In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype

Abstract

Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide-metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/ aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.

The Geoglobus acetivorans Genome: Fe(III) Reduction, Acetate Utilization, Autotrophic Growth, and Degradation of Aromatic Compounds in a Hyperthermophilic Archaeon

“…The most probable operon of Fe(III) reduction in G. acetivorans consists of the genes Gace_1843 to -1847, encoding five multiheme c-type cytochromes with predicted membrane localizations that are necessary to contact the insoluble electron acceptor (ferrihydrite). Among these genes, Gace_1847 encodes a putative protein that includes several c-type multiheme domains, an outer surface membrane anchor region, and two hematite-binding motifs, described previously for a putative terminal Fe(III)-oxide reductase of Shewanella oneidensis (58). One of these motifs in Gace_1847 is adjacent to a heme c-binding motif, supporting the idea of the involvement of putative hematite-binding residues in electron transfer processes performed by this protein.…”

Binding of Silver Nanoparticles to Bacterial Proteins Depends on Surface Modifications and Inhibits Enzymatic Activity

“…For example, the TFTY motif in the 1055 Da fragment of TNase is similar to hydroxyland aromatic-rich sequences found in synthetic peptides with high affinity for AgNPs (42). Due to the small sample size of protein fragments listed in Table 1, we were unable to identify specific recurring binding motifs or sequence similarities across all peptides that have been observed for Ag or other metals using high-throughput screening methods (42)(43)(44).…”

Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella oneidensis Outer Membrane Cytochromes MtrC and OmcA

“…Consistent with this hypothesis, MtrC and OmcA are predicted to possess a putative binding site for solid metal oxide (17) and purified MtrC and OmcA bind and directly transfer electrons to the oxide (10). The MtrC and OmcA also are found in the extracellular polymeric substance produced by the bacterial cells under anaerobic, uranyl-reducing conditions, where they are spatially colocated with nano-domain uraninite (UO 2 ) (18).…”