Two silica-precipitating peptides, silaffin-1A₁ and-1A ₂, both encoded by the sill gene from the diatom Cylindrotheca fusiformis, were extracted from cell walls and purified to homogeneity. The chemical structures were determined by protein chemical methods combined with mass spectrometry. Silaffin-1A₁ and -1A₂ consist of 15 and 18 amino acid residues, respectively. Each peptide contains a total of four lysine residues, which are all found to be post-translationally modified. In silaffin-1A₂ the lysine residues are clustered in two pairs in which the ε-amino group of the first residue is linked to a linear polyamine consisting of 5 to 11 N-methylated propylamine units, whereas the second lysine is converted to ε-N,N-dimethyllysine. Silaffin-1A₁ contains only a single lysine pair exhibiting the same structural features. One of the two remaining lysine residues was identified as ε-N,N,N-trimethyl-δ -hydroxylysine, a lysine derivative containing a quaternary ammonium group. The fourth lysine residue again is linked to a long-chain polyamine. Silaffin-1A₁ is the first peptide shown to contain ε-N,N,N-trimethyl-δ-hydroxylysine. In vitro, both peptides precipitate silica nanospheres within seconds when added to a monosilicic acid solution.