CXC and CC chemokines form mixed heterodimers: Association free energies from molecular dynamics simulations and experimental correlations

Journal of Biological Chemistry

Volumn 283, Issue 35, 2008, Pages 24155-24166

  Nesmelova, Irina V ^a   Sham, Yuk ^b   Gao, Jiali ^a,c   Mayo, Kevin H ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROLIFERATION; DYNAMICS; FREE ENERGY; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; SECURITY OF DATA;

BIOLOGICAL IMPLICATIONS; BIOLOGICAL PROCESSES; CHEMOKINE; CHEMOKINES; EXPERIMENTAL CORRELATIONS; HETERO DIMERS; HETERODIMER FORMATIONS; IN-SITU; MOLECULAR DYNAMICS SIMULATIONS; PROLIFERATION ACTIVITIES; RELATIVE FREE ENERGIES; STRUCTURAL HOMOLOGIES;

PEPTIDES;

ALPHA CHEMOKINE; BETA CHEMOKINE; CXCL1 CHEMOKINE; CXCL4 CHEMOKINE; CXCL7 CHEMOKINE; HETERODIMER; HOMODIMER; INTERLEUKIN 8; MONOCYTE CHEMOTACTIC PROTEIN 1; MONOCYTE CHEMOTACTIC PROTEIN 2; RANTES; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SIMULATION; ANIMAL; CHEMISTRY; COMPUTER SIMULATION; DIMERIZATION; ELECTRICITY; HUMAN; THERMODYNAMICS;

ANIMALS; CHEMOKINES, CC; CHEMOKINES, CXC; COMPUTER SIMULATION; DIMERIZATION; ELECTROSTATICS; HUMANS; THERMODYNAMICS;

EID: 53049103896     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M803308200     Document Type: Article

References (64)

1. Baggiolini, M. (1998) Nature 392, 565-568
2. Mackay, C. R. (2001) Nat. Immunol. 2, 95-101
3. Youn, B. S., Mantel, C., and Broxmeyer, H. E. (2000) Immunol. Rev. 177, 150-174
4. Belperio, J. A., Keane, M. P., Arenberg, D. A., Addison, C. L., Ehlert, J. E., Burdick, M. D., and Strieter, R. M. (2000) J. Leukocyte Biol. 68, 1-8
5. Koch, A. E., Polverini, P. J., Kunkel, S. L., Harlow, L. A., DiPietro, L. A., Elner, V. M., Elner, S. G., and Strieter, R. M. (1992) Science 258, 1798-1801
6. Zlotnik, A., and Yoshie, O. (2000) Immunity 12, 121-127
7. Clore, G. M., and Gronenborn, A. M. (1995) FASEB J. 9, 57-62
8. Clark-Lewis, I., Kim, K. S., Rajarathnam, K., Gong, J. H., Dewald, B., Moser, B., Baggiolini, M., and Sykes, B. D. (1995) J. Leukocyte Biol. 57, 703-711
9. Mayo, K. H., and Chen, M. J. (1989) Biochemistry 28, 9469-9478
10. St Charles, R., Walz, D. A., and Edwards, B. F. (1989) J. Biol. Chem. 264, 2092-2099
11. Clore, G. M., Appella, E., Yamada, M., Matsushima, K., and Gronenborn, A. M. (1990) Biochemistry 29, 1689-1696
12. Handel, T. M., and Domaille, P. J. (1996) Biochemistry 35, 6569-6584
13. Yang, Y., Mayo, K. H., Daly, T. J., Barry, J. K., and La Rosa, G. J. (1994) J. Biol. Chem. 269, 20110-20118
14. Czaplewski, L. G., McKeating, J., Craven, C. J., Higgins, L. D., Appay, V., Brown, A., Dudgeon, T., Howard, L. A., Meyers, T., Owen, J., Palan, S. R., Tan, P., Wilson, G., Woods, N. R., Heyworth, C. M., Lord, B. I., Brotherton, D., Christison, R., Craig, S., Cribbes, S., Edwards, R. M., Evans, S. J., Gilbert, R., Morgan, P., Randle, E., Schofield, N., Varley, P. G., Fisher, J., Waltho, J. P., and Hunter, M. G. (1999) J. Biol. Chem. 274, 16077-16084
15. Mayo, K. H., Roongta, V., Ilyina, E., Milius, R., Barker, S., Quinlan, C., La Rosa, G., and Daly, T. J. (1995) Biochemistry 34, 11399-11409
16. Nesmelova, I. V., Sham, Y., Dudek, A. Z., van Eijk, L. I., Wu, G., Slungaard, A., Mortari, F., Griffioen, A. W., and Mayo, K. H. (2005) J. Biol. Chem. 280, 4948-4958
17. Dudek, A. Z., Nesmelova, I., Mayo, K., Verfaillie, C. M., Pitchford, S., and Slungaard, A. (2003) Blood 101, 4687-4694
18. Guan, E., Wang, J., and Norcross, M. A. (2001) J. Biol. Chem. 276, 12404-12409
19. von Hundelshausen, P., Koenen, R. R., Sack, M., Mause, S. F., Adriaens, W., Proudfoot, A. E., Hackeng, T. M., and Weber, C. (2005) Blood 105, 924-930
20. Paoletti, S., Petkovic, V., Sebastiani, S., Danelon, M. G., Uguccioni, M., and Gerber, B. O. (2005) Blood 105, 3405-3412
21. Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E., III (2000) Acc. Chem. Res. 33, 889-897
22. Srinivasan, J., Miller, J., Kollman, P. A., and Case, D. A. (1998) J. Biomol. Struct. Dyn. 16, 671-682
23. Wang, W., and Kollman, P. A. (2000) J. Mol. Biol. 303, 567-582
24. Gilson, M. K., Given, J. A., Bush, B. L., and McCammon, J. A. (1997) Biophys. J. 72, 1047-1069
25. Warshel, A. (2002) Acc. Chem. Res. 35, 385-395
26. Warshel, A. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 425-443
27. Lazaridis, T., and Karplus, M. (2003) Biophys. Chem. 100, 367-395
28. Xu, Y., and Wang, R. (2006) Proteins 64, 1058-1068
29. Gohlke, H., Kiel, C., and Case, D. A. (2003) J. Mol. Biol. 330, 891-913
30. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) J. Mol. Biol. 112, 535-542
31. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. (1983) J. Comput. Chem. 4, 187-217
32. MacKerell, A. D., Jr., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., Evanseck, J., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph, 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., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) J. Phys. Chem. 102, 3586-3616
33. Darden, T. A., York, D. M., and Pedersen, L. G. (1993) J. Chem. Phys. 98, 10089-10092
34. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) J. Comp. Physics 23, 327-341
35. Case, D. A. (1994) Curr. Opin. Struct. Biol. 4, 285-290
36. Sitkoff, D., Sharp, K. A., and Honig, B. (1994) J. Phys. Chem. 98, 1978-1988
37. Grasberger, B. L., Gronenborn, A. M., and Clore, G. M. (1993) J. Mol. Biol. 230, 364-372
38. Ye, J., Mayer, K. L., and Stone, M. J. (1999) J. Biomol. NMR 15, 115-124
39. Ye, J., Mayer, K. L., Mayer, M. R., and Stone, M. J. (2001) Biochemistry 40, 7820-7831
40. LiWang, A. C., Cao, J. J., Zheng, H., Lu, Z., Peiper, S. C., and LiWang, P. J. (1999) Biochemistry 38, 442-453
41. Cornell, W., Abseher, R., Nilges, M., and Case, D. A. (2001) J. Mol. Graph. Model. 19, 136-145
42. Shaw, J. P., Johnson, Z., Borlat, F., Zwahlen, C., Kungl, A., Roulin, K., Harrenga, A., Wells, T. N., and Proudfoot, A. E. (2004) Structure (Lond.) 12, 2081-2093
43. Crown, S. E., Yu, Y., Sweeney, M. D., Leary, J. A., and Handel, T. M. (2006) J. Biol. Chem. 281, 25438-25446
44. Beveridge, D. L., and DiCapua, F. M. (1989) Annu. Rev. Biophys. Biophys. Chem. 18, 431-492
45. Straatsma, T. P., and McCammon, J. A. (1992) Annu. Rev. Phys. Chem. 43, 407-435
46. Aqvist, J., Medina, C., and Samuelsson, J. E. (1994) Protein Eng. 7, 385-391
47. Sham, Y. Y., Chu, Z. T., Tao, H., and Warshel, A. (2000) Proteins 39, 393-407
48. Swanson, J. M., Henchman, R. H., and McCammon, J. A. (2004) Biophys. J. 86, 67-74
49. Luo, H., and Sharp, K. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 10399-10404
50. Villa, J., Strajbl, M., Glennon, T. M., Sham, Y. Y., Chu, Z. T., and Warshel, A. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 11899-11904
51. Karlsson, M., Martensson, L. G., Karlsson, C., and Carlsson, U. (2005) Biochemistry 44, 3487-3493
52. Weber, C., and Koenen, R. R. (2006) Trends Immunol. 27, 268-273
53. Gouwy, M., Struyf, S., Catusse, J., Proost, P., and Van Damme, J. (2004) J. Leukocyte Biol. 76, 185-194
54. Broxmeyer, H. E., Sherry, B., Cooper, S., Lu, L., Maze, R., Beckmann, M. P., Cerami, A., and Ralph, P. (1993) J. Immunol. 150, 3448-3458
55. Gouwy, M., Struyf, S., Mahieu, F., Put, W., Proost, P., and Van Damme, J. (2002) Mol. Pharmacol. 62, 173-180
56. Chen, M. J., and Mayo, K. H. (1991) Biochemistry 30, 6402-6411
57. Mayo, K. H. (1991) Biochemistry 30, 925-934
58. Burrows, S. D., Doyle, M. L., Murphy, K. P., Franklin, S. G., White, J. R., Brooks, I., McNulty, D. E., Scott, M. O., Knutson, J. R., Porter, D., Young, P. R., and Hensley, P. (1994) Biochemistry 33, 12741-12745
59. Paolini, J. F., Willard, D., Consler, T., Luther, M., and Krangel, M. S. (1994) J. Immunol. 153, 2704-2717
60. Lowman, H. B., Fairbrother, W. J., Slagle, P. H., Kabakoff, R., Liu, J., Shire, S., and Hebert, C. A. (1997) Protein Sci. 6, 598-608
61. Schnitzel, W., Monschein, U., and Besemer, J. (1994) J. Leukocyte Biol. 55, 763-770
62. Rajarathnam, K., Kay, C. M., Dewald, B., Wolf, M., Baggiolini, M., Clark-Lewis, I., and Sykes, B. D. (1997) J. Biol. Chem. 272, 1725-1729
63. Hanzawa, H., Haruyama, H., Konishi, K., Watanabe, K., and Tsurufuji, S. (1997) J. Biochem. (Tokyo) 121, 835-841
64. Skelton, N. J., Aspiras, F., Ogez, J., and Schall, T. J. (1995) Biochemistry 34, 5329-5342