Aragonite-associated biomineralization proteins are disordered and contain interactive motifs

Bioinformatics

Volumn 28, Issue 24, 2012, Pages 3182-3185

  Evans, John Spencer ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; MOLLUSCA;

CALCIUM CARBONATE; SCLEROPROTEIN;

ANIMAL; ARTICLE; BONE MINERALIZATION; CHEMISTRY; METABOLISM; MOLLUSC; NACRE; PROTEIN CONFORMATION; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

ANIMALS; CALCIFICATION, PHYSIOLOGIC; CALCIUM CARBONATE; EXTRACELLULAR MATRIX PROTEINS; MOLLUSCA; NACRE; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84870838761     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts604     Document Type: Article

References (31)

1. Amos, F.F. et al. (2010) The N-and C-terminal regions of the pearl-associated EF Hand protein, PFMG1, promote the formation of the aragonite polymorph in vitro. Cryst. Growth Des., 10, 4211-4216.
2. Amos, F.F. et al. (2011) A C-RING-like domain participates in protein self-assembly and mineral nucleation. Biochemistry, 50, 8880-8887.
3. Berland, S. et al. (2011) Coupling proteomics and transcriptomics for the identification of novel and variant forms of mollusk shell proteins: a study with P. margaritifera. Chembiochem, 12, 950-961.
4. Bryan, A.W. et al. (2009) BETASCAN: probable beta-amyloids identified by pairwise probabilities analysis. PLoS Comput. Biol., 5, 1-11.
5. Conchillo-Sole, O. et al. (2007) AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics, 8, 65-82.
6. Dosztányi, Z. et al. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
7. Falini, G. et al. (2011) The interstitial crystal-nucleating sheet in molluscan Haliotis rufescens shell: a bio-polymeric composite. J. Struct. Biol., 173, 128-137.
8. Garbuzynsky, S.O. et al. (2010) FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence. Bioinformatics, 26, 326-332.
9. Greenwald, J. and Riek, J. (2012) On the possible amyloid origin of protein folds. J. Mol. Biol., 421, 417-426.
10. Keene, E.C. et al. (2010) Matrix interactions in biomineralization: aragonite nucleation by an intrinsically disordered nacre polypeptide, n16N, associated with a-chitin substrate. Cryst. Growth Des., 10, 1383-1389.
11. Levi-Kalisman, Y. et al. (2001) Structure of the nacreous organic matrix of a bivalve mollusk shell examined in the hydrated state using cryo-TEM. J. Struct. Biol., 135, 8-17.
12. Linding, R. et al. (2003) GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res., 31, 3701-3708.
13. Linding, R. et al. (2004) A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins (TANGO). J. Mol. Biol., 342, 345-353.
14. Liu, H.L. et al. (2007) Identification and characterization of a biomineralization related gene PFMG1 highly expressed in the mantle of Pinctada fucata. Biochemistry, 46, 844-851.
15. Marchler-Bauer, A. et al. (2011) CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res., 39, 225-229.
16. Marie, B. et al. (2010) Proteomic analysis of the acid-soluble nacre matrix of the bivalve Unio pictorum: detection of novel carbonic anhydrase and putative protease inhibitor proteins. Chembiochem, 11, 2138-2147.
17. Mészáros, B. et al. (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput. Biol., 5, 1-18.
18. Michenfelder, M. et al. (2003) Characterization of two molluscan crystal-modulating biomineralization proteins and identification of putative mineral binding domains [published erratum appears in Biopolymers (2004), 73, 291]. Biopolymers, 70, 522-533.
19. Petersen, T.N. et al. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods, 8, 785-786.
20. Peysselon, F. et al. (2011) Intrinsic disorder of the extracellular matrix. Mol. Biosyst., 7, 3353-3365.
21. Ponce, C.B. and Evans, J.S. (2011) Polymorph crystal selection by n16, an intrinsically disordered nacre framework protein. Cryst. Growth Des., 11, 4690-4696.
22. Samata, T. et al. (1999) A new matrix protein family related to the nacreous layer formation in Pinctada fucata. FEBS Lett., 462, 225-229.
23. Smith, B.L. et al. (1999) Molecular mechanistic origin of the toughness of natural adhesives, fibres, and composites. Nature, 399, 761-763.
24. Suzuki, M. et al. (2010) An acidic matrix protein Pif is a key macromolecule for nacre formation. Science, 325, 1388-1390.
25. Suzuki, M. et al. (2011) Identification and characterization of a calcium carbonate-binding protein, blue mussle shell protein (BMSP), from the nacreous layer. Chembiochem, 12, 2478-2487.
26. Tompa, P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci., 27, 527-533.
27. Uversky, V.N. and Dunker, A.K. (2010) Understanding protein non-folding. Biochim. Biophys. Acta, 1804, 1231-1264.
28. Ward, J.J. et al. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
29. Weiss, I.M. et al. (2000) Purification and characterization of perlucin and perlustrin, two new proteins from the shell of the mollusc Haloitis laevigata. Biochem. Biophys. Res. Commun., 267, 17-21.
30. Weiss, I.M. et al. (2001) Perlustrin, a Haloitis laevigata (abalone) nacre protein, is homologous to the insulin-like growth factor binding protein N-terminal module of vertebrates. Biochem. Biophys. Res. Commun., 285, 244-249.
31. Xie, H. et al. (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res., 6, 1882-1898.