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Molecular Biomimetics: Linking Polypeptides to Inorganic Structures

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Molecular Biomimetics: Linking Polypeptides to Inorganic Structures Molecular Biomimetics: Linking Polypeptides to Inorganic 8 Structures Candan Tamerler and Mehmet Sarikaya Abstract Introduction In developing novel materials, Mother Na- Mother Nature has provided a high degree ture gave us enormous inspiration with its of sophistication in materials and systems already existing highly organized structures at the nanometer scale. Naturally occurring varying from macro to nano- and molecu- materials have remarkable functional prop- lar scales. Biological hard tissues are the ex- erties derived from their highly organized amples of composite hybrid materials hav- structures from the molecular to the nano-, ing both inorganic and organic phases that micro-, and macroscales, with intricate ar- exhibit excellent physical properties, all chitectures (Fig. 8.1). They are self-direct- based on their evolved architectural design. ed in their organization and formation, Biocomposites incorporate both structural operate in water environment, dynamic in macromolecules, such as proteins, lipids their interaction with the surroundings, and polysaccharides and minerals, such as complex in their structures and functions hydroxyapatite, silica, magnetite, and cal- self-healing in damage control. Yet, they are cite. Among these, proteins are the most not achievable in purely synthetic systems instrumental components for use in mate- under the same efficient energy conserving, rials fabrication because of their molecu- no waste delivering manner (Lowenstam, lar recognition, binding and self-assembly 1989; Sarikaya, 1999; Ball, 2001; Sanchez characteristics. Consequently, based on this et al., 2005). With the integration of recent premise, inorganic surface specific polypep- developments in molecular and nanoscale tides could be a key in the molecular engi- engineering in physical sciences, and the neering of biomimetic materials. Peptides advances in molecular biology, materials can now be selected by directed evolution, fabrication through biology, biomimetics, adapted from molecular biology, by using is now entering the molecular scale (Sari- combinatorial peptide libraries, analogous kaya et al., 1995; 2003). Utilizing closely to natural selection. Adapting genetic ap- controlled molecular, nano- and micro- proaches further allow to redesign, modify structures through molecular recognition, or engineer the selected first generation templating and self assembling properties peptides for their ultimate utilization in of Nature, molecular biomimetics is evolv- bionanotechnological applications as mo- ing from the true marriage of physical and lecular erectors, couplers, growth modifiers biological sciences (Niemeyer, 2001; Sari- and bracers. kaya et al., 2004). 1 | Tamerler and Sarikaya Figure .1 Examples of biologically fabricated complex nanomaterials. (A) Layered nanocomposite: growth edge of nacre (pearl) of abalone (Haliotis rufescens): Aragonite platelets separated by a thin-film of organic matrix. (B) Nanomagnetics: magnetite (Fe3O4) particles in magnetotactic bacteria: Aquaspirillum magnetotacticum. (C) Hierarchical structure: 3D woven enamel rods of hydroxyapatite crystallites of mouse teeth. (D) Biofiber-optics: a layered siliceous spicular optical fiber of a sponge (Rosella) and its apex (inset), novel design of a lens, a light collector. Biological hard tissues are the ex- modifiers, brazers and molecular erector amples of composite hybrid materials sets, for self assembly of materials with having both inorganic and organic phases controlled organization and desired func- and exhibiting excellent physical proper- tions. The realization of heterofunctional ties thereby creating ecological intakes for nanostructure materials and systems could the host organisms (Mann 1996; Mann et be at three levels, all occurring simulta- al., 1998; Ball, 2001). Biocomposites have neously feed backing each other as the incorporated both structural macromol- Mother Nature produces her materials and ecules such as proteins, lipids and polysac- components. The first is that the inorganic charides and minerals, such as hydroxyap- specific peptides are identified and pep- atite, silica, magnetite, and calcite (Berman tide/protein templates are designed at the et al., 1988; Ratner et al., 1996; Cha et al., molecular level through directed evolution 1999; Mayer et al., 2002). Among these, using the tools of molecular biology. This proteins are the most promising molecules ensures the molecular-scale up process- because of their recognition, binding and ing for nanostructural control at the low- self assembly characteristics. The advan- est dimensional scale possible. The second tage of a molecular biomimetic approach is that these peptide building blocks can to nanotechnology, therefore, is that in- be further engineered to tailor their rec- organic surface-specific proteins could be ognition and assembly properties similar used as couplers, growth initiators and to the Nature’s way of successive cycles of Tools for Bionanotechnology | 1 mutation and generation can lead to prog- tems, polypeptides are the major displayed eny with improved features eventually for molecules, which can be screened for the their utilization as couplers or molecular specific properties. erector sets to join synthetic entities, includ- In the following sections, we provide ing nanoparticles, functional polymers, an overview of molecular biomimetics ap- or other nanostructures onto molecular proaches to achieve the premises of nano- templates (molecular and nanoscale rec- technology and summarize its potentials ognition). Finally, the third is that the bio- and limitations. Then, we look into the logical molecules self- and coassemble into ways finding polypeptides that recognize ordered nanostructures. This ensures an inorganics, and describe the protocols energy efficient robust assembly process of combinatorial biology for identifying, for achieving complex nano-, and possibly characterizing and engineering peptides to hierarchical-structures, similar to those utilize them as molecular buildings blocks found in Nature (self-assembly) (Sarikaya of future bimimetic materials and systems. et al., 2004). Here we emphasize on the cell surface and There are different ways to obtain the phage display technologies that are well inorganic surface specific proteins such as adapted for the identification of inorganic extraction from hard tissue, designing them surface specific peptides, and to further tai- via theoretical approaches or utilizing the lor the characterized peptides using post- limited number of already existing ones selection engineering. We then discuss (Carlolou et al., 1988; Paine et al., 1996; the possible mechanisms through which a Schneider et al., 1998; Kroger et al., 1999; given protein might selectively bind to an Cha et al., 1999; Liou et al., 2000). Each of inorganic based on their thoroughly bind- these approaches has its own major limita- ing characterization. We present examples tions and may not be practical enough to of current achievements in utilizing engi- serve in all nanoscale-engineering applica- neered polypeptides are given to demon- tions. Inorganic surface specific peptides strate their potential use and, finally, we could be the key in the molecular engi- present future prospects of molecular bio- neering of bioinspired materials. However, mimetics in bio- to nanotechnologies. there are only a few polypeptides have been identified that specifically bind to the in- Potentials and limitations organics. With the recent developments in of nanotechnology recombinant DNA technology, these inor- The fundamental premise in the field of ganic surface specific proteins can now be nanotechnology has been that the length designed, modified or engineered for the scales, which characterize materials struc- production of nanostructured materials. ture and organization, predominantly de- During the last decades, combinatorial bi- termine their physical properties (Drexler, ology based molecular library systems have 1992; Schmid, 1994; Ferry et al., 1997; been developed for selecting substrate- Katz et al., 2004). Mechanical properties specific peptide units, mostly for medical of nanocomposites, light harvesting prop- applications but only recently they are ap- erties of nanocrystals, stain defender prop- plied for selecting short peptides for inor- erties of nanoparticles, magnetic properties ganic surfaces (Brown, 1997; Whaley et al., of single-domained particles, barrier prop- 2000; Gaskin et al., 2000; Naik et al., 2002; erties of nanoclays to extend the shelf lifes Sarikaya et al., 2004). In these library sys- of bottles, and solution properties of col- 1 | Tamerler and Sarikaya loidal suspensions are all examples to show etry or functionality. One way to overcome that nanotechnology is not a futuristic tech- this problem is to combine “self-assembly” nology, it is already establishing its place in with more conventional “bottom-up tech- our daily life (Jackson et al., 2002; Shipway nology” to provide suitable functionalities et al., 2001; Hoenlein et al., 2003; Thayer with specific structures. However, there a et al., 2004). All of the given examples number of challenges to be overcome such correlate directly to the nanometer-scale as if the structures available from “self-as- structures that characterize these systems. sembly” technique can provide function- In building the nanometer scale structures, ality comparable to that realized by “bot- the approach is to design molecule by mol- tom-up” process, or if the architectures
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