Homology model and molecular dynamics simulation of carp ovum cystatin

Biotechnology Progress

Volumn 21, Issue 4, 2005, Pages 1315-1320

  Su, Yuan Chen ^a   Lin, Jin Chung ^a   Liu, Hsuan Liang ^a  

^a NATIONAL TAIPEI UNIVERSITY OF TECHNOLOGY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CRYSTAL STRUCTURE; ELECTROSTATICS; MOLECULAR DYNAMICS;

CYSTATIN; DISULFIDE BONDS; ELECTROSTATIC INTERACTION; HOMOLOGY MODELS;

PROTEINS;

CYSTATIN; CYSTATIN, EGG WHITE; CYSTATIN, EGG-WHITE;

AMINO ACID SEQUENCE; ANIMAL; ANTIGEN ANTIBODY REACTION; ARTICLE; CARP; CHEMISTRY; ELECTRICITY; FEMALE; GENETICS; MALE; METABOLISM; MOLECULAR GENETICS; MUTATION; OOCYTE; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; SPERMATOZOON; STRUCTURAL HOMOLOGY;

AGGLUTINATION; AMINO ACID SEQUENCE; ANIMALS; CARPS; CYSTATINS; ELECTROSTATICS; FEMALE; MALE; MOLECULAR SEQUENCE DATA; MUTATION; OVUM; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SPERMATOZOA; STRUCTURAL HOMOLOGY, PROTEIN;

CYPRINUS CARPIO;

EID: 23244440144     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp0501017     Document Type: Article

References (25)

1. Wang, S.-C.; Huang, F.-L. Carp ovarian cystatin binds and agglutinates spermatozoa via electrostatic interaction. Biol. Reprod. 2002, 66, 1318-1327.
2. Tsai, Y.-J.; Chang, G.-D.; Huang, C.-J.; Chang, Y.-S.; Huang, F.-L. Purification and molecular cloning of carp ovarian cystatin. Comp. Biochem. Physiol. 1996, 113B, 573-580.
3. Margis, R.; Reis, E. M.; Vincent, V. Structural and phylogenetic relationships among plant and animal cystatins. Arch. Biochem. Biophys. 1998, 359, 24-30.
4. Bell, J. E.; Cunningham, E.; Belt, C.; Featherstone, J. D. B.; Bell, J. Examination of the potential structure of human salivary cystatins based on computer modeling. Arch. Oral Biol. 1997, 42, 761-772.
5. Dieckmann, T.; Mitschang, L.; Hofmann, M.; Kos, J.; Turk, V.; Auerswald, E. A.; Jaenicke, R.; Oschkinat, H. The structures of native phosphorylated chicken cystatin and of a recombinant unphorylated variant in solution. J. Mol. Biol. 1993, 234, 1048-1059.
6. Engh, R. A.; Dieckmann, T.; Bode, W.; Auerswald, E. A.; Turk, V.; Huber, R.; Oschkinat, H. Conformational variability of chicken cystatin. J. Mol. Biol. 1993, 234, 1060-1069.
7. Hall, A.; Hakansson, K.; Mason, R. W.; Grubb, A.; Abrahamson, M. Structural basis for the biological specificity of cystatin C. Identification of leucine 9 in the N-terminal binding region as a selectivity-conferring residue in the inhibition of mammalian cysteine peptidases. J. Biol. Chem. 1995, 270, 5115-5121.
8. Sato, C. Alzheimer's and prion disease as disorders of protein conformation: implications for the design of novel therapeutic approaches. J. Mol. Med. 1999, 77, 412-418.
9. Dehouck, Y.; Biot, C.; Gilis, D.; Kwasigroch, J. M.; Rooman, M. Sequence-structure signals of 3D domain swapping in proteins. J. Mol. Biol. 2003, 330, 1215-1225.
10. Beyer, K.; Lao, J. I.; Gomez, M.; Riutort, N.; LaTorre, P.; Mate, J. L.; Ariza, A. Alzheimer's disease and the cystatin C gene polymorphism: an association study. Neurosci. Lett. 2001, 315, 17-20.
11. Staniforth, R. A.; Giannini, S.; Lee, D. H.; Conroy, M. J.; Hounslow, A. M.; Jerala, R.; Craven, C. J.; Waltho, J. P. Three-dimensional domain swapping in the folded and molten-globule states of cystatins, an amyloid-forming structural superfamily. EMBO J. 2001, 20, 4774-4781.
12. Bode, W.; Engh, R.; Musil, D.; Thiele, U.; Huber, R.; Karshikov, A.; Brzin, J.; Kos, J.; Turk, V. The 2.0 Å X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases. EMBO J. 1988, 7, 2593-2599.
13. Greer, J. Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins 1990, 7, 317-334.
14. Schuler, G. D.; Altschul, S. F.; Lipman, D. J. A workbench for multiple alignment construction and analysis. Proteins: Struct. Funct. Genet. 1991, 9, 180-190.
15. Shenkin, P. S.; Yarmush, D. L.; Fine, R. M.; Wang, H.; Levinthal, C. Predicting antibody hypervariable loop conformation. I. ensembles of random conformations for ringlike structures. Biopolymers 1987, 26, 2053-2085.
16. Ponder, J. W.; Richards, F. M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 1987, 193, 775-791.
17. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.
18. 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.
19. Maple, J. R.; Hwang, M.-J.; Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T. Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds. J. Comput. Chem. 1998, 19, 430-458.
20. Peng, Z.; Ewig, C. S.; Hwang, M.-J.; Waldman, M.; Hagler, A. T. Derivation of class II force fields. 4. van der Waals parameters of alkali metal cations and halide anions. J. Phys. Chem. A 1997, 101, 7243-7252.
21. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Comput. Phys. 1984, 81, 3684-3690.
22. Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 1963, 7, 95-99.
23. Nosih, Y.; Sekiguchi, T. Protein Stability and Stabilization through Protein Engineering; Ellis Horwood: London, 1991.
24. Bjiirk, I.; Ylinenjlrvi, K. Different roles of the two disulfide bonds of the cysteine proteinase inhibitor, chicken cystatin, for the conformation of the active protein. Biochemistry 1992, 31, 8597-8602.
25. Engleman, D. M.; Steitz, T. A. The spontaneous insertion of proteins into and across membranes: the helical hairpin hypothesis. Cell 1981, 23, 411-422.