Molecular dynamics simulations of human cystatin c and its l68q varient to investigate the domain swapping mechanism

Journal of Biomolecular Structure and Dynamics

Volumn 25, Issue 2, 2007, Pages 135-144

  Liu, Hsuan Liang ^a,b   Lin, Yuan Min ^a   Zhao, Jian Hua ^a   Hsieh, Man Ching ^b   Lin, Hsin Yi ^b   Huang, Chih Hung ^b   Fang, Hsu Wei ^b   Ho, Yih ^c   Chen, Wen Yih ^d  

^a Department of Chemical Engineering and Biotechnology ^*  (Taiwan)

^b University of Technology   (Taiwan)

^c TAIPEI MEDICAL UNIVERSITY   (Taiwan)

^d NATIONAL CENTRAL UNIVERSITY   (Taiwan)

Author keywords

Alzheimer's disease; Domain swapping; Hereditary cystatin C amyloid angiopathy; Human cystatin C; Hydrophobic core; Molecular dynamics simulation; Zip up

Indexed keywords

AMYLOID PROTEIN; CYSTATIN C; DIMER; MONOMER;

ACIDITY; ALZHEIMER DISEASE; ARTICLE; BETA SHEET; HYDROPHOBICITY; MOLECULAR DYNAMICS; PH; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE; PROTEIN VARIANT; SIMULATION; TEMPERATURE DEPENDENCE; VASCULAR AMYLOIDOSIS; WILD TYPE;

EID: 34548848283     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2007.10507162     Document Type: Article

References (35)

1. Grubb, A., 2000. Adv Clin Chem, 35:63–99.
2. Shlipak, M. G., Katz, R., Fried, L. F., Jenny, N. S., Stehman-Breen, C. O., Newman, A. B., Siscovick, D., and et al. 2005. J Am Coll Cardiol, 45:268–271.
3. Carrell, R. W., and Lomas, D. A., 1997. Lancet, 350:134–138.
4. Olafsson, I., and Grubb, A., 2000. Amyloid, 7:70–79.
5. Abrahamson, M., and Grubb, A., 1994. Proc Natl Acad Sci USA, 91:1416–1420.
6. Janowski, R., Abrahamson, M., Grubb, A., and Jaskólski, M., 2004. J Mol Biol, 341:151–160.
7. Ekiel, I., Abrahamson, M., Fulton, D. B., Lindahl, P., Storer, A. C., Levadoux, W., Lafrance, M., and et al. 1997. J Mol Biol, 271:266–277.
8. Kozak, M., Jankowska, E., Janowski, R., Grzonka, Z., Grubb, A., Fernandez, M. A., Abrahamson, M., and Jaskólski, M., 1999. Acta Crystallogr D Biol Crystallogr, 55:1939–1942.
9. Bode, W., Engh, R., Musil, D., Thiele, U., Huber, R., Karshikov, A., Brzin, J., Kos, J., and Turk, V., 1988. EMBO J, 7:2593–2599.
10. Engh, R., Dieckmann, T., Bode, W., Auerswald, E. A., Turk, V., Huber, R., and Oschkinat, H., 1993. J Mol Biol, 234:1060–1069.
11. Sinha, N., Tsai, C. J., and Nussinov, R., 2001. Protein Eng, 14:93–103.
12. Jaskólski, M., 2001. Acta Biochim Polo, 48:807–827.
13. Nilsson, M., Wang, X., Rodziewicz-Motowidlo, S., Janowski, R., Lindström, V., Önnerfjord, P., Westermark, G., and et al. 2004. J Biol Chem, 279:24236–24245.
14. Wei, L., Walker, L. C., and Levy, E., 1996. Stroke, 27:2080–2085.
15. Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Grubb, A., Abrahamson, M., and Jaskólski, M., 2001. Nat Struct Biol, 8:316–320.
16. Bennett, M. J., Choe, S., and Eisenberg, D., 1994. Proc Natl Acad Sci USA, 91:3127–3131.
17. Gerhartz, B., Ekiel, I., and Abrahamson, M., 1998. Biochemistry, 37:17309–17317.
18. Esposito, L., and Daggett, V., 2005. Biochemistry, 44:3358–3368.
19. Day, R., Bennion, B. J., Ham, S., and Daggett, V., 2002. J Mol Biol, 322:189–203.
20. Li, B., and Daggett, V., 2003. Biopolymers, 68:121–129.
21. Rodziewicz-Motowidlo, S., Wahlbom, M., Wang, X., Lagiewka, J., Janowski, R., Jaskólski, M., Grubb, A., and Grzonka, Z., 2006. J Struct Biol, 154:68–78.
22. Lin, Y.-M., Liu, H.-L., Zhao, J.-H., Huang, C.-H., Fang, H.-W., Ho, Y., and Chen, W.-Y., 2007. Biotech-nol Prog, in press, DOI:10.1021/bp060380d
23. Hwang, M.-J., Ni, X., Waldman, M., Ewig, C. S., and Hagler, A. T., 1998. Biopolymers, 45:435–468.
24. Allen, M. P., and Tildesley, D. J., 1987. Computer Simulation of Liquids. Oxford:Clarendon Press.
25. Kell, G. S., 1967. J Chem Eng Data, 12:66–69.
26. Jankowska, E., Wiczk, W., and Grzonka, Z., 2004. Eur Biophys J, 33:454–461.
27. Trzesniak, D., Lins, R. D., and van Gunsteren, W. F., 2006. Proteins:Struct Funct Bioinformatics, 65:136–144.
28. Su, Y.-C., and Liu, H.-L., 2006. J Chin Chem Soc, 53:713–720.
29. Liu, H.-L., and Hsu, C.-M., 2003. J Chin Chem Soc, 50:1235–1240.
30. Kabsch, W., and Sander, C., 1983. Biopolymers, 22:2577–2637.
31. Calero, M., Pawlik, M., Soto, C., Castano, E. M., Sigurdsson, E. M., Kumar, A., Gallo, G., Frangione, B., and Levy, E., 2001. J Neurochem, 77:628–637.
32. Janowski, R., Kozak, M., Abrahamson, M., Grubb, A., and Jaskólski, M., 2005. Proteins:Struct Funct Bioinformatics, 61:570–578.
33. Rose, G., Geselowitz, A., Lesser, G., Lee, R., and Zehfus, M., 1985. Science, 229:834–838.
34. Liu, H.-L., and Lin, Y.-M., 2003. J Chin Chem Soc, 50:799–808.
35. Nelson, R., and Eisenberg, D., 2006. Curr Opin Struct Biol, 16:260–265.