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Selection of peptides binding to metallic borides by screening M13 phage display libraries.

Ploss M, Facey SJ, Bruhn C, Zemel L, Hofmann K, Stark RW, Albert B, Hauer B - BMC Biotechnol. (2014)

Bottom Line: The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni3B emerged as the best binder for both substrates.Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni3B nanoparticles.We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany. bernhard.hauer@itb.uni-stuttgart.de.

ABSTRACT

Background: Metal borides are a class of inorganic solids that is much less known and investigated than for example metal oxides or intermetallics. At the same time it is a highly versatile and interesting class of compounds in terms of physical and chemical properties, like semiconductivity, ferromagnetism, or catalytic activity. This makes these substances attractive for the generation of new materials. Very little is known about the interaction between organic materials and borides. To generate nanostructured and composite materials which consist of metal borides and organic modifiers it is necessary to develop new synthetic strategies. Phage peptide display libraries are commonly used to select peptides that bind specifically to metals, metal oxides, and semiconductors. Further, these binding peptides can serve as templates to control the nucleation and growth of inorganic nanoparticles. Additionally, the combination of two different binding motifs into a single bifunctional phage could be useful for the generation of new composite materials.

Results: In this study, we have identified a unique set of sequences that bind to amorphous and crystalline nickel boride (Ni3B) nanoparticles, from a random peptide library using the phage display technique. Using this technique, strong binders were identified that are selective for nickel boride. Sequence analysis of the peptides revealed that the sequences exhibit similar, yet subtle different patterns of amino acid usage. Although a predominant binding motif was not observed, certain charged amino acids emerged as essential in specific binding to both substrates. The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni3B emerged as the best binder for both substrates. Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni3B nanoparticles.

Conclusions: This study is, to our knowledge, the first to identify peptides that bind specifically to amorphous and to crystalline Ni3B nanoparticles. We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.

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Amino acid distribution of the isolated peptide sequences. A total of 15 peptide sequences were analysed for amorphous Ni3B (grey bars) and a total of 28 peptide sequences were analysed for crystalline Ni3B (black bars).
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Figure 1: Amino acid distribution of the isolated peptide sequences. A total of 15 peptide sequences were analysed for amorphous Ni3B (grey bars) and a total of 28 peptide sequences were analysed for crystalline Ni3B (black bars).

Mentions: Due to the fact that cysteines interfere with the p3-mediated M13 infection process, no cysteines were present in the identified binding peptides [33]. The binding peptides showed approximately three-times more positively charged residues (K, R, and H) than negatively charged residues (D and E) (Table 3). Compared with the peptides binding to amorphous Ni3B, the binding peptides to crystalline nickel boride show a two-times higher occurrence of the positively charged amino acids arginine and lysine, and a three-times higher occurrence of histidine, respectively. Although the distribution of charged amino acids in the library is comparable in frequency, the increased abundance of these amino acids within the identified sequences could be possibly attributed to the surface composition of the nickel borides. The characterisation of the surface of different amorphous nickel borides by Okamoto et al. and Caputo et al. by X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD), respectively, revealed that the electron densities on nickel are increased by electron transfer from boron to the metal [6,34]. Based on the shift of the charge, specific binding peptides could therefore interact with the nickel boride substrates via electrostatic interactions. The majority of the peptides identified on Ni3B prevalently possess alanine, leucine, proline, serine and threonine residues (Figure 1) which is a consequence of the amino acid distribution of the applied phage display library. In addition, the binding peptides identified on amorphous Ni3B possess 2.5-times more asparagine residues as compared with the peptides identified on crystalline Ni3B. This is vice versa with proline residues binding to crystalline Ni3B. The strong presence of asparagine in the peptide sequences binding to amorphous Ni3B, and asparagine and histidine in the peptide sequences binding to crystalline Ni3B suggests that the binding between the Ni3B and peptides could furthermore occur via hydrogen bonding interactions. The almost complete absence of tryptophan, phenylalanine, and methionine residues is also due to the low frequencies of these amino acids within the library. An amino acid position consensus was not evident from the 7-mer library screening of Ni3B nanoparticles as substrates. However, besides the predominantly hydrophobic amino acids (A and L) and hydrophilic amino acids (S and T) the variety of amino acids with charged side groups implies that these groups could be essential in specific binding to both substrates via electrostatic interactions. The Ni3B-binding peptides identified possess calculated theoretical isoelectric points (pI) ranging from strongly acidic (4.0) to highly basic (9.75). 60% of the peptides binding to amorphous Ni3B show a pI value < 7.5 while 40% of the peptides have pI > 7.5. 57% of the peptides binding to crystalline Ni3B show a pI value < 7.5 and 43% of the peptides have pI > 7.5. Therefore the identified peptides can be grouped into the categories acidic (pI 3.0 - 5.9; 35.7% of the peptides), neutral (pI 6.0 – 8.9; 52.4% of the peptides), and basic (pI 9.0 – 12; 11.9% of the peptides), respectively.


Selection of peptides binding to metallic borides by screening M13 phage display libraries.

Ploss M, Facey SJ, Bruhn C, Zemel L, Hofmann K, Stark RW, Albert B, Hauer B - BMC Biotechnol. (2014)

Amino acid distribution of the isolated peptide sequences. A total of 15 peptide sequences were analysed for amorphous Ni3B (grey bars) and a total of 28 peptide sequences were analysed for crystalline Ni3B (black bars).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3924706&req=5

Figure 1: Amino acid distribution of the isolated peptide sequences. A total of 15 peptide sequences were analysed for amorphous Ni3B (grey bars) and a total of 28 peptide sequences were analysed for crystalline Ni3B (black bars).
Mentions: Due to the fact that cysteines interfere with the p3-mediated M13 infection process, no cysteines were present in the identified binding peptides [33]. The binding peptides showed approximately three-times more positively charged residues (K, R, and H) than negatively charged residues (D and E) (Table 3). Compared with the peptides binding to amorphous Ni3B, the binding peptides to crystalline nickel boride show a two-times higher occurrence of the positively charged amino acids arginine and lysine, and a three-times higher occurrence of histidine, respectively. Although the distribution of charged amino acids in the library is comparable in frequency, the increased abundance of these amino acids within the identified sequences could be possibly attributed to the surface composition of the nickel borides. The characterisation of the surface of different amorphous nickel borides by Okamoto et al. and Caputo et al. by X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD), respectively, revealed that the electron densities on nickel are increased by electron transfer from boron to the metal [6,34]. Based on the shift of the charge, specific binding peptides could therefore interact with the nickel boride substrates via electrostatic interactions. The majority of the peptides identified on Ni3B prevalently possess alanine, leucine, proline, serine and threonine residues (Figure 1) which is a consequence of the amino acid distribution of the applied phage display library. In addition, the binding peptides identified on amorphous Ni3B possess 2.5-times more asparagine residues as compared with the peptides identified on crystalline Ni3B. This is vice versa with proline residues binding to crystalline Ni3B. The strong presence of asparagine in the peptide sequences binding to amorphous Ni3B, and asparagine and histidine in the peptide sequences binding to crystalline Ni3B suggests that the binding between the Ni3B and peptides could furthermore occur via hydrogen bonding interactions. The almost complete absence of tryptophan, phenylalanine, and methionine residues is also due to the low frequencies of these amino acids within the library. An amino acid position consensus was not evident from the 7-mer library screening of Ni3B nanoparticles as substrates. However, besides the predominantly hydrophobic amino acids (A and L) and hydrophilic amino acids (S and T) the variety of amino acids with charged side groups implies that these groups could be essential in specific binding to both substrates via electrostatic interactions. The Ni3B-binding peptides identified possess calculated theoretical isoelectric points (pI) ranging from strongly acidic (4.0) to highly basic (9.75). 60% of the peptides binding to amorphous Ni3B show a pI value < 7.5 while 40% of the peptides have pI > 7.5. 57% of the peptides binding to crystalline Ni3B show a pI value < 7.5 and 43% of the peptides have pI > 7.5. Therefore the identified peptides can be grouped into the categories acidic (pI 3.0 - 5.9; 35.7% of the peptides), neutral (pI 6.0 – 8.9; 52.4% of the peptides), and basic (pI 9.0 – 12; 11.9% of the peptides), respectively.

Bottom Line: The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni3B emerged as the best binder for both substrates.Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni3B nanoparticles.We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany. bernhard.hauer@itb.uni-stuttgart.de.

ABSTRACT

Background: Metal borides are a class of inorganic solids that is much less known and investigated than for example metal oxides or intermetallics. At the same time it is a highly versatile and interesting class of compounds in terms of physical and chemical properties, like semiconductivity, ferromagnetism, or catalytic activity. This makes these substances attractive for the generation of new materials. Very little is known about the interaction between organic materials and borides. To generate nanostructured and composite materials which consist of metal borides and organic modifiers it is necessary to develop new synthetic strategies. Phage peptide display libraries are commonly used to select peptides that bind specifically to metals, metal oxides, and semiconductors. Further, these binding peptides can serve as templates to control the nucleation and growth of inorganic nanoparticles. Additionally, the combination of two different binding motifs into a single bifunctional phage could be useful for the generation of new composite materials.

Results: In this study, we have identified a unique set of sequences that bind to amorphous and crystalline nickel boride (Ni3B) nanoparticles, from a random peptide library using the phage display technique. Using this technique, strong binders were identified that are selective for nickel boride. Sequence analysis of the peptides revealed that the sequences exhibit similar, yet subtle different patterns of amino acid usage. Although a predominant binding motif was not observed, certain charged amino acids emerged as essential in specific binding to both substrates. The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni3B emerged as the best binder for both substrates. Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni3B nanoparticles.

Conclusions: This study is, to our knowledge, the first to identify peptides that bind specifically to amorphous and to crystalline Ni3B nanoparticles. We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.

Show MeSH