Molecular Biomimetics: Linking Polypeptides to Inorganic Structures 6 Candan Tamerier and Mehmet Sarikaya Abstract In developing novel materials, Mother Na: ture gave us enormous inepiarion with is already existing highly organized structures varying feo macro to nano- and molecu- lar scales. Biological hard tissues are the ex- ampies of composite hybrid materials hav ing both inorganic and organic phases that exhibit excellene physical properties, all based on their evolved architectural design. Biocomposites incorporate both structural ‘macromolecules, such as proteins, lipids and polysaccharides and minerals, such as tydroxyapatee silica, magnetite, and cal- cite. Among these, proteins are the most instrumental components for use in mate~ tials fabrication because of their molecu~ lar recognition, binding and self-assembly characteristics. Consequently, based on this premise inorganic surface specific polypep- Sides could be a key in the molecular engi- neering of biomimerie materials. Peptides can now be selected by dieected evolution, adapted from molecular biology, by using combinatorial peptide libraries, analogous ro natural selection. Adapting genetic ap- proaches farther allow ro redesign, modify or engineer the selected first generation peptides for their ultimate utilization in bionanovechnological applications as mo- lecular erectors, couplers geoweh modifiers introduction “Mother Narure has provided a high degree of sophistication in materials and systems atthe nanometer sale Naturally occurring raterials have remarkable functional prop eries derived from thei highly organized seructres from the molecular co the nano-, riero-, and macrescaes, with intricate ar- chivecrutes (Fig, 81). They ae self-direce: ed in cheir orgarization and formation, operat in water environment, dynamic in their interaction with the sorroundings, complex in ther structures and functions self-heatingin damage conte. Yet chey are not achievable in purely synthetic asters ander she same eff cient energy conserving, no waste delivering manner (Lovenstam, 1989; Sarikaya, 1999; Ball, 2001; Sanchez etal, 2005), With the integration of recent Gevelopments in molecular and nanoseale engineering in physical sciences, and the aavances in. moleclae biology, materials fabrication through biology, biomimeies, is now entering the molecular seal (Sar kaya etal, 1995; 2003). Ussing closely controlled moleclar, nano- and) micro- feeuctutes through molecular recognition, templating and self assembling properties of Nature, molecu'ar biomimesis is evolv- ing fom the true marrage of physical and biological sciences (Niemeyer, 2001: Sar aya et at, 2004)192 | Tamer and Saray MAGNETIC (@)_ Magnetotactie Bacteri PIEZOELECTRIC Figure 8.1 Examples of biologicaly fabricated complex nanomaterials. iievot pear of molluaks | (A) OPTICAL if It ) Layered nanocomposite: growth adge of nacre (pear!) of abalone (Hafotisrufescens) Aragonite platelets ‘separated by a thin-film of organic matrix. (8) Nanomagneties: magnetite FeO.) particles in ‘magnetotactc bacteria: Aquaspinilum magnetotacticum. (0) Hierarchical structure: 3D woven enamel rods of hydroxyanatite crystallites of mouse teeth (0) Blofiber-opics: a layered siiceous spicular optical fiber of a sponge (Rosella) and its apex (inset), novel design of a lens, a light collector. Biological hard issues are the ex amples of composite hybrid materials having both inorganic and organic phases and exhibiting excellere physical proper- ties thereby creating ecological intakes for the host organisms (Mann 1996; Mann et sl, 1998; Ball, 2001). Biocomposites have incorporated both structural macromol- ecules such as proteins lipids and polysac charides and minerals, such as hydroxyap- atte, silica, magnerite, and calcite (Berman ct al, 1988; Ratner ¢a!, 1996; Cha etal, 1999; Mayer et al, 2002). Among these, proteins are the most promising molecules because of theit recognition, binding and self assembly characterstis. The advan- tage of a molecular biemimetic approach 0 nanotechnology, therefore, is that in organic surface-specific proceins could be used as couplers, growth initiators and modifiers, brazers and molecular er sets, for'self assembly of materials with controlled organization and desired func: tions. The realization of heterotunctional nanoscructure materials and systems could be at ehres neously feed backing each other as che Mother Nature produces her materials and levels, all occurring simulta components. The firs is that che inorganic specific peptides are identified and pep tide/protein cemplates are designed at the molecular level chrough dieecced evolutior using the tools of molecular biology. This ensures the molecular-scale up process ing for nanostruceural control ar the low est dimensional scale possible. The second is that these peptide building be further engineered to tailor thei rec cognition and assembly propercies similar 0 the Nature's way of successive cycles of ks can‘mutation and generation can lead to prog: iy with improved feacures eventually for their utilization as couplers or molecular rector sets o join synthetic entities, includ- ing nanoparticles, functional polymers, for other nanostructures onto molecular templates (molecular and nanoscale rec~ cognition). Finally, che third is that the bio molecules self- and coassemble into be ordered nanoseractutes. This ensures an energy efficient robust assembly process for achieving complex nano-, and possibly hicrarchical-struccures, similar co chose found in Nature (self-assembly) (Sarikaya ct al, 2004) “There are different ways to obsain the inorganic surface specific proteins such as excraction fromhard issu, designing shem via cheoretical approaches or utilizing che limited number of already existing ones (Casolou et al, 1988; Paine et al, 1996: Schneider etal, 1998; Kroger etal, 1999; Cha et al., 1999; Liou et al., 2000). Bach of these approaches has its own major limita- tions and may not be practical enough serve in all nanoscale-engineering applica- sions. Inorganic surface specific peptides could be the key in the molecular engi- neering of bioinspited materials. However, there are only afew polypeptides have been identified chat specifically bind to the in organics. With che recent developments in recombinant DNA technology, these inor- sanic surface specific proteins can now be designed, modified or engineered for the production of nanostructured materials. Daring the lase decades, combinatorial bi- ology based molecular library systems have been developed for selecting substate- specific peptide units, mostly for medical applications bue only recently they are ap- plied for selecting shore peptides for inor- ganic surfaces (Brown, 1997; Whaley et al, 2000; Gaskin et al., 2000; Naik et al., 2002; Satikaya et al, 2004). these library sys- Tools for Bioranotoctrology | 198 tems, polypeptides are the major displayed molecules, which can be screened for the specific properties In the following sections, we provide an overview of molecular biomimetic proaches co achieve the premises of nano- technology and summarize its potentials and limitations. Then, we look into che ways finding polrpeptides that recognize inorganics, and describe the protocols of combinatorial biology for identifying, characterizing and engineering peptides t0 ucilize chem as molecular buildings blocks ‘of furure bimimetic materials and systems. Here we emphasize on the cell surface and phage display technologies char are well adapted forthe identification of inorganic surface specific peptides, and to fureher ta Jor the characterized peptides using post selection engineering, We then discuss the possible mechanisms through which a given protein might selectively bind ro an inorganic based o1 their thoroughly bind- ing characterization. We present examples of current achievements in utilizing engi- necred polypeptices are given co demon: strate their potential use and, finally, we present farure prespects of molecular bio ‘mimetics in bio~ e0 nanotechnologies. Potentials and limitations of nanotechnology The fundamental premise in the field of nanotechnology has been that che length scales, which characterize materials steuc- ture and organiza, predominanely de- termine their physial properties (Deedes, 1992; Schmid, 1994; Ferry et al, 1997; Kate etal, 2004), Mechanical properties of nanocomposites, light harvesting prop- certes of nanocrystals, rain defender prop erties of anoparies, magnetic properties of single-domained particles, barrier prop- erties of nanoclaysto extend the shelf lifes of bottles, and solution properties of col-