Expression and molecular dynamics studies on effect of amino acid substitutions at Arg344 in human cathepsin A on the protein local conformation

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1794, Issue 11, 2009, Pages 1693-1699

  Yoshida, Tatsusada ^a   Kadota, Yoshito ^b   Hitaoka, Seiji ^a   Kori, Eri ^a   Horikawa, Yasushi ^a   Taguchi, Masahiro ^a   Tsuji, Daisuke ^a   Hirokawa, Takatsugu ^c   Chuman, Hiroshi ^a   Itoh, Kohji ^a  

^a UNIVERSITY OF TOKUSHIMA   (Japan)

^b TOKUSHIMA BUNRI UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Accessible surface area (ASA); B factor; Cathepsin A; Conformational similarity; Excision peptide; Galactosialidosis; Lysosomal protective protein; Maturation molecular dynamics (MD); Mutation; Proteolysis

Indexed keywords

AMINO ACID; ARGININE DERIVATIVE; CARBOXYPEPTIDASE C; ENZYME PRECURSOR; GENE PRODUCT;

AMINO ACID SUBSTITUTION; ARTICLE; CELL CULTURE; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ENZYME ACTIVITY; FIBROBLAST CULTURE; GALACTOSIALIDOSIS; HUMAN; HUMAN CELL; MOLECULAR DYNAMICS; MUTANT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN EXPRESSION; SIMULATION; WILD TYPE;

AMINO ACID SUBSTITUTION; CATHEPSIN A; HUMANS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MUCOLIPIDOSES; PROTEIN CONFORMATION; WATER;

CATHA; TRITICUM AESTIVUM;

EID: 70249101347     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.08.004     Document Type: Article

References (32)

1. Rudenko G., Bonten E., dAzzo A., and Hol W.G.L. Three dimensional structure of the human protective protein: structure of the precursor form suggests a complex activation mechanism. Structure 3 (1995) 1249-1259
2. Matsuda K. Studies on cathepsins of rat liver lysosomes. III. Hydrolysis of peptides, and inactivation of angiotensin and bradykinin by cathepsin. Am. J. Biochem. 80 (1976) 659-669
3. Jackman H.L., Tan F.L., Tamei H., Beurling-Harbury C., Li X.Y., Skidgel R.A., and Erdos E.G. A peptidase in human platelets that deamidates tachykinins. Probable identity with the lysosomal 'protective protein'. J. Biol. Chem. 265 (1990) 11265-11272
4. Jackman H.L., Morris P.W., Deddish P.A., Skidgel R.A., and Erdos E.G. Inactivation of endothelin I by deamidase (lysosomal protective protein). J. Biol. Chem. 267 (1992) 2872-2875
5. Itoh K., Kase R., Shimmoto M., Satake H., and Suzuki Y. Protective protein as an endogenous endothelin degradation enzyme in human tissues. J. Biol. Chem. 270 (1995) 515-518
6. Itoh K., Oyanagi K., Takahashi H., Sato T., Hashizume Y., Shimmoto M., and Sakuraba H. Endothelin-1 in the brain of patients with galactosialidosis: its abnormal increase and distribution pattern. Ann. Neurol. 47 (2000) 122-126
7. Galjart N.J., Gillemans N., Harris G., van der Horst G.T., Verheijen F.W., Galjaard H., and d'Azzo A. Expression of cDNA encoding the human 'protective protein' associated with lysosomal β-galactosidase and neuraminidase; homology to yeast proteases. Cell 54 (1988) 755-764
8. Pshezhetsky A.V., and Potier M. Direct affinity purification and supramolecular organization of human lysosomal cathepsin A. Arch. Biochem. Biophys. 313 (1994) 64-70
9. Wang D., Zaitsev S., Taylor G., d'Azzo A., and Bonten E. Protective protein/Cathepsin A rescues N-glycosylation defects in Neuraminidase-1. Biochim. Biophys. Acta 1790 (2009) 275-282
10. Galjart N.J., Morreau H., Willemsen R., Gillemans N., Bonten E.J., and d'Azzo A. Human lysosomal protective protein has cathepsin A-like activity distinct from its protective function. J. Biol. Chem. 266 (1991) 14754-14762
11. Itoh K., Takiyama N., Kase R., Kondoh K., Sano A., Oshima A., Sakuraba H., and Suzuki Y. Purification and characterization of human lysosomal protective protein expressed in stably transformed Chinese hamster ovary cells. J. Biol. Chem. 268 (1993) 1180-1186
12. d'Azzo A., Hoogeveen A., Reuser A.J., Robinson D., and Galjaard H. Molecular defect in combined β-galactosidase and neuraminidase deficiency in man. Proc. Natl. Acad. Sci. U. S. A. 79 (1982) 4535-4539
13. d'Azzo A., Andria G., Strisciuglio G., and Galjaard H. Galactosialidosis. In: Scriver C.R., Beaudet A.L., Sly W.S., and Valle D. (Eds). Metabolic and Molecular Bases of Inherited Disease (2001), McGraw-Hill, NewYork 3811-3826
14. Shimmoto M., Fukuhara Y., Itoh K., Oshima A., Sakuraba H., and Suzuki Y. Protective protein gene mutations in galactosialidosis. J. Clin. Invest. 91 (1993) 2393-2398
15. Oheda Y., Kotani M., Murata M., Sakuraba H., Kadota Y., Tatano Y., Kuwahara J., and Itoh K. Elimination of abnormal sialylglycoproteins in fibroblasts with sialidosis and galactosialidosis by normal gene transfer and enzyme replacement. Glycobiol. 16 (2006) 271-280
16. Adcock S.A., and McCammon J.A. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem. Rev. 106 (2006) 1589-1615
17. Smith L.J. Computational methods for generating models of denatured and partially folded proteins. Methods 34 (2004) 144-150
18. Karplus M., and McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Mol. Biol. 9 (2002) 646-652
19. Dobson C.M., Šali A., and Karplus M. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. 37 (1998) 868-893
20. Yoshida T., Lepp Z., Kadota Y., Satoh Y., Itoh K., and Chuman H. Comparative analysis of binding energy of chymostatin with human cathepsin A and its homologous proteins by molecular orbital calculation. J. Chem. Inf. Model. 46 (2006) 2093-2103
21. SYBYL7.0 Tripos Inc., 1699 South Hanley Road, St. Louis, MI 63144, USA.
22. Case D.A., Cheatham III T.E., Darden T., Gohlke H., Luo R., Merz Jr. K.M., Onufriev A., Simmerling C., Wang B., and Woods R.J. The Amber biomolecular simulation programs. J. Comput. Chem. 26 (2005) 1668-1688
23. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
24. Darden T.A., York D.M., and Pedersen L.G. Particle mesh Ewald-an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
25. Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23 (1977) 327-341
26. McCammon J.A., and Harvey S.C. Dynamics of Proteins and Nucleic Acids (1987), Cambridge University Press, Cambridge 96-105
27. Shao J., Tanner S.W., Thompson N., and Cheatham III T.E. Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3 (2007) 2312-2334
28. Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
29. Chothia C. Hydrophobic bonding and accessible surface area in proteins. Nature 248 (1974) 338-339
30. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
31. Bondi A. Van der Waals volumes and radii. J. Phys. Chem. 68 (1964) 441-451
32. Bonten E.J., Galjart N.J., Willemsen R., Usmany M., Vlak J.M., and d'Azzo A. Lysosomal protective protein/cathepsin A. Role of the "linker" domain in catalytic activation. J. Biol. Chem. 270 (1995) 26441-26445