12.3.2 Matrix Proteins
12.3.2.1 General Features
Predominant Amino Acids
Analysis of the amino acid composition of matrix proteins shows that some amino
acids are predominant, e.g., Asp, Gly, and Ser. These amino acids organize some
repeat regions or modular structure of the proteins to perform specific functions
involved in biomineralization. Different proteins may have different predominant
amino acid residues which determine their different functions. The acidic protein
N16 (Pearlin) has a high content of Gly, Tyr, Asn, and Cys, whereas basic Lustrin A
contains a high proportion of Ser, Pro, Gly, and Cys. Alanine-rich is one of the
features of silk-like proteins, whereas Gly-rich represents one of the characteristics
of framework proteins. Asp-rich acidic proteins are thought to be the sites of crystal
nucleation (Weiner and Traub 1984) on which Asp presumably binds and interacts
with calcium by providing carboxyl groups, and may therefore initiate crystal
nucleation (Addadi and Weiner 1985). This is why the soluble matrix of shells
contains a high content of aspartic residues (Simkiss and Wilbur 1989). Extremely
acidic shell proteins (pI < 4.5) with a high proportion of Asp are preferentially
associated with calcitic prismatic layers rather than with aragonitic nacreous layers
(Marin et al. 2008). Only one Asp-rich protein, Pif, which has been identified from
nacreous layers, specifically binds to aragonite crystal and induces aragonite formation (Suzuki et al. 2009).
Sequence Repeats and Modular Structure
One of the most remarkable structural features of matrix proteins is the existence of
modular units, which means that their primary structure contains one or more
functional domains. Several proteins have a modular structure. For example,
Nacrein (Miyamoto et al. 1996) and N66 (Kono et al. 2000) contain a carbonic
anhydrase domain, Perlucin (Mann et al. 2000) has a C-type functional lectin
domain, Perlustrin (Weiss et al. 2001) is similar to insulin-like growth factor
binding protein, and Lustrin A (Shen et al. 1997) contains a similar domain of
protease inhibitors and another domain that is similar to the sequence of extracellular matrix proteins. These modular multidomain proteins are probably produced
by exon shuffling (Patthy 1999), which is assumed to be a “fast tool” of evolution.
This is why similar domains were found to be widespread among seemingly
unrelated extracellular proteins (Bork 1991).
Having sequence repeats is another common structural feature of matrix
proteins, which also has some specific roles. For example, MSI60 contains 11
poly(alanine) blocks and 39 poly(glycine) blocks. Because polyalanine is one of
the features of fibroin (Guerette et al. 1996), MSI60 is therefore referred to as a
12 Molecular Approaches to Understand Biomineralization of Shell Nacreous Layer
337
12.3.2.1 General Features
Predominant Amino Acids
Analysis of the amino acid composition of matrix proteins shows that some amino
acids are predominant, e.g., Asp, Gly, and Ser. These amino acids organize some
repeat regions or modular structure of the proteins to perform specific functions
involved in biomineralization. Different proteins may have different predominant
amino acid residues which determine their different functions. The acidic protein
N16 (Pearlin) has a high content of Gly, Tyr, Asn, and Cys, whereas basic Lustrin A
contains a high proportion of Ser, Pro, Gly, and Cys. Alanine-rich is one of the
features of silk-like proteins, whereas Gly-rich represents one of the characteristics
of framework proteins. Asp-rich acidic proteins are thought to be the sites of crystal
nucleation (Weiner and Traub 1984) on which Asp presumably binds and interacts
with calcium by providing carboxyl groups, and may therefore initiate crystal
nucleation (Addadi and Weiner 1985). This is why the soluble matrix of shells
contains a high content of aspartic residues (Simkiss and Wilbur 1989). Extremely
acidic shell proteins (pI < 4.5) with a high proportion of Asp are preferentially
associated with calcitic prismatic layers rather than with aragonitic nacreous layers
(Marin et al. 2008). Only one Asp-rich protein, Pif, which has been identified from
nacreous layers, specifically binds to aragonite crystal and induces aragonite formation (Suzuki et al. 2009).
Sequence Repeats and Modular Structure
One of the most remarkable structural features of matrix proteins is the existence of
modular units, which means that their primary structure contains one or more
functional domains. Several proteins have a modular structure. For example,
Nacrein (Miyamoto et al. 1996) and N66 (Kono et al. 2000) contain a carbonic
anhydrase domain, Perlucin (Mann et al. 2000) has a C-type functional lectin
domain, Perlustrin (Weiss et al. 2001) is similar to insulin-like growth factor
binding protein, and Lustrin A (Shen et al. 1997) contains a similar domain of
protease inhibitors and another domain that is similar to the sequence of extracellular matrix proteins. These modular multidomain proteins are probably produced
by exon shuffling (Patthy 1999), which is assumed to be a “fast tool” of evolution.
This is why similar domains were found to be widespread among seemingly
unrelated extracellular proteins (Bork 1991).
Having sequence repeats is another common structural feature of matrix
proteins, which also has some specific roles. For example, MSI60 contains 11
poly(alanine) blocks and 39 poly(glycine) blocks. Because polyalanine is one of
the features of fibroin (Guerette et al. 1996), MSI60 is therefore referred to as a
12 Molecular Approaches to Understand Biomineralization of Shell Nacreous Layer
337