Molecular dynamics simulations to investigate the domain swapping mechanism of human cystatin C

Biotechnology Progress

Volumn 23, Issue 3, 2007, Pages 577-584

  Lin, Yuan Min ^a   Liu, Hsuan Liang ^a   Zhao, Jian Hua ^a   Huang, Chi Hung ^a   Fang, Hsu Wei ^a   Ho, Yih ^b   Chen, Wen Yih ^c  

^a NATIONAL TAIPEI UNIVERSITY OF TECHNOLOGY   (Taiwan)

^b TAIPEI MEDICAL UNIVERSITY   (Taiwan)

^c NATIONAL CENTRAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DISEASES; MOLECULAR DYNAMICS; MONOMERS; PROTONATION;

ALZHEIMER'S DISEASE; DOMAIN SWAPPING; HUMAN CYSTATIN C; SALT-BRIDGE INTERACTIONS;

PROTEINS;

CYSTATIN; CYSTATIN C;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HUMAN; METABOLISM; PH; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; CYSTATINS; HUMANS; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 34250368085     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp060380d     Document Type: Article

References (47)

1. Grubb, A. Cystatin C-properties and use as diagnostic marker. Adv. Clin. Chem. 2000, 35, 63-99.
2. Olafsson, I.; Grubb, A. Hereditary cystatin C amyloid angiopathy. Amyloid 2000, 7, 70-79.
3. Carrell, R. W.; Lomas, D. A.; Conformational disease. Lancet 1997, 350, 134-138.
4. Janowski, R.; Kozak, M.; Jankowska, E.; Grzonka, Z.; Grubb, A.; Abrahamson, M.; Jaskolski, M. Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat. Struct. Biol. 2001, 8, 316-320.
5. Janowski, R.; Abrahamson, M.; Grubb, A.; Jaskolski, M. Domain swapping in N-truncated human cystatin C. J. Mol. Biol. 2004, 341, 151-160.
6. Ekiel, I.; Abrahamson, M.; Fulton, D. B.; Lindahl, P.; Storer, A. C.; Levadoux, W.; Lafrance, M.; Labelle, S.; Pomerleau, Y.; Groleau, D.; LeSauteur, L.; Gehring, K. NMR structural studies of human cystatin C dimers and monomers. J. Mol. Biol. 1997, 271, 266-277.
7. Kozak, M.; Jankowska, E.; Janowski, R.; Grzonka, Z.; Grubb, A.; Alvarez Fernandez, M.; Abrahamson, M.; Jaskolski, M. Expression of a selenomethionyl derivative and preliminary crystallographic studies of human cystatin C. Acta Crystallogr. D 1999, 55, 1939-1942.
8. Bode, W.; Engh, R.; Musil, D.; Thiele, U.; Huber, R.; Karshikov, A.; Brzin, J.; Kos, J.; Turk, V. The 2.0 A X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases. EMBO J. 1988, 7, 2593-2599.
9. Engh, R.; Dieckmann, T.; Bode, W.; Auerswald, E. A.; Turk, V.; Huber, R.; Oschkinat, H. Conformational variability of chicken cystatin. Comparison of structures determined by X-ray diffraction and NMR spectroscopy. J. Mol. Biol. 1993, 234, 1060-1069.
10. Sinha, N.; Tsai, C. J.; Nussinov, R. A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer. Protein Eng. 2001, 14, 93-103.
11. Rodziewicz-Motowidlo, S.; Wahlbom, M.; Wang, X.; Lagiewka, J.; Janowski, R.; Jaskolski, M.; Grubb, A.; Grzonka, Z. Checking the conformational stability of cystatin C and its L68Q variant by molecular dynamics studies: why is the L68Q variant amyloidogenic? J. Struct. Biol. 2006, 154, 68-78.
12. Abrahamson, M.; Grubb, A. Increased body temperature accelerates aggregation of the Leu-68→Gln mutant cystatin C, the amyloid-forming protein in hereditary cystatin C amyloid angiopathy. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 1416-1420.
13. Nilsson, M.; Wang, X.; Rodziewicz-Motowidlo, S.; Janowski, R.; Lindstrom, V.; Onnerfjord, P.; Westermark, G.; Grzonka, Z.; Jaskolski, M.; Grubb, A. Prevention of domain swapping inhibits dimerization and amyloid fibril formation of cystatin C: use of engineered disulfide bridges, antibodies, and carboxymethylpapain to stabilize the monomelic form of cystatin C. J. Biol. Chem. 2004, 279, 24236-24245.
14. Ekiel, I.; Abrahamson, M. Folding-related dimerization of human cystatin C. J. Biol. Chem. 1996, 271, 1314-1321.
15. Gerhartz, B.; Ekiel, I.; Abrahamson, M. Two stable unfolding intermediates of Disease-Causing L68Q variant of human cystatin C. Biochemistry 1998, 37, 17309-17317.
16. Alonso, D. O.; Alm, E.; Daggett, V. Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure 2000, 8, 101-110.
17. Esposito, L.; Daggett, V. Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations. Biochemistry 2005, 44, 3358-3368.
18. Day, R.; Bennion, B. J.; Ham, S.; Daggett, V. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J. Mol. Biol. 2002, 322, 189-203.
19. Li, B.; Daggett, V. The molecular basis of the temperature- and pH-induced conformational transitions in elastin-based peptides. Biopolymers 2003, 68, 121-129.
20. Hwang, M. J.; Ni, X.; Waldman, M.; Ewig, C. S.; Hagler, A. T. Derivation of class II force fields. VI. Carbohydrate compounds and anomeric effects. Biopolymers 1998, 45, 435-468.
21. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Clarendon Press: Oxford, 1987.
22. Kell, G. S. Precise representation of volume properties of water at one atmosphere. J. Chem. Eng. Data 1967, 12, 66-69.
23. Yang, A. S.; Honig, B. Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin. J. Mol. Biol. 1994, 237, 602-614.
24. van't Hof, W.; Blankenvoorde, M. F.; Veerman, E. C.; Amerongen, A. V. The salivary lipocalin von Ebner's gland protein is a cysteine proteinase inhibitor. J. Biol. Chem. 1997, 272, 1837-1841.
25. Liu, H.-L.; Hsu, C.-M. The effects of solvent and temperature on the structural integrity of monomeric melittin by molecular dynamics simulations. Chem. Phys. Lett. 2003, 375, 119-125.
26. Liu, H.-L.; Wang, W.-C. The predicted unfolding order of the β-strands in the starch binding domain from Aspergillus niger glucoamylase. Chem. Phys. Lett. 2003, 366, 284-290.
27. Liu, H.-L.; Wang, W.-C. Molecular dynamics simulations of the unfolding of the starch binding domain from Aspergillus niger glucoamylase, J. Biomol. Struct. Dyn. 2003, 20, 615-622.
28. Liu, H.-L.; Wang, W.-C. Predicted unfolding order of the 13 α-helices in the catalytic domain of glucoamylase from Aspergillus awamori var. X100 by molecular dynamics simulations. Biotechnol. Prog. 2003, 19, 1583-1590.
29. Liu, H.-L.; Lin, J.-C.; Hsieh, W.-C.; Chen, C.-W.; Su, Y.-C. Molecular dynamics simulations to investigate the temperature effect on the main proteinases from various coronaviruses. J. Biomol. Struct. Dyn. 2004, 22, 65-77.
30. Liu, H.-L.; Hsieh, W.-C. Molecular dynamics simulations to investigate the thermal unfolding behaviors of N-carbamyl-D-amino acid amidohydrolase. J. Chin. Inst. Chem. Eng. 2005, 36, 185-194.
31. Chen, C.-W.; Lin, J.-C.; Liu, H.-L. Molecular dynamics simulations of the tetramerization domain of Shaker and Kv1.1 potassium channels. J. Chin. Inst. Chem. Eng. 2005, 36, 649-660.
32. Liu, H.-L.; Wu, Y.-C.; Zhao, J.-H.; Fang, H.-W.; Ho, Y. Structural analysis of human lysozyme using molecular dynamics simulations. J. Biomol. Struct. Dyn. 2006, 24, 229-238.
33. Trzesniak, D.; Lins, R. D.; van Gunsteren, W. F. Protein under pressure: molecular dynamics simulation of the Arc repressor. Proteins: Struct. Funct. Bioinformatics 2006, 65, 136-144.
34. Su, Y.-C.; Liu, H.-L. The effects of salt and pH on the spermatozoa agglutinating activity of carp ovum cystatin by molecular dynamics simulations. J. Chin. Chem. Soc. 2006, 53, 713-720.
35. Liu, H.-L.; Hsu, C.-M. The effects of various alcohols on the stability of melittin: A molecular dynamics study. J. Chin. Chem. Soc. 2003, 50, 1235-1240.
36. Liu, H.-L.; Hsieh, W.-C.; Liu, H.-S. Molecular dynamics simulations to determine the effect of supercritical carbon dioxide on the structural integrity of hen egg white lysozyme. Biotechnol. Prog. 2004, 20, 930-938.
37. Zhao, J.-H.; Liu, H.-L. The effects of various alcohols on the structural stability of melittin, TH-10Aox, and Tc1 by molecular dynamics simulations. Chem. Phys. Lett. 2006, 420, 235-240.
38. Miyazawa, S.; Jernigan, R. L.; Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18, 534-552.
39. Treptow, W. L.; Barbosa, M. A.; Garcia, L. G.; Pereira de Araujo, A. F. Non-native interactions, effective contact order, and protein folding: a mutational investigation with the energetically frustrated hydrophobic model. Proteins 2002, 49, 167-180.
40. Takano, K.; Tsuchimori, K.; Yamagata, Y.; Yutani, K. Contribution of salt bridges near the surface of a protein to the conformational stability. Biochemistry 2000, 39, 12375-12381.
41. Xiao, L.; Honig, B. Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 1999, 289, 1435-1444.
42. Jankowska, E.; Wiczk, W.; Grzonka, Z. Thermal and guanidine hydrochloride-induced denaturation of human cystatin C. Eur. Biophys. J. 2004, 33, 454-461.
43. Liu, H.-L.; Lin, Y.-M.; Stability and Unfolding Mechanism of the N-terminal β-Hairpin from [2Fe-2S] Ferredoxin 1 by Molecular Dynamics Simulations J. Chin. Chem. Soc. 2003, 50, 799-808.
44. Shlipak, M. G.; Katz, R.; Fried, L. F.; Jenny, N. S.; Stehman-Breen, C. O.; Newman, A. B.; Siscovick, D.; Psaty, B. M.; Sarnak, M. J. Cystatin-C and mortality in elderly persons with heart failure. J. Am. Coll. Cardiol. 2005, 45, 268-271.
45. Nelson, R.; Eisenberg, D. Recent atomic models of amyloid fibril structure. Curr. Opin. Struct. Biol. 2006, 16, 260-265.
46. Janowski, R.; Kozak, M.; Abrahamson, M.; Grubb, A.; Jaskolski, M. 3D domain-swapped human cystatin C with amyloidlike intermolecular beta-sheets. Proteins 2005, 61, 570-578.
47. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.