Water interaction differences determine the relative energetic stability of the polyproline II conformation of the alanine dipeptide in aqueous environments

Biopolymers

Volumn 97, Issue 10, 2012, Pages 789-794

  Mirkin, Noemi G ^a   Krimm, Samuel ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

ab initio; conformation; hydrogen bonds; peptides; polyproline II; water

Indexed keywords

AB INITIO; ALANINE DIPEPTIDES; AQUEOUS ENVIRONMENT; ENERGETIC STABILITY; EXPLICIT WATER; INTERACTION ENERGIES; PERSISTENCE LENGTH; POLYPEPTIDE CHAIN; POLYPROLINE II; REACTION FIELDS; RELATIVE STABILITIES; THREE COMPONENT; WATER INTERACTIONS; WATER STRUCTURE;

AMINO ACIDS; BIOPOLYMERS; CONFORMATIONS; HYDROGEN BONDS; WATER;

PEPTIDES;

ALANINE; BIOPOLYMER; DIPEPTIDE; POLYPROLINE II; PROLINE; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; CIRCULAR DICHROISM; ENERGY; MOLECULAR MECHANICS; PROTEIN CONFORMATION; PROTEIN STABILITY; PROTEIN STRUCTURE; TEMPERATURE; WATER STRUCTURE;

ALANINE; DIPEPTIDES; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; WATER;

EID: 84863910282     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.22064     Document Type: Article

References (92)

1. Tanford, C.; Kawahara, K.; Lapanje, S., J Biol Chem 1966, 241, 1921-1923.
2. Flory, P. J., Statistical Mechanics of Chain Molecules; John Wiley and Sons: New York, 1969.
3. Greenfield, N.; Fasman, G. D., Biochemistry 1969, 8, 4108-4116.
4. Tiffany, M. L.; Krimm, S., Biopolymers 1968, 6, 1379-1381.
5. Tiffany, M. L.; Krimm, S., Biopolymers 1969, 8, 347-359.
6. Tiffany, M. L.; Krimm, S., Biopolymers 1972, 11, 2309-2316.
7. Tiffany, M. L.; Krimm, S., Biopolymers 1973, 12, 575-587.
8. Ronish, E. W.; Krimm, S., Biopolymers 1972, 11, 1919-1928.
9. Ronish, E. W.; Krimm, S., Biopolymers 1974, 13, 1635-1651.
10. Krimm, S.; Mark, J. E., Proc Natl Acad Sci USA 1969, 60, 1122-1129.
11. Krimm, S.; Tiffany, M. L., Isr J Chem 1974, 12, 189-200.
12. Woody, R. W., J Polym Sci Macromol Rev 1977, 12, 181-320.
13. Woody, R. W., Adv. Biophys Chem 1992, 2, 37 -> 79.
14. Shi, Z.; Woody, R. W.; Kallenbach, N. R., Adv Protein Chem 2002, 62, 163-240.
15. Shi, Z.; Chen, K.; Liu, Z.; Kallenbach, N. R., Chem Rev 2006, 106, 1877-1897.
16. Chen. K.; Liu, Z.; Bracken, W. C.; Lu, M.; Kallenbach, N. R., In Unfolded Proteins: From Denatured to Intrinsically Disordered;, Creamer, T. P., Eds.; Nova Science Publishers, Hauppauge, N.Y. 2008; pp 71-99.
17. Chellgren, V. M.; Chellgren, B. W.; Creamer, T. P., In Unfolded Proteins: From Denatured to Intrinsically Disordered;, Creamer, T. P., Eds.; Nova Science Publishers, 2008; pp 143-167.
18. Gaigeot, M.-P., Phys Chem Chem Phys 2010, 12, 10198-10209.
19. Woody, R. W., J Am Chem Soc 2009, 131, 8234-8245.
20. Woody, R. W., Chirality 2010, 22, E22-E29.
21. Zagrovic, B.; Lipfert, J.; Sorin, E. J.; Millett, I. S.; van Gunsteren, W. F.; Doniach, S.; Pande, V. S., Proc Natl Acad Sci USA 2005, 102, 11698-11703.
22. Makowska, J.; Rodziewicz-Motowidlo, S.; Baginska, K.; Vila, J. A.; Liwo, A.; Chmurzynski, L.; Scheraga, H. A., Proc Natl Acad Sci USA 2006, 103, 1744-1749.
23. Makowska, J.; Rodziewicz-Motowidlo, S.; Baginska, K.; Makowski, M.; Vila, J. A.; Liwo, A.; Chmurzynski, L.; Scheraga, H. A., Biophys J 2007, 92, 2904-2917.
24. Makowska, J.; Baginska, K.; Skwierawska, A.; Liwo, A.; Chmurzynski, L.; Scheraga, H. A., Biopolymers (Pept Sci) 2008, 90, 772-782.
25. Shi, Z.; Olson, C. A.; Rose, G. D.; Baldwin, R. L.; Kallenbach, N. R., Proc Natl Acad Sci USA 2002, 99, 9190-9195.
26. Chen, K.; Liu, Z.; Zhou, C.; Bracken, W. C.; Kallenbach, N. R., Angew Chem Int Ed 2007, 46, 9036-9039.
27. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A., J Am Chem Soc 1997, 119, 5908-5920.
28. Hu, H.; Elstner, M.; Hermans, J., Proteins 2003, 50, 451-463.
29. Mu, Y.; Kosov, D. S.; Stock, G., J Phys Chem B 2003, 107, 5064-5073.
30. Yoda, T.; Sugita, Y.; Okamoto, Y., Chem Phys 2004, 307, 269-283.
31. Gnankaran, S.; Garcia, A., Proteins 2005, 59, 773-782.
32. Kwac, K.; Lee, K. -K.; Han, J. B.; Oh, K. -I.; Cho, M., J Chem Phys 2008, 128, 105-106.
33. Aliev, A. E.; Courtier-Murias, D., J Phys Chem B 2010, 114, 12358-12375.
34. Hu, Z.; Jiang, J., J Comput Chem 2010, 31, 371-380.
35. Mittal, J.; Best, R. B., Biophys J 2010, 99, L26-L28.
36. Florova, P.; Sklenovsky, P.; Banas, P.; Otyepka, M., J Chem Theory Comput 2010, 6, 3569-3579.
37. Cerutti, D. S.; Freddolino, P. L.; Duke, Jr., R. E.; Case, D. A., J Phys Chem B 2010, 114, 12811-12824.
38. Piana, S.; Lindorff-Larsen, K.; Shaw, D. E., Biophys J 2011, 100, L47-L49.
39. Nerenberg, P. S.; Head-Gordon, T., J Chem Theory Comput 2011, 7, 1220-1230.
40. Patapati, K. K.; Glykos, N. M., Biophys J 2011, 101, 1766-1771.
41. Feynman, R. P., Phys Rev 1939, 56, 340-343.
42. Palmo, K.; Mannfors, B.; Mirkin, N. G.; Krimm, S., Chem Phys Lett 2006, 429, 628-632.
43. Palmo, K.; Mannfors, B.; Mirkin, N. G.; Krimm, S., Biopolymers 2003, 68, 383-394.
44. Hermans, J., Adv Protein Chem 2006, 72, 105-119.
45. Mannfors, B.; Palmo, K.; Krimm, S., J Phys Chem A 2008, 112, 12667-12678.
46. Li, X.-Z.; Walker, B.; Michaelides, A., Proc Natl Acad Sci USA 2011, 108, 6369-6373.
47. Mirkin, N. G.; Krimm, S., J Phys Chem A 2004, 108, 10923-10924.
48. Mirkin, N. G.; Krimm, S., J Phys Chem A 2007, 111, 5300-5303.
49. Mirkin, N. G.; Krimm, S., Biopolymers 2009, 91, 791-800.
50. Mirkin, N. G.; Krimm, S., Biopolymers 2010, 93, 1065-1071.
51. Creamer, T. P.; Campbell, M. N., Adv Protein Chem 2002, 62, 263-282.
52. Pappu, R. V.; Rose, G. D., Protein Sci 2002, 11, 2437-2455.
53. Drozdov, A. N.; Grossfield, A.; Pappu, R. V., J Am Chem Soc 2004, 126, 2574-2581.
54. Law, P. H.; Daggett, V., Prot Eng, Des Sel 2010, 23, 27-33.
55. Woutersen, S.; Hamm, P., J Phys Chem B 2000, 104, 11316-11320.
56. Oh, K.-I.; Lee, K.-K.; Park, E.-U.; Yoo, D.-G.; Hwang, G.-S.; Cho, M., Chirality 2010, 22, E186-E201.
57. Toal, S.; Amidi, O.; Schweitzer-Stenner, R., J Am Chem Soc 2011, 133, 12728-12739.
58. Krimm, S.; Venkatachalam, C. M., Proc Natl Acad Sci USA 1971, 68, 2468-2471.
59. Venkatachalam, C. M.; Krimm, S., In Conformation of Biological Molecules and Polymers;, Bergmann, E. D.; Pullman, B., Eds.; Academic Press: New York, 1973; pp 141-154
60. Rossky, P. J.; Karplus, M., J Am Chem Soc 1979, 101, 1913-1937.
61. Hagler, A. T.; Osguthorpe, D. J.; Robson, B., Science 1980, 208, 599-601.
62. Mezei, M.; Mehrota, P. K.; Beveridge, D. L., J Am Chem Soc 1985, 107, 2239-2245.
63. Pettitt, B. M.; Karplus, M., Chem Phys Lett 1985, 121, 194-201.
64. Anderson, A. G.; Hermans, J., Proteins 1988, 3, 262-265.
65. Tobias, D. J.; Brooks III, C. L., J Phys Chem 1992, 96, 3864-3870.
66. Smith, P. E., J Chem Phys 1999, 111, 5568-5579.
67. Seabra, G. de M.; Walker, R. C.; Elstner, M.; Case, D. A.; Roitberg, A. E., Phys Chem A 2007, 111, 5655-5664.
68. Ishizuka, R.; Huber, G. A.; McCammon, J. A., J Phys Chem Lett 2010, 1, 2279-2283.
69. Cruz, V.; Ramos, J.; Martinez-Salazar, J., J Phys Chem B 2011, 115, 4880-4886.
70. Gaigeot, M.-P., J Phys Chem B 2009, 113, 10059-10062.
71. Sreerama, N.; Woody, R.W., Proteins 1999, 36, 400-406.
72. Garcia, A. E., Polymer 2004, 45, 669-676.
73. Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D., Proteins 2004, 55, 502-507.
74. Kentsis, A.; Mezei, M.; Gindin, T.; Osman, R., Proteins 2004, 55, 493-501.
75. Kentsis, A.; Mezei, M.; Osman, R., Proteins 2005, 61, 769-776.
76. Sorin, E. J.; Rhee, Y. M.; Shirts, M. R.; Pande, V. S., J Mol Biol 2006, 356, 248-256.
77. Czapiewski, D.; Zielkiewicz, J., J Phys Chem B 2010, 114, 4536-4550.
78. Jalkanen K. J.; Suhai, S., Chem Phys 1996, 208, 81-116.
79. Han, W.-G.; Jalkanen, K. J.; Elstner, M.; Suhai, S., J Phys Chem B 1998, 102, 2587-2602.
80. Poon, C.-D.; Samulski, E.T.; Weise, C. F.; Weisshaar, J. C., J Am Chem Soc 2000, 122, 5642-5643.
81. Weise, C. F.; Weisshaar, J. C., J Phys Chem B 2003, 107, 3265-3277.
82. Jalkanen, K. J.; Degtyarenko, I. M.; Nieminen, R. M.; Cao, X.; Nafie, L. A.; Zhu, F.; Barron, L. D., Theor Chem Acc 2008, 119, 191-210.
83. Mirkin N. G.; Krimm, S., J Phys Chem B 2008, 112, 15267-15268.
84. Avbelj, F.; Baldwin, R. L., Proc Natl Acad Sci USA 2003, 100, 5742-5747.
85. Gaussian 09, Revision A.2, Frisch, M. J., et al., Gaussian, Wallingford CT, 2009.
86. Anthony, J.; Grimme, S., Phys Chem Chem Phys 2006, 8, 5287-5293.
87. Bouteiller, Y.; Poully, J. C.; Desfrançois, C.; Grégoire, G., J Phys Chem A 2009, 113, 6301-6307.
88. Drake, A. F.; Siligardi, G.; Gibbons, W. A., Biophys Chem 1988, 31, 143-146.
89. Eker, F.; Griebenow, K.; Schweitzer-Stenner, R., J Am Chem Soc 2003, 125, 8178-8185.
90. Chen, K.; Liu, Z.; Kallenbach, N. R., Proc Natl Acad Sci USA 2004, 101, 15352-15357.
91. He, L.; Navarro, A. E.; Shi, Z.; Kallenbach, N. R., J Am Chem Soc 2012, 134, 1571-1576.
92. Nicholls, A., J Comput Aided Mol Des 2011, DOI 10.1007/s10822-011-9520-3.