Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon

Journal of Biomolecular Structure and Dynamics

Volumn 21, Issue 4, 2004, Pages 555-565

  Shepherd, Craig M ^a   Spoel, David van der ^b   Vogel, Hans J ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Salt bridges; helix stabilization; helix

Indexed keywords

CALDESMON; GLUTAMIC ACID; MUSCLE PROTEIN; PEPTIDE; REPETITIVE PEPTIDE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID REPEAT; AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; ELECTRICITY; MOLECULAR DYNAMICS; PI HELIX; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STABILITY; PROTEIN STRUCTURE; SALT BRIDGE; SIMULATION; SMOOTH MUSCLE;

INSERTION SEQUENCES;

EID: 1642433348     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2004.10506948     Document Type: Article

References (35)

1. Wang, C. L., Chalovich, J. M., Graceffa, P., Lu, R. C., Mabuchi, K., and Stafford, W. F., 1991. J. Biol. Chem., 266:13958–13963.
2. Marston, S. B., Moody, C., and Smith, C., 1984. Biochem. Soc. Trans., 12:945–948.
3. Ngai, P. K., and Walsh, M. P., 1984. J. Biol. Chem., 259:13656–13659.
4. Lash, J. A., Sellers, J. R., and Hathaway, D. R., 1986. J. Biol. Chem., 261:16155–16160.
5. Hemric, M. E., and Chalovich, J. M., 1988. J. Biol. Chem., 263:1878–1885.
6. Ikebe, M., and Reardon, S., 1988. J. Biol. Chem., 263:3055–3058.
7. Lehman, W., Vibert, P., and Craig, R., 1997. J. Mol. Biol., 274:310–317.
8. Zhou, N., Yuan, T., Mak, A. S., and Vogel, H. J., 1997. Biochemistry, 36:2817–2825.
9. Mabuchi, K., and Wang, C. L., 1991. J. Muscle Res. Cell Motil., 12:145–151.
10. Bryan, J., Imai, M., Lee, R., Moore, P., Cook, R. G., and Lin, W. G., 1989. J. Biol. Chem., 264:13873–13879.
11. Hayashi, K., Kanda, K., Kimizuka, F., Kato, I., and Sobue, K., 1989. Biochem. Biophys. Res. Commun., 164:503–511.
12. Wang, E., and Wang, C. L., 1996. Arch. Biochem. Biophys., 329:156–162.
13. Babu, Y. S., Sack, J. S., Greenhough, T. J., Bugg, C. E., Means, A. R., and Cook, W. J., 1985. Nature, 315:37–40.
14. Berendsen, H. J. C., van derSpoel, D., and vanDrunen, R., 1995. Comp. Phys. Comm., 91:43–56.
15. vanGunsteren, W. F., and Berendsen, H. J. C., 1987. GROMOS-87 Manual Nijenborgh 4, 9747 AG Groningen, The Netherlands:Biomos B.V.
16. VanBuuren, A. R., Marrink, S. J., and Berendsen, H. J. C., 1993. J. Phys. Chem., 97:9206–9212.
17. Darden, T., York, D., and Pedersen, L., 1993. J. Chem. Phys., 98:10089–10092.
18. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G., 1995. J. Chem. Phys., 103:8577–8593.
19. Weber, W., Hünenberger, P. H., and McCammon, J. A., 2000. J. Phys. Chem. B, 104:3668–3675.
20. Berendsen, H. J. C., Postma, J. P. M., vanGunsteren, W. F., and Hermans, J., 1981. Intermolecular Forces Edited by:Pullman, B. D., 331–342. Dordrecht, The Netherlands:Reidel Publishing Company.
21. Berendsen, H. J. C., Postma, J. P. M., DiNola, A., and Haak, J. R., 1984. J. Chem. Phys., 81:3684–3690.
22. Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M., 1997. J. Comp. Chem., 18:1463–1472.
23. Young, W. S., and Brooks, C. L., III. 1996. J. Mol. Biol., 259:560–572.
24. Lee, K. H., Benson, D. R., and Kuczera, K., 2000. Biochemistry, 39:13737–13747.
25. Sundaralingam, M., and Sekharudu, Y. C., 1989. Science, 244:1333–1337.
26. Olson, C. A., Spek, E. J., Shi, Z., Vologodskii, A., and Kallenbach, N. R., 2001. Proteins, 44:123–132.
27. Smith, J. S., and Scholtz, J. M., 1998. Biochemistry, 37:33–40.
28. Huyghues-Despointes, B. M., and Baldwin, R. L., 1997. Biochemistry, 36:1965–1970.
29. Marqusee, S., Robbins, V. H., and Baldwin, R. L., 1989. Proc. Natl. Acad. Sci. USA, 86:5286–5290.
30. Marqusee, S., and Baldwin, R. L., 1987. Proc. Natl. Acad. Sci. USA, 84:8898–8902.
31. Poland, D., and Scheraga, H. A., 1970. Theory of Helix-Coil Transitions in Biopolymers New York, N.Y.:Academic Press.
32. Armen, R., Alonso, D. O., and Daggett, V., 2003. Protein Sci., 12:1145–1157.
33. Duneau, J. P., Crouzy, S., Chapron, Y., and Genest, M., 1999. Theor. Chem. Acc., 101:87–91.
34. Feig, M., MacKerell, A. D., and Brooks, C. L., III. 2003. J. Phys. Chem. B, 107 (2831):2836
35. Kabsch, W., and Sander, C., Biopolymers, 222577–2637. 362817–2825