Effects of solute-solvent proton exchange on polypeptide chain dynamics: A constant-pH molecular dynamics study

Journal of Physical Chemistry B

Volumn 109, Issue 28, 2005, Pages 13777-13784

  Dlugosz M ^a   Antosiewicz, J M ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR DYNAMICS SIMULATIONS; PENTAPEPTIDES; PROTON EXCHANGE; PROTONATION;

COMPUTER SIMULATION; CONFORMATIONS; ION EXCHANGE; MOLECULAR STRUCTURE; PH EFFECTS; POLYPEPTIDES; PROBABILITY; SOLVENTS;

MOLECULAR DYNAMICS;

ASPARTIC ACID; LYSINE; PEPTIDE; PROTON; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; HYDROGEN BOND; PH; PROTEIN CONFORMATION; STATISTICAL MODEL; THERMODYNAMICS; TIME;

ASPARTIC ACID; COMPUTER SIMULATION; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; LYSINE; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PEPTIDES; PROTEIN CONFORMATION; PROTONS; SOLVENTS; THERMODYNAMICS; TIME FACTORS;

EID: 23144435711     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0505779     Document Type: Article

References (48)

1. Stryer, L. Biochemistry, 4th ed.; W. H. Freeman and Co.: New York, 1995.
2. Pace, C. N.; Laurents, D. V.; Thomson, J. A. Biochemistry 1990, 29, 2564-2572.
3. Pace, C. N.; Laurents, D. V.; Erickson, R. E. Biochemistry 1992, 31, 2728-2734.
4. Yang, A.; Honig, B. J. Mol. Biol. 1993, 231, 459-474.
5. Yang, A.; Honig, B. J. Mol. Biol. 1994, 257, 602-614.
6. Swint-Kruse, L.; Robertson, A. D. Biochemistry 1996, 35, 171-180.
7. Tollinger, M.; Crowhurst, K. A.; Kay, L. E.; Forman-Kay, J. D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 4545-4550.
8. Pletcher, C. H.; Bouhoutsos-Brown, E. F.; Bryant, R. G.; Nelsestuen, G. L. Biochemistry 1981, 20, 6149-6155.
9. Anderson, D. E.; Becktel, W. J.; Dahlquist, F. W. Biochemistry 1990, 29, 2403-2408.
10. Ripoll, D. R.; Vorobjev, Y. N.; Liwo, A.; Vila, J. A.; Scheraga, H. A. J. Mol. Biol. 1996, 264, 770-783.
11. Horng, J.; Cho, J.; Raleigh, D. P. J. Mol. Biol. 205, 345, 163-173.
12. Abbruzzetti, S.; Vlappiani, C.; Small, J. R.; Libertini, L. J.; Small, E. W. Biophys. J. 2000, 79, 2714-2731.
13. McCammon, J. A.; Harvey, S. C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, U. K., 1987.
14. Tuckerman, M. E.; Laasonen, K.; Sprik, M.; Parrinello, M. J. Chem. Phys. 1995, 103, 150-161.
15. Hammes-Schiffer, S.; Tully, J. C. J. Chem. Phys. 1994, 101, 4657-4667.
16. Bała, P.; Grochowski, P.; Lesyng, B.; McCammon, J. A. J. Phys. Chem. 1996, 100, 2535-2545.
17. Billeter, S. R.; van Gunsteren, W. F. J. Phys. Chem. A 2000, 104, 3276-3286.
18. Lill, M. A.; Helms, V. J. Chem. Phys. 2001, 115, 7993-8005.
19. Baptista, A. M.; Martel, P. J.; Petersen, S. B. Proteins: Struct., Funct., Genet. 1997, 27, 523-544.
20. Börjesson, U.; Hünenberger, P. H. J. Chem. Phys. 2001, 114, 9706-9719.
21. Lee, M. S.; Salsbury, F. R.; Brooks, C. L. Proteins: Struct., Funct., Bioinf. 2004, 56, 738-752.
22. Börjesson, U.; Hünenberger, P. H. J. Phys. Chem. B 2004, 108, 13551-13559.
23. Bürgi, R.; Kollman, P. A.; van Gunsteren, W. F. Proteins: Struct., Funct., Genet. 2002, 47, 469-480.
24. Baptista, A. M.; Teixeira, V. H.; Soares, C. M. J. Chem. Phys. 2002, 117, 4184-4200.
25. Walczak, A. M.; Antosiewicz, J. M. Phys. Rev. E 2002, 66, 051911.
26. Dlugosz, M.; Antosiewicz, J. M.; Robertson, A. D. Phys. Rev. E 2004, 69, 021915.
27. Dlugosz, M.; Antosiewicz, J. M. Chem. Phys. 2004, 502, 161-170.
28. Mongan, J.; Case, D. A.; McCammon, J. A. J. Comput. Chem. 2004, 25, 2038-2048.
29. Antosiewicz, J.; Briggs, J. M.; Elcock, A. H.; Gilson, M. K.; McCammon, J. A. J. Comput. Chem. 1996, 17, 1633-1644.
30. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
31. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473-486.
32. Bashford, D. An object-oriented programming suite for electrostatic effects in biological molecules. In Scientific Computing in Object-Oriented Parallel Environments; Ishikawa, Y., Oldehoeft, R. R., Reynolds, J. V. W., Tholburn, M., Eds.; Lecture Notes in Computer Science 1343; Springer; Berlin, Germany, 1997, p 233.
33. Schaefer, M.; Karplus, M. J. Phys. Chem. 1996, 100, 1578.
34. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684.
35. MacKerell, A. D., Jr.; Bashford, D.; Bellott, R. L.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
36. Długosz, M.; Antosiewicz, J. M. J. Phys.: Condens. Matter 2005, 17, S1607-S1616.
37. Schmidt, G. R.; Brickmann, J. Solid State Ionics 1996, 77, 3-9.
38. Hu, -P. W.; You, -R. M.; Yen, -Y, S.; Hung, -T. F.; Chou, -H. P.; Chou, -T. P. Chem. Phys. Lett. 2003, 370, 139-146.
39. Rini, M.; Magnes, B.-Z.; Pines, E.; Nibbering, E. T. J. Science 2003, 301, 349-352.
40. Keiding, S. R.; Madsen, D.; Larsen, J.; Jensen, S. K.; Thøgersen, J. Chem. Phys. Lett. 2004, 390, 94-97.
41. Auffinger, P.; Louise-May, S.; Westhof, E. J. Am. Chem. Soc. 1995, 117, 6720-6726.
42. Kenney, J. F.; Keeping, E. S. Moving Averages. In Mathematics of Statistics, 3rd ed.; Van Nostrand: Princeton, NJ, 1962; Part 1, pp 221-223.
43. Xie, X. S.; Lu, H. P. J. Biol. Chem. 1999, 274, 15967-15970.
44. Brooks, C. L., III; Karplus, M.; Pettit, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics; Advances in Chemical Physics 71; John Wiley and Sons: New York, 1988.
45. Bieri, O.; Kiefhaber, T. Biol. Chem. 1999, 380, 923-929.
46. Spörlein, S.; Carstens, H.; Satzger, H.; Renner, C.; Berrendt, R.; Moroder, L.; Tavan, P.; Zinth, W.; Wachtveitl, J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7998-8002.
47. Hummer, G.; Kevrekidis, G. I. J. Chem. Phys. 2003, 118, 10762-10773.
48. Humphreys, W.; Dalke, A.; Schulten, K. VMD-Visual molecular dynamics. J. Mol. Graphics 1996, 44, 33-38.