Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine
Hannes H. Loeffler
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorChristoph A. Sotriffer
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorRudolf H. Winger
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorKlaus R. Liedl
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorCorresponding Author
Bernd M. Rode
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, AustriaSearch for more papers by this authorHannes H. Loeffler
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorChristoph A. Sotriffer
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorRudolf H. Winger
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorKlaus R. Liedl
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Search for more papers by this authorCorresponding Author
Bernd M. Rode
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
Department of Theoretical Chemistry, Institute of General, Inorganic, and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, AustriaSearch for more papers by this authorAbstract
The relative free energies of hydration of the dipeptides glycylalanine and alanyl-glycine in their naturally occurring form have been calculated both for the zwitterionic and protonated species. Emphasis was laid on comparisons between the conventional cutoff method and the Particle Mesh Ewald method to account for possible differences in electrostatic contributions to the free energy. Furthermore, the convergence behavior of the total free energy and its individual contributions were examined. The results, obtained by means of the thermodynamic integration technique as implemented in the free energy module of the AMBER program suite, suggest that in aqueous solution glycylalanine is more stable than alanylglycine by 2.7 kcal/mol in the zwitterionic form and by 3.5 kcal/mol in the protonated form. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 846–860, 2001
References
- 1Creighton, T. Proteins; Freeman and Company: New York, 1993, 2nd ed.
- 2Rode, B. M. Peptides 1999, 20, 773.
- 3 These molecules are the blocked amino acid residues Ac-Ala-NHMe and Ac-Gly-NHMe, respectively. Ac denotes the N-terminal blocking group, COCH3, Ala, and Gly are the alanine and glycine residues, and NHMe is the C-terminal blocking group, NHCH3.
- 4Brooks, C. L., III; Case, D. A. Chem Rev 1993, 93, 2487.
- 5Pettitt, B. M.; Karplus, M. Chem Phys Lett 1985, 121, 194.
- 6Lau, W. F.; Pettitt, B. M. Biopolymers 1987, 26, 1817.
- 7Pettitt, B. M.; Karplus, M. J Phys Chem 1988, 92, 3994.
- 8Mezei, M.; Mehrotra, P. K.; Beveridge, D. L. J Am Chem Soc 1985, 107, 2239.
- 9Kumar, S.; Payne, P. W.; Vásquez, M. J Comput Chem 1996, 17, 1269.
- 10Tobias, D. J.; Brooks, C. L., III. J Am Chem Soc 1992, 96, 3864.
- 11Straatsma, T. P.; McCammon, J. A. J Chem Phys 1994, 101, 5032.
- 12Gilson, M. K.; McCammon, J. A.; Madura, J. D. J Comput Chem 1995, 17, 1081.
- 13Wan, S. Z.; Wang, C. X.; Xiang, Z. X.; Shi, Y. Y. J Comput Chem 1997, 18, 1440.
- 14Smart, J. L.; Marrone, T. J.; McCammon, J. A. J Comput Chem 1997, 18, 1750.
- 15Head-Gordon, T.; Head-Gordon, M.; Frisch, M. J.; Brooks, C. L., III.; Pople, J. A. J Am Chem Soc 1991, 113, 5959.
- 16Gould, I. R.; Kollman, P. A. J Phys Chem 1992, 96, 9255.
- 17Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. J Am Chem Soc 1997, 119, 5908.
- 18Shang, H. S.; Head-Gordon, T. J Am Chem Soc 1994, 116, 1528.
- 19Gould, I. R.; Cornell, W. D.; Hillier, L. H. J Am Chem Soc 1994, 116, 9250.
- 20Cortis, C. M.; Langlois, J.-M.; Beachy, M. D.; Priesner, R. A. J Chem Phys 1996, 105, 5472.
- 21Schwendinger, M. G.; Rode, B. M. Inorg Chimica Acta 1991, 186, 247.
- 22McQuarrie, D. A. Statistical Mechanics; Harper & Row: New York, 1976.
- 23Reynolds, C. A.; King, P. M.; Richards, W. G. Mol Phys 1991, 76, 251.
- 24Beveridge, D. L.; DiCapua, F. M. Annu Rev Biophys Biophys Chem 1989, 18, 431.
- 25Straatsma, T. P.; McCammon, J. A. Annu Rev Phys Chem 1992, 43, 407.
- 26Kollman, P. A. Chem Rev 1993, 93, 2395.
- 27Kollman, P. A. Acc Chem Res 1996, 29, 461.
- 28Meirovitch, H. In Reviews in Computational Chemistry; K. B. Lipkowitz; D. B. Boyd, Eds.; VCH Publishers: New York, 1998, p. 1, vol. 12.
10.1002/9780470125892.ch1 Google Scholar
- 29Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J Chem Phys 1953, 21, 1087.
- 30Jorgensen, W. L. J Phys Chem 1983, 87, 5304.
- 31Jorgensen, W. L.; Ravimohan, C. J Chem Phys 1985, 83, 3050.
- 32Leach, A. R. Molecular Modelling, Principles and Applications; Addison Wesley Longman Limited: England, 1996.
- 33van Gunsteren, W. F.; Berendsen, H. J. C. Angew Chem 1990, 102, 1020.
- 34Helms, V.; Wade, R. C. J Am Chem Soc 1998, 120, 2710.
- 35Kirkwood, J. G. J Chem Phys 1935, 3, 300.
- 36Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, L. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
- 37Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, R. A. J Phys Chem 1993, 97, 10269.
- 38Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. GAUSSIAN 94; Gaussian, Inc.: Pittsburgh, PA, 1994.
- 39Cornell, W. D.; Cieplak, R.; Bayly, C. I.; Kollman, P. A. J Am Chem Soc 1993, 115, 9620.
- 40Cieplak, R.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J Comput Chem 1995, 16, 1357.
- 41Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comp Phys Commun 1995, 91, 1.
- 42Case, D. A.; Pearlman, D. A.; Caldwell, J. W.; Cheatham, T. E., III.; Ross, W. S.; Simmerling, C. L.; Darden, T.; Merz, K. M., Jr.; Stanton, R. V.; Cheng, A. L.; Vincent, J. J.; Crowley, M.; Ferguson, D. M.; Radmer, R. J.; Seibel, G. L.; Singh, U. C.; Weiner, P. K.; Kollman, P. A. Amber 5; University of California: San Francisco, 1997.
- 43Straatsnia, T. P.; McCammon, J. A. J Chem Phys 1991, 95, 1175.
- 44Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
- 45Alder, B. J.; Frankel, S. P.; Lewinson, V. A. J Chem Phys 1955, 23, 417.
- 46Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J Phys Chem 1984, 81, 3684.
- 47Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
- 48Tobias, D. J.; Brooks, C. L., III. J Chem Phys 1988, 89, 5115.
- 49Chipot, C.; Kollman, P. A.; Pearlman, D. A. J Comput Chem 1996, 17, 1112.
- 50Pearlman, D. A.; Kollman, P. A. J Chem Phys 1991, 94, 4532.
- 51Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. J Am Chem Soc 1992, 114, 6798.
- 52Pearlman, D. A. J Chem Phys 1993, 98, 8946.
- 53Levy, R. M.; Gallicchio, E. Annu Rev Phys Chem 1998, 49, 531.
- 54Ewald, R. Ann Phys 1921, 64, 253.
- 55Darden, T.; York, D.; Pedersen, L. J Chem Phys 1993, 98, 10089.
- 56Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577.
- 57Simmerling, C.; Fox, T.; Kollman, P. A. J Am Chem Soc 1998, 120, 5771.
- 58Singh, U. C.; Brown, F. B.; Bash, P. A.; Kollman, P. A. J Am Chem Soc 1987, 109, 1607.
- 59Bash, P. A.; Singh, U. C.; Brown, F. B.; Langridge, R.; Kollman, P. A. Science 1987, 235, 574.
- 60Harris, D.; Loew, G. J Comput Chem 1996, 17, 273.
- 61Fox, T.; Scanlan, T. S.; Kollman, P. A. J Am Chem Soc 1997, 119, 11571.
- 62Mark, A. E.; van Gunsteren, W. F. J Mol Biol 1994, 240, 167.
- 63Smith, P. E.; van Gunsteren, W. F. J Phys Chem 1994, 98, 13735.
- 64Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M. Science 1989, 244, 1069.
- 65Tidor, B.; Karplus, M. Biochemistry 1991, 30, 3217.
- 66Boresch, S.; Archontis, G.; Karplus, M. Proteins Struct Funct Genet 1994, 20, 25.
- 67Boresch, S.; Karplus, M. J Mol Biol 1995, 254, 801.
- 68Brady, G. P.; Szabo, A.; Sharp, K. A. J Mol Biol 1996, 263, 123.
- 69Morgantini, P.-Y.; Kollman, P. A. J Am Chem Soc 1995, 117, 6057.
