A synthetic hexapeptide designed to resemble a proteinaceous p‐loop nest is shown to bind inorganic phosphate

Abstract

The hexapeptide Ser-Gly-Ala-Gly-Lys-Thr has been synthesized and characterized. It was designed as a minimal soluble peptide that would be likely to have the phosphate-binding properties observed in the P-loops of proteins that bind the β-phosphate of GTP or ATP. The β-phosphate in such proteins is bound by a combination of the side chain ε-amino group of the lysine residue plus the concavity formed by successive main chain peptide NH groups called a nest, which is favored by the glycines. The hexapeptide is shown to bind HPO(4) (2-) strongly at neutral pH. The affinities of the various ionized species of phosphate and hexapeptide are analyzed, showing that they increase with pH. It is likely the main chain NH groups of the hexapeptide bind phosphate in much the same way as the corresponding P-loop atoms bind the phosphate ligand in proteins. Most proteinaceous P-loops are situated at the N-termini of α-helices, and this observation has frequently been considered a key aspect of these binding sites. Such a hexapeptide in isolation seems unlikely to form an α-helix, an expectation in accord with the CD spectra examined; this suggests that being at the N-terminus of an α-helix is not essential for phosphate binding. An unexpected finding about the hexapeptide-HPO(4) (2-) complex is that the side chain ε-amino group of the lysine occurs in its deprotonated form, which appears to bind HPO(4) (2-) via an N···H-O-P hydrogen bond.

Nitrogen Oxides in Early Earth's Atmosphere as Electron Acceptors for Life's Emergence

“…Alanine could then have condensed to a 5-mer peptide on carbonate surfaces in the mound (Kawamura et al, 2011). Such peptides have the potential to render iron-nickel sulfides and pyrophosphate clusters that are more stable and catalytically active, thus quickening the reactions along the pathway that had previously relied on the unadorned inorganic clusters themselves (Milner-White and Russell, 2011;Bianchi et al, 2012). Such a positive feedback would lock this cycle in as the foundation for an autocatalytic pathway at the emergence of life (e.g., Mielke et al, 2011).…”

Separation of Peptides with Forward Osmosis Biomimetic Membranes

“…The peptide sequence Ser-Gly-Ala-Gly-Lys-Thr (SGA GKT) is a reconstructed P-loop in which proteins are able to bind phosphate groups of GTP and ATP. This hexapeptide has previously been reported to bind to ${\mathrm{HPO}}_4^{2-}$ at high pH [28] and may therefore be able to bind phosphorous compounds as a means to address the future issues with diminishing phosphorous resources.…”

“…( a ) AGKT (375 Da) and ( b ) GGG SGA GKT (692 Da). The peptides are constructs based on the amino acid configuration described by Bianchi et al [28]. The peptide amine (N–H) backbone groups form a ‘nest’ structure toward phosphate anions and the Lysine side chain participates in the binding when phosphorous compounds are present.…”

Novel molecular fossils of bacteria: Insights into hydrothermal origin of life

“…SKA58 . DndC shows ATP pyrophosphatase activity and has a unique P-loop (SGGKDS) of the PPi synthetase family (Zhou et al, 2005), which is a phosphate binding motif and glycine-rich (Bianchi et al, 2012;Bork and Koonin, 1994). This characteristic is shared by the H þ -pyrophosphatase (Via et al, 2000), a synthase that catalyzes the phosphorylation of orthophosphate (Pi) to PPi (Holm and Baltscheffsky, 2011).…”