301, 347-349.
55. W. Kunz, Curr Opin. Colloid Interface Sci. 2010, 15, 34-39.
56. J. Dzubiella, J. Am. Chem. Soc. 2008, 130, 14000-14007.
57. J. Dzubiella, J. Phys. Chem. B 2009, 113, 16689-16694.
58. Y. von Hansen, I. Kalcher, J. Dzubiella, J. Phys. Chem. B 2010, 114, 13815-13822.
59. A. Crevenna, N. Naredi-Rainer, D. Lamb, R. Wedlich-Söldner, J. Dzubiella, Biophys. J. 2012, 102, 907-915.
60. Y. Zhang, S. Furyk, D. E. Bergbreiter, P. S. Cremer, J. Am. Chem. Soc. 2005, 127, 14505-14510.
61. V. Blum, R. Gehrke, F. Hanke, P. Havu, V. Havu, X. Ren, K. Reuter, M. Scheffler, Comput. Phys. Commun. 2009, 180, 2175-2196.
62. F. Neese, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012, 2, 73-78.
63. D. G. Truhlar, Chem. Phys. Lett. 1998, 294, 45-48.
64. T. H. Dunning Jr., J. Chem. Phys. 1989, 90, 1007-1023.
65. A. Tkatchenko, M. Rossi, V. Blum, J. Ireta, M. Scheffler, Phys. Rev. Lett. 2011, 106, 118102.
66. N. Marom, A. Tkatchenko, M. Scheffler, L. Kronik, J. Chem. Theory Comput. 2010, 6, 81-90.
67. G.-X. Zhang, A. Tkatchenko, J. Paier, H. Appel, M. Scheffler, Phys. Rev. Lett. 2011, 107, 245501.
68. J. A. Pople, J. S. Binkley, R. Seeger, Int. J. Quantum Chem. 1976, 10, 1-19.
69. C. Adamo, V. Barone, J. Chem. Phys. 1999, 110, 6158-6170.
70. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiõrkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586-3616.
71. M. Schnieders, J. Ponder, J. Chem. Theory Comput. 2007, 3, 2083-2097.
72. J. Oomens, B. Sartakov, G. Meijer, G. von Helden, Int. J. Mass Spectrom. 2006, 254, 1-19.