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Carole C. Perry
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Silica Structure: Molecules, Materials and Methods of Analysis . . . . . . . . . . . . . . . . . . . Siliciﬁcation in Sponges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Siliciﬁcation in Diatoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Siliciﬁcation in Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Role of Silica in Stress Relief . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Laboratory Studies of Silica Condensation, Polymerisation and Materials Formation. . . The Effect of Biologically Relevant Solution Additives on Condensation, Polymerisation and Materials Formation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 Applications Using the Biomolecules as Identiﬁed from Diatoms, Sponges and Higher Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 Technological and Model Advances Utilising Diatoms . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Abstract Biomineralisation is widespread in the biological world and occurs in bacteria, single-celled protists, plants, invertebrates and vertebrates. Minerals formed in the biological environment often show unusual physical properties (e.g. strength, degree of hydration) and often have structures that exhibit order on many length scales. Biosilica, found in single cell organisms through to higher plants and primitive animals (sponges), is formed from an environment that is undersaturated with respect to silicon and under conditions of around neutral pH and low temperature, ca. 4–40°C. Formation of the mineral may occur intra- or extra-cellularly, and specific biochemical locations for mineral deposition that include lipids, proteins and carbohydrates are known. In most cases, the formation of the mineral phase is linked to cellular processes, understanding of which could lead to the design of new materials for biomedical, optical and other applications. This Chapter briefly describes the occurrence of silica in biology including known roles for the mineral
C.C. Perry School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS e-mail: firstname.lastname@example.org W.E.G. Müller and M.A. Grachev (eds.), Biosilica in Evolution, Morphogenesis, and Nanobiotechnology, Progress in Molecular and Subcellular Biology, Marine Molecular Biotechnology 47, DOI: 10.1007/978-3-540-88552-8, © Springer-Verlag Berlin Heidelberg 2009 295
amounting to gigatons per annum. Materials and Methods of Analysis Plants and primitive organisms. including a vast range of proteins. The terminology which is used in this and other contributions within this volume is as follows: Si: the chemical symbol for the element and the generic term used when the nature of the specific silicon compound is not known. it is apparent that the organic environment.C. however. are capable of accumulating. For example. and this production. radiolaria through to primitive animals such as sponges and molluscs such as limpets. SiO32−). polymerised material. term also used to describe salts (e.g. the associated biomolecules and some recent applications of this knowledge in materials chemistry. Oligomerisation: the formation of dimers and small oligomers from orthosilicic acid by removal of water. carbohydrates. Perry phase. SiO2•nH2O or SiO2−x(OH)2x•2H2O: amorphous. tetrethoxy or tetramethoxysilane Silanol: hydroxyl group bonded to silicon atom Silicate: a chemically specific ion having negative charge (e. the fundamental building block used in the formation of silicas. The methods by which this can be achieved in organisms have been the subject of immense study and debate. 1 Silica Structure: Molecules. Si(OH)4: orthosilicic acid. such as diatoms. 2Si(OH)4 ↔ (HO)3Si–O–Si(OH)3 + H2O Polymerisation: the mutual condensation of silicic acid to give molecularly coherent units of increasing size. the chemistry of the material. storing and processing ‘silicon’ to create ornate hierarchical patterned biosilicas.296 C. sodium silicate Na2SiO3) Opal: the term used to describe the gem-stone and often used to describe the type of amorphous silica produced by biological organisms. but at higher levels of structural organisation are distinct from one another. e.g. The production of silica by biological organisms is carried out in an aqueous environment from under-saturated solutions of silicic acid. choanoflagellates.g. lipids. vastly outweighs that produced industrially. Organosilicon compound: must contain silicon covalently bonded to carbon within a distinct chemical species Silane: a compound having silicon atom(s) and organic chemical groups often connected through an oxygen linkage. The two are similar in structure at the molecular level (disordered or amorphous). at atmospheric pressure and with temperatures ranging between 4°C and 40°C. . hydrated.
An Overview of Silica in Biology 297 metal ions and. small molecules and polymers (Iler 1979). is a weakly acidic molecule (pKa 9. temperature. at least for exemplars of the three main classes (the most well studied) of silicified organisms (diatoms. 1990). phenolic compounds. but in all cases the materials that form are built up from SiO4 tetrahedra with variable Si–O–Si bond angles and Si–O bond distances that are amorphous at the 1 nm length scale (Mann and Perry 1986). sponges and higher plants). growth of nuclei to form spherical particles and aggregation of particles to form branched chains or structural motifs (Perry and KeelingTucker 2000). in plants. where the concentration of silicic acid is in excess of 100– 200 ppm. auto polycondensation reactions occur that lead to the formation of stable nuclei with critical size. Although the mineral phase that forms is amorphous. This can also be true for silica formed within a single cell of an organism with evidence for this being observed in diatoms (Wetherbee et al. solubility. The simplest form of silica. viscosity and composition (Perry and Keeling-Tucker 2000). This monomeric unit is found universally (seawater. An interesting feature of silicic acids is that although the pKa of the silanol groups in the monomer is mildly basic. 1998. soil water) at low concentrations (a few parts per million. 2006). In all organisms. there are now a wide range of techniques that are being used to probe the structure of these complex materials (Perry 2003). The techniques that provide information on the nanoscopic through to the microscopic length scales include the following: electron microscopy (scanning and transmission modes) which is used to identify the sizes of fundamental particles and their interconnection to one another and.8. and it is these particles what will be interacting with the cell wall or the environment in which they are found. 2000) and plant hairs (Perry et al. The materials contain hydroxyl groups and. This means that. analysis of which should yield information on the pathway/mechanism by which the mineral has formed. Beyond this. Ma et al. It is most likely that it is in this form that all organisms are able to take silica into their bodies although it is known that. 2004. 1 nm in size is 6. silicic acid transporters are available to at least transport silicic acid into the organism (Hildebrand et al. The mineralised structures are built up from nanosized particles intermixed with organic material. the pKa of silanol groups on the outside of oligomers ca. they will carry a surface negative charge. as the silica particles grow and approach a couple of nanometres in size (as found in nature). including concentration. in conjunction with energy . hardness. silica from different organisms/precipitation conditions can vary greatly with regard to density.8) with silicon tetrahedrally coordinated to four hydroxyl groups (Iler 1979). Many factors affect the process of silica condensation from the molecular level upwards. ppm). the monomer orthosilicic acid. The structure that the composite adopts arises from a complex interplay between inorganic chemistry (silica formation) and cellular biology (biomolecule structure and location of both phases). Schröder et al. freshwater. 1997. according to the reaction environment in which the mineral forms. is likely to play a fundamental role (Perry 2003). the exact transport mechanism for all these classes of organism through to the final place of deposition is largely unknown. pH and the presence of other ions.
Atomic force microscopy (AFM) with a range of viewing modes can be used to great effect to measure particle sizes in three dimensions. none of these techniques has identified any crystallinity within biosilicas but USAXS has been used successfully to identify structures on different length scales including pore structures (Vrieling et al. in order to obtain information on direct connections between the inorganic and organic phase. 2 Silicification in Sponges Sponges are one class of organisms known to make structural objects out of silica and for which much is known concerning the mineral phase.C. etc. ultra small angle and wide angle X-ray diffraction (SAXS. Of the three classes of sponges. Infrared spectroscopy and Raman spectroscopy are both molecular spectroscopies that probe vibrational motion and can be used to provide information on the internal structure of siliceous phases as well as on the composition and conformation of components of the organic phase. It is to be hoped that if costs reduce then more experiments will be performed to provide information on the extent of and molecular nature of any interactions occurring between the mineral phase and associated biomolecules within the composite material as it forms. NMR spectroscopy (solution and solid state) provides information on the immediate local environment around the chosen nucleus and by judicious use of single pulse and multiple pulse methods can give information on speciation (including level of hydroxylation) and the extent of interaction between the inorganic phase and any organic material present. 1990). the costs of preparing enriched samples are prohibitive and very few experiments have been performed.) that can be of great use in planning further biochemical investigations.298 C. can be used to locate the mineral within an organism as well as locate co-localised inorganic species and additionally. 2002). Silicon-29 only occurs at 4. Another technique which gives information on bulk samples is nitrogen (or other gas) adsorption analysis and this can be used to provide evidence on porosity. The use of these instruments in ‘mapping’ modes can be used to identify any co-localisation of the mineral with specific molecule types (protein. carbohydrate. Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy.67% natural abundance which means that. There are also a wide range of spectroscopic techniques that provide information at the molecular level and these include 29Si nuclear magnetic resonance (NMR) spectroscopy. 2000). including the distribution of pore sizes. two produce silicified spicules as their body support (Hexactinellida and . At present. isotopically enriched Si sources must be used. the extent of hydration of a particular mineral form can be explored by use of reactive heavy metal compounds that react with hydroxyl groups (Perry et al. associated biomolecules and the biology of mineralisation. Perry dispersive X-ray analysis (EDXa). including height (Wetherbee et al. USAXS and WAXS) that can detect order at the nm level. small angle.
The axial filament contains silicatein molecules organised into a filamentous form. 1999). Furthermore. 1998. 1999) and able to catalyse the formation of silica from alkoxysilanes. The spicules range in size over several length scales with the largest measuring ca. It is reported that. These particles are then arranged into larger scale structures admixed with the biomolecules that include silicatein. Silicatein is enzymatically active (Shimizu et al. Zhou et al. a silicatein-associated protein (26 kDa). 2005) which is inactive until cleavage of a signal peptide and a propeptide occurs. . a galectin (Schröder et al. 14 kDa). 36.3 kDa (Muller et al. silicatein. Silicatein is a hydrolytic enzyme that has some structural analogies with cathepsin for which crystal structures are known. histidine and asparagine.1 kDa) (Schröder et al. 43. 2000). The smallest silica particles that have been measured by electron microscopy are of the order of 2–3 nm in size with little space between the particles. 2006) and collagen (Schröder et al. see later in this Chapter for an overview (including appropriate references) and elsewhere in the book for other chapters containing more detailed information.An Overview of Silica in Biology 299 Demospongiae) with the silica being deposited around an axial filament largely made up of protein. 8 mm in diameter by 3 m in length (Levi et al. 23 kDa involved in silica formation. a putative silicic acid transporter has been isolated (Schröder et al. Papers by Morse and coworkers and Muller and coworkers provide great detail on the structure and function of the principal protein. 1999) as well as a cluster of hydroxyl containing amino acids and hydrophobic patches on the surface that are probably used in the self-assembly of the protein molecules to form the axial filament. sponge collagen and other proteins. at least from S. The catalytic centre contains three amino acids. galectin. a selenoprotein (ca. although most recent studies have indicated that there is organic material intimately associated with the silica throughout the width of the spicule (Pisera 2003). 2004) with high sequence similarity to the Na+/ HCO3− cotransporter. In addition to this. Application of molecular biology techniques to the production of recombinant silicatein have used both Escherichia coli and the bacterial expression vector pQE-30 with some success and His-tag labelled and non His-tag labelled recombinant silicatein has been produced for biotechnological applications. silicase. a relatively small protein of molecular weight ca. all required for activity (Shimizu et al. domuncula include silicase (ca. Silicatein has also been detected in the extracellular space during spicule formation as a pro-enzyme of molecular weight ca. an enzyme that has been proposed to depolymerise amorphous silica. Cha et al. Spicules are synthesised by special cells. 1989) and the smallest having dimensions on the micron scale. 2005). with the diversity thought to be affected by the amount of silicon available to the organism (Maldonado et al. the sclerocytes. at least for Suberites domuncula. although some sponge species only generate one spicule type. 1998. only the phosphorylated form of silicatein is able to oligomerise to form silicatein dimers and trimers (Müller et al. Other proteins identified from silicified spicules. with synthesis occurring in a membrane (silicalemma)-bounded compartment (Simpson 1984). serine. others are known to produce many different spicule forms. 2003).
25 kDa for the polyamines (Kröger et al. 2005). More recently. The frustule has two halves with the upper half being known as the epitheca and the lower half as the hypotheca. All these observations indicate that the silica formation process is regulated. Perry 3 Silicification in Diatoms More than 100. This information combined with the fact that chemical inhibition of protein synthesis during valve development produced structural irregularities (Blank and Sullivan 1983) all pointed to the fact that protein synthesis is an essential part of the silicified valve formation process. 2000). 1970). The mineral structures are formed from ca. 2000).6–1.C. 1999. Reproduction involves division of the cell and the formation of new mineralised valves within a membrane-bounded compartment known as the silica deposition vesicle (SDV). 4–17 kDa for the silaffins and 0. . Both halves of the frustule are known as valves and the structures that overlap the two valves are known as the girdle bands. by methylation and hydroxylation or by the incorporation of an oligomeric structure built up from N-propylamine units showing various levels of methylation (Kröger et al. The serine units are modified by phosphorylation (Kröger et al. Biochemical analysis of cell wall isolates identified unusual amino acids including a dihydroxyproline and a trimethylated lysine derivative as well as its phosphorylated analogue (Nakajima and Volcani 1969. 2000) using mild etching methods in conjunction with AFM analysis have shown that the packing density of the silica particles varies between different parts of the mineralised structure. They occur in both freshwater and in seawater and different species contain different amounts of amorphous silica in their cell walls that are known as frustules.000 species of single-celled algae (diatoms) are currently known.300 C. 40 nm in diameter that are then packed in specific patterns within the developing structure. The silaffin that has been most studied is Sil-1 which contains a series of repeating units containing high levels of posttranslationally-modified lysine and serine. The peptide sequence derived from the sil1p gene is known as R5 and has been used in model studies of silica formation as well as in nanobiotechnological applications. Early experimental studies on cultures of diatoms found that silica formation occurred when cells were also synthesising proteins (Coombs and Volcani 1968). a variety of biomolecules have been found specifically associated with the mineral phase of the diatom Cylindrotheca fusiformis that include silaffins and polyamines. although a wider range of functionality has been identified and now includes tertiary ammonium groups (Sumper et al. Electron microscopy studies of the early stages of valve development and studies by others (Wetherbee et al. 2001). These families of molecules are all of low molecular weight. 5 nm amorphous particles that initially appear to form small aggregates ca. The valve structures are composed of a range of organic molecules and silica and can be porous with each diatom species having a very specific pattern of mineral/ pore structures. The further class of molecules identified in a range of diatoms are low molecular weight (by comparison with proteins) linear polyamines composed of N-methylaminopropyl or aminopropyl units (Kröger at al. ca. 2002) and the lysine units by dimethylation.
Urticales and Commelinaceae show intermediate Si accumulation (2–4% Si).5 g/kg in polished rice through 50 g/kg in rice bran. Although biomolecules are clearly involved in the formation of the patterned silica deposits it should be remembered that the shape of the SDV is also governed by microtubules derived from actin and that microfilaments are also involved (Chiappino and Volcani 1977. roots leaves and other spaces. the uptake of silicon from solution is the result of the operation of two different transport mechanisms. a good example is the variation between 0. There have been few detailed studies of Si-uptake. Studies of cucumber (moderate accumulator) and tomato (low level accumulator) have shown much lower levels of LSi1 with further transport of any silicic acid into the xylem being by passive diffusion. cell lumens. 130 g/kg in rice straw. glutamate acetyltransferase. was identified. Silica deposition in diatoms occurs within the silica deposition vesicle which itself is surrounded by a membrane. Their role in the growth of the SDV. Plants deprived of silicon are often weaker structurally and more prone to abnormalities of growth. intracellular spaces. while most other species demonstrate little accumulation (Epstein 1994). and through the use of synchronised cultures and the measurement of mRNA levels they were able to identify many (>10) proteins that correlated with mRNA levels of silaffin synthesis (taken as a marker for cell wall formation) during cell growth. Silica can occur in cell walls. 1998) which are coupled with the transport of sodium but beyond this little is know concerning transport within the diatom itself. The second transporter is responsible for xylem loading of Si (Mitani and Ma 2005). Even within single hair cells more than one type of silica . One specific enzyme. development and reproduction (Epstein 1999). 2006) has probed the synthesis of membrane-associated proteins. but for rice. and different parts of the same plant can show large differences in Si accumulation. In the lateral roots. The silica structures formed and their localisation show great variation between individual plant families. 4 Silicification in Plants Silica deposition occurs in many plant families though the highest levels are found in the primitive plants such as the Equisetaceae and the Gramineae (>4% Si).An Overview of Silica in Biology 301 Molecular biology approaches to the understanding of silica formation in diatoms have identified silicic acid transporters (Hildebrand et al. the silicalemma. the manipulation of its shape and their relationship to the biomolecules such as the silaffins and polyamines remains to be determined. Van der Meene and Pickett-Heaps 2002). A very elegant study by Hildebrand and co workers (Frigeri et al. providing evidence for the direct involvement of this enzyme in the formation of the silica frustule. a low affinity transporter (Lsi1) is responsible for the uptake of silicic acid from the external solution to the root cortical cells (Ma and Yamaji 2006). 230 g/kg in rice hulls to 350 g/kg in rice joints (found at the base of the grain) (Van Hoest 2006). Application of a specific enzymic inhibitor for ornithine decarboxylase resulted in dramatic changes to the silica structures produced. 1997. Cucurbitales.
fibrillar and globular) that differ in terms of their fundamental particle size. three distinct types of silica have been identified (sheet-like. aggregation characteristics. In many other plants. The cell wall is the site of deposition for most plant silica deposits and is a highly complex matrix that contains cellulose. the silica structures so formed perform a structural role (Currie and Perry 2007). Perry can be identified. An alternative hypothesis is that silicon is a biologically active element capable of triggering a broad range of natural defences. notably those that produce food crops. in detailed studies of plant hairs on the lemma of the grass Phalaris canariensis L. These gross silica structures (known as phytoliths) when found at archaeological sites have proved useful in identifying the plant species used by a population at a given time. 1994. but studies in the early 1990s identified that plant silicas contained protein and carbohydrate-containing biomolecules intimately associated with the mineral phase (Harrison 1996). Progress in the understanding of plant silicification is not as far advanced as for sponges and diatoms.C. and silica bodies found for example on bulliform cells of rice leaves. silica infills certain cells such as silica cells. 2003). more complex polysaccharides such as hemicelluloses and pectins rich in galacturonic acid residues that are cross linked by the coordination of Ca ions. This biochemical environment may be capable of modifying the solubility and binding possibilities of the silica phase as it develops (Perry and Keeling-Tucker 1998. Similar biologically active defence agents (increased production of glycosylated phenolics and antimicrobial products such as flavonoid phytoalexins) have been induced in the presence of silica for wheat and rice blast . For example. however. 1984).302 C. Much experimental work is still required to increase our understanding of the relationship between the silica deposits and the biochemical environment in which they are found. proteins and phenolic compounds including lignin. 1992). studies on plants containing ‘silicon’ have shown that the presence of the element in some form has been found to alleviate many abiotic and biotic stresses. 5 Role of Silica in Stress Relief In all three main classes of silicifying organisms. Beyond this. The deposition of silica as a physical barrier to penetration and reduction in the susceptibility to enzymatic degradation by fungal pathogens has been explored (Yoshida et al. This was first demonstrated in cucumbers whereby silicon-treated plants demonstrated enhanced activity of a range of enzymes such as chitinases. extent of hydration and location within the plant hair (Perry et al. Fawe et al. As a consequence of this. 1998). Similar structures and others have also been observed in other plant species such as members of the Equisetaceae family and in nettle hairs (Perry and Fraser 1991). It is not known how the presence of silicon exerts such a protective effect although roles including provision of a physical and/or biochemical defence system have been proposed. Cherif et al.. dumb-bell-shaped cells located on vascular bundles. silicates are incorporated into many fertilisers. peroxidases and polyphenoloxydases as well as flavenoid phytoalexins to protect against fungal pathogens (Cherif et al. 1962.
A variety of silicic acid precursors including salts of silicates (e. 2007). Perry and Lu 1992 and all later publications from the Perry group). drought and temperature stresses (Liang et al. and alkylsilanes (e. Experiments performed on cucumber leaves following fungal infection identified that further resistance to infection is acquired by expression of a proline-rich protein together with the presence of silica at the site of attempted penetration (Kauss et al. 2004. 2005). with clear analogies being observed with the composition of the R5 peptide found within the silica of selected diatom species (Currie and Perry 2007). Si(OCH3)4 (TMOS). Polymerisation and Materials Formation In order to understand how silica-associated biomolecules affect silicic acid polymerisation and materials formation. ascorbate) against Mn toxicity (Shi et al. and increased release of phenolics with a strong Al chelating ability for Al tolerance (Kidd et al.g. but in solutions of alkoxysilanes. All the silicic acid precursor . 1999. Rodrigues et al. Si(OC2H5)(OH)3 and Si(OH)4). but many of the experiments designed to understand the process are performed in largely non-aqueous solutions using alkoxysilanes as the silicon precursor. CH3Si(OCH3)3. superoxide dismutase. Kröger et al. K2[Si(C6H4O2)3]·xH2O). Cha et al. all of which show different reactivity towards condensation and hence polymerisation. and the presence of silicified structures in plants has also been shown to improve plant tolerance to high temperatures (Wang et al. and Si(OC2H5)4 (TEOS)). salts of silicon complexes (e. Moussa 2006). diluted and buffered Na2SiO3. In addition. Coradin and Livage 2001).g. All species present in the reaction mixture have some effect on the silica formation process (Iler 1979) and this fact should not be ignored. 2003). The proposed mechanism for the alleviation of Mn. Si(OC2H5)2(OH)2. All biological silica forms from an aqueous environment. 1999) have been used.g. alkoxysilanes (e. tetraethoxysilane (Si(OC2H5)4).g. 2003.An Overview of Silica in Biology 303 (Bélanger et al.g. silicon application has been found to alleviate metal toxicity. hydrolysis yields a mixture of monomers (Si(OC2H5)3OH. Zhou et al. increased enzymatic (e. salinity. 2001).g. The c-terminal end of this protein contained a high density of lysine and arginine residues that were proposed to catalyse the localised deposition of silica at the site of vulnerability. e. 2005). 1999. SOD) and non-enzymatic antioxidant production (e. 6 Laboratory Studies of Silica Condensation. The resistance to salt stress has been found to be due to the enhancement of antioxidants such as SOD and catalase preventing oxidative membrane damage (Zhu et al. If we only consider the differences in the molecules available for silica formation. Al and Zn toxicities is through accumulation of Zn as a silicate (Neuman and zur Nieden 2001).g. several laboratory-based model systems have been developed. Cd. Application of silicon (usually as a soluble silicate) can also bring about drought tolerance possibly as a result of decreased transpiration (Epstein 1999). then for reaction in an aqueous environment the building block is orthosilicic acid (Si(OH)4) or its anion (Si(OH)3O−). 2003).
sold state 29Si NMR and electron microscopy in order to determine particle sizes. Tilburey et al. partly because of the very limited quantities available. porosity. The nature of the side chain and the number of these within a peptide both affect the silica formation process. or incomplete breakdown to monomeric silicic acid (silicate solutions). Coradin and Livage (2001) have studied the effect of four amino acids (lysine. (2004) explored the effect of eleven amino acids (lysine. the silaffins (diatom cell wall proteins) and long-chain polyamines of diatoms (Sumper and Kroger 2004) influence both the rate of silicate polymerisation and also the structures formed. tyrosine. polymerisation and aggregation behaviour. very fast kinetics preventing detailed analysis of kinetics (alkoxysilanes). 2007.304 C.g. threonine. aspartic acid and proline) and their homopeptides (n = ca. presence of methanol. and n = ca. ethanol or catechol as breakdown products. Tomczak et al. Perry systems listed above have their disadvantages. with positively charged side chains showing the largest effect via electrostatic interactions between positively charged . gas adsorption. 2006. alanine.C. atomic absorption and inductively coupled plasma analysis are all methods that have been used to measure silicon concentrations in solution (Iler 1979. serine. 7 The Effect of Biologically Relevant Solution Additives on Condensation. 2004. other researchers have used chemical mimics of these biomolecules to further explore the capacity of these and similar molecules to modify silica condensation. 2005. glutamine. as well as morphological characteristics on a range of length scales as described earlier in this chapter. Belton et al. aspartic acid and proline. Analysis of the materials formed is possible by a number of methods including dynamic light scattering. which are most sensitive to low concentrations). glycine. surface area. FTIR. Patwardhan et al. aggregate characteristics. 50 for poly(-l-) lysine. Polymerisation and Materials Formation In vitro studies of silica formation using molecules extracted from biosilica have shown that silicatein (sponge protein). arginine. either as the extracted axial filament or as single molecules. amino acids and recombinant proteins have also been performed (e. Coradin and Livage 2001. while plant intrasilica isolates modify condensation kinetics and silica form (Perry and Keeling-Tucker 1998. Charged side chains have the most effect. Perry 2003). asparagine. Complementary in vitro studies using peptides. Such studies have indicated that all these bioextracts can act as catalysts and/or as templating agents and. serine. glutamic acid and proline) together with homopeptides of glycine (1–5 amino acid units) and lysine (1–5 amino acids units) on silica formation from solutions containing monomeric silicic acid derived from a silicon catecholate complex. and surface and local molecular chemistry. Belton et al. 2007). 1999). 130 for poly(-l-)serine) on silica formation using buffered solutions of diluted sodium silicate over a range of pH values. Colorimetric methods (molybdenum yellow and blue. 2003). catalyses the hydrolysis and condensation of alkoxysilanes (Cha et al.
together with reduced silica surface area as n increased (Belton et al. 2007).An Overview of Silica in Biology 305 amino acid side chains and negatively charged silica species. bioengineers. with particularly strong effects on the dissolution process suggesting the promotion of structural reorganisation. Putrescine. 2005a). influenced aggregation according to molecule length. 2007). spermidine and putrescine. a simple alkyldiamine. In solution. pore volume and average pore diameter that could be correlated with increasing amounts of organic material entrapped within the precipitated silica (alpha helical < beta sheet < random coil. Other molecules of biological relevance that have been examined in model reaction systems are the polyamines. 2004). these conclusions were verified by the analysis of a number of synthetically produced homologues (Belton et al. Studies with longer chain poly-l-lysines (Tomczak et al. all of the proteins exhibited self-assembled structures that were disrupted by the presence of the negatively charged. While only two natural polyamines were examined. Detailed studies have also been performed with recombinant silicatein (26 kDa) and with three highly basic recombinant proteins pYT320 (alpha helical). 2005. 2006) have demonstrated the ability of this macromolecule to form silica hexagons with either TMOS or waterglass as the silicic acid precursors. R5 < silicatein). spermidine and spermine. Patwardhan et al. The hexagons are composed of amorphous silica templated on packed arrays of alpha helical poly-l-lysine molecules. The small positively charged peptides are thought to be able to bridge particles to produce extended structures. The pI of the side chain functionality correlates positively with acceleration of the early stage reaction kinetics and the hydrophobicity of the side chain with the surface area of the silica material formed. Analysis of silicas produced by thermogravimetric analysis and nitrogen gas adsorption showed a decreasing trend in surface area. Reactions using nitrogen-containing amino acids modified the morphology of the silica formed with granular structures being created suggesting their ability to stabilise aggregates. The addition of L-lysine homopeptides of increasing length (n = 1–5) to the model reaction system showed increases in rates of oligomer formation and aggregate growth. Longer chain amines. as well as recombinant proteins and synthetic peptides based on the biomolecules . silica particles. which are sometimes found conjugated to phenolic acids. Sponges and Higher Plants Materials scientists. 2005b). Similar studies on highly hydroxylated proteins (sericin) and other hydroxyl-containing molecules found little effect on silica formation in highly aqueous media due to competition with water for hydrogen bonded interactions between the additives used and the forming silica structures (Tilburey et al. chemists and theoretical chemists have begun to utilise the molecules isolated from the silica of mineralised organisms. All the recombinant proteins investigated affected the early stages of silica formation. pYT338 (beta sheet) and pYT287 (random coil) (Patwardhan et al. 8 Applications Using the Biomolecules as Identified from Diatoms. early stage. spermine. was able to increase the rate of condensation and the rate of particle aggregation (Belton et al.
2001). The first application of the R5 (repeating peptide sequence within Sil-1A) peptide was to create an ordered organic/inorganic array of silica nanospheres within a polymer hologram originally created by two-photon-induced polymerisation. 1999. with the R5 peptide being used to promote localised condensation under pH neutral reaction conditions that were compatible with the polymer matrix (Brott et al. The peptide has also been used to generate unusual silica morphologies including arched and elongated structures (Naik et al. fusiformis showed that the naturally occurring protein was able to generate spheres (sphere diameter size range 50–700 nm depending on whether single silaffins or mixtures of silaffins were used) in vitro from metastable solutions of silicic acid generated from alkoxysilanes at neutral pH (Kröger et al. The authors found that the presence of the RRIL motif in the peptide was crucial for activity and that this was related to the ability of the peptide to form a supramolecular self-assembled structure. The incorporation of a regular array of silica nanospheres in the polymer hologram lead to a nearly 50-fold increase in diffraction efficiency. These materials have potential use in the biomaterials field including replacement bone and dental materials. isolated or prepared without the posttranslational modifications was found to promote sphere formation down to pH 4 provided that phosphate ions were present in the reaction medium. Perry previously identified by others. 2004) to produce composite materials with improved stability of the enzyme and no loss of activity. The formation of silica under physiologically compatible (benign) reaction conditions has also been exploited by the same group in the encapsulation of enzymes (Luckarift et al. More recently. 2006). to perform experiments (including in silico) aimed at understanding the biological process of silicification or for developing new materials using a biomimetic approach.C. The presence of the highly positively charged side chains is thought to be required for the formation of silica under mildly acidic conditions with the presence of the phosphate groups providing an intrinsic source of anions.306 C. Silaffin-1A. The chimeric proteins have been used to generate silica polymer nanocomposites in the form of films and fibers whose composite morphology and structure can be regulated by changes to processing conditions. 2003). the R5 peptide has been attached as a fusion to a protein from Nephila clavipes spider dragline silk to generate a novel family of chimeric proteins for use in model materials-forming reactions (Foo et al. and the authors proposed that the adopted experimental approach may find use in photonic applications. A synthetic site-directed mutagenesis study of non-posttranslationally-modified R5 has explored the effect of amino acid sequence on the activity of the peptides on silica formation in vitro (Knecht and Wright 2003). . 2002). 9 Technological and Model Advances Utilising Diatoms The scientists who identified the presence of silaffins or isolated and characterised them from C.
ZrO2. The technique has the acronym BaSIC (biosculpting and shape-preserving inorganic conversion) (Dickerson et al. 2005. and synthetic propylamines built from the N-methyl propylamine as found in diatom silica (Annenkov et al. 2004) and polypropyleneimine (PPI) amine terminated dendrimers (Knecht and Wright 2004). In the simulations. R5) under a range of volume fractions (concentrations). BaTiO3: Weatherspoon et al...g. the element silicon (Bao et al. Cai et al. together with diamines of various chain length (Belton et al. polylysine (PLL) of different chain lengths (Coradin and Livage 2001. automotive and defence applications. 2007) and boron nitride (Kusari et al. 2005). 2007) with complex shapes for potential use in environmental. 2006). namely the presence of charged amine groups.. diatom silica frustules have been used to fabricate a range of different materials using the frustule as the shaped template which is then converted into a different material at high temperatures (at least compared with biological synthesis) whilst retaining the shape of the organism. the model peptides selfassemble to form spherical clusters.to 100-nm silica building blocks from which diatom skeletons and synthetic nanospheres are constructed (Lenoci and Camp 2006). polymers such as poly(allylamine hydrochloride) (PAH). aerospace. as well as small molecules such as amino acids and small peptide oligomers (Belton et al. 2005. Thermal treatment to 600°C was still required for conversion to crystalline anatase. poly(2-(dimethylamino)ethyl methacrylate) (poly(DMAEMA)) (Kim et al. Shian et al.. In some instances. porosity and surface chemistry. 2006). 2006) with entrapment of the peptide in both materials as formed. have been explored as catalysts and templates in the formation of . 2006.An Overview of Silica in Biology 307 More recently. Native silicateins. later studies have utilised diatoms with a wide range of morphologies to generate a range of ceramics (MgO. Most recent uses to which R5 have been put include the synthesis of amorphous titania from titanium bis(ammonium lactate)dihydroxide (Sewell and Wright 2006) and the synthesis of amorphous titanium phosphate in the form of spheres and fused structures (Cole et al. but the temperature at which conversion to rutile occurred was some 125°C lower than found for similar experiments performed with silicatein from sponges (Sewell and Wright 2006). In a totally different chemical approach. domuncula. have all been found to affect the silica formation process at physiological pH. Many similar studies have been made using peptides of simpler composition that retain a key feature of the R5 peptide. telecommunications. Tomczak et al. as extracted from sponges such as Tethya aurantia and S. 2004).. Patwardhan et al. and whilst the earliest studies used silica generated in the presence of the R5 peptide. 2006). the mechanism by which this happens has been identified and should lead to greater predictive ability in the generation of silica with different structure including particle sizes. chemical. 2005a) and amines with varied spacing (Belton et al. networks of strands or bicontinuous structures with characteristic length scales from 12 to 45 nm. theoretical chemists using a coarse-grained simulation model have looked at the self-assembly of model peptides (e. polyethylenimine (PEI) (Patwardhan and Clarson 2002). For example. biomedical. density. The authors suggest that the self-assembled structures act as either nucleation points or scaffolds for the deposition of the 10. 2005b).
the metals silver (Schröder et al. It is less clear how precursors such as nitrates of gallium and silver. galectin. Another difference between the naturally occurring silicatein and that produced by recombinant methods is that it can be produced with a His-tag at the c-terminus. 2007) and gold (Tahir et al. One approach has been to use molecular biology techniques to create whole cell biocatalysts for inorganic and organic/polymer applications through the recombinant expression and presentation of folded functional silicatein-alpha at the external surfaces of cells (Curnow et al. 2005) and gallium (Kisailus et al. titania and zirconia: Tahir et al. a whole range of different inorganic materials. 2005) which is why reactions with substrates having significant organic mass (e. 2006). The use of silicatein in nano(bio)technology is expanding due to the ability of scientists to produce recombinant material. 2005). collagen and other as yet unidentified proteins that make up the mineralising environment into which silica forms and is moulded (Schröder et al. probably has an active site that recognises substrates primarily through main chain and side chain interactions (Curnow et al. Silicatein.g. isopropoxide. Perry silica (Cha et al. 2006) and organic materials such as poly (l-lactide) (Curnow et al. bis(ammonium lactato)) have perhaps been successful. zirconium (Tahir et al. including oxides of titanium (Sumerel et al. It is clear from the data accumulated to date that the hydrolytic activity of silicatein is somewhat unspecific! In all cases. Silicatein attached to culture plate plastic has been used to generate silica which was then used to culture human osteosarcoma SaOS-2 cells that were found to generate more calcium phosphate in the presence of the silica (Schröder et al.C.308 C. 2005). 2005). 2007). 2007) or can be used to advantage in the preparation of surfaces functionalised with the protein. 1999) and. The initial study generated layered titanium phosphates at the outer membrane of the silicatein-displaying cells at . It is possible using different methods of extraction to produce filaments of silicatein alone by HF treatment or by use of lysis media combined with urea to retain the intricate assembly of proteins that includes silicatein. as well as phosphates of titanium (Curnow et al. albeit without the posttranslational modifications found in nature. and silver: Schröder et al. 2003). 2006. Several routes are currently being explored by scientists to surmount this problem. 2005) However. 2005. 2007) and oxides (silica. 2006). (Kisailus et al. other less expensive methods could be used to prepare the silica under the same biocompatible conditions! Problems with expression and reconstitution of recombinant silicatein due to its high degree of hydrophobicity have limited the applications to date as efficient expression to generate large quantities of protein has not been possible. have been generated. by structural analogy with the cathepsin family of enzymes. 2005). This tag can be cleaved enzymatically during purification using an enterokinase (Schröder et al. more latterly. ethyl. Silicatein-functionalised surfaces been used in the formation of metals (gold: Tahir et al. water-soluble precursors were used and reactions performed under approximately physiological conditions. fluoride anions of zirconium and chloride containing anions of gold fit the same proposed mechanism although interaction of active silicatein with a metal and its precursor ligands with modification of the partial charges on species present has been used to explain the activity of silicatein in the generation of oxides and oxyhydroxides of gallium.
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