We report on the secondary structure of the recombinant silaffin protein, rSilC, at liquid-solid and air-solid interfaces with polyelectrolyte layer-by-layer (LbL) films serving as templates to mediate protein adsorption. By exploiting in situ ATR-FTIR spectroscopy directly we revealed that the molecular layer of rSilC adsorbed on the LbL surface exhibits a random coil conformation in a hydrated state. In contrast, the partial transition into β-sheet state is observed when the protein is deposited by spin casting with fast water removal. Both forms of rSilC surface layers are capable of mineralization of titania nanostructures at ambient conditions. We suggest that the careful tailoring of the silaffin secondary structure both at interfaces and in solution with particular amino acid sequences capable of intra- and inter-molecular transformations is essential for directing the "bio-titania" mineralization resulting in nanoparticles to large microstructures. © 2010 The Royal Society of Chemistry.