Combinatorial Discovery and Validation of Heptapeptides with UTP Binding Induced Structure

Abstract

In biology, supramolecular recognition typically involves an ‘induced‐fit’ mechanism, where structures rearrange upon complexation to accommodate binding ligands. Designing minimalistic compounds with such adaptability is challenging as they involve subtle conformational changes that are energetically similar. Here, we demonstrate the integration of combinatorial screening with molecular modelling to identify heptapeptides that form a stable loop upon recognition of uridine triphosphate (UTP). Peptide sequences selected using phage display were refined computationally and correlated with experimental KD values. This combined approach may serve as a method for the de novo selection and subsequent rationalization of the compositional and organizational principles that dictate chemical functionality in flexible structures with dynamic conformations.

Peptide-Based Supramolecular Systems Chemistry

“…In particular, they identified the unstructured peptide ADARYKS that was shown to have modest, sequence specific binding affinity for ATP, 79 and later, using an integrated experimental screening and molecular modeling approach, the peptide KAIHPMR-NH 2 was demonstrated to form a stable, induced loop upon recognition of UTP. 43 Peptide sequences selected using phage display were refined computationally and correlated with experimental K D values down to sub-mM. Unstructured functional peptides may form condensates that engage in the formation of spatially confined compartments in a phenomenon known as coacervation, as has been known in polymer chemistry since the 1920s, 80 or liquid−liquid phase separation (LLPS).…”

“…313 The peptide functionalization of three different chromophores were investigated. Specifically, two sides of oligo(p-phenylenevinylene) i.e., OPV were conjugated with the N terminal of VVD tripeptides (43) 10F. Interestingly, kinetic control over the self-assembly through slow acidification resulted in the formation of self-sorted coassembly due to the difference in pK a of the two peptides.…”

“…Remarkably, single peptide molecular dynamics simulations to calculate spectroscopic and crystallographic data aligned well with these preferred orientations, suggesting predictive potential based on the peptide sequence (Figure C). There are more and more examples in the literature of computationally guided sequence design, − leaving us hopeful that the deliberate design of ordered/disordered peptides is not far out of reach.…”

“…Kroiss et al adapted the phage display technique to identify peptides as short as heptamers that could bind to small molecules, as exemplified by ATP and UTP. In particular, they identified the unstructured peptide ADARYKS that was shown to have modest, sequence specific binding affinity for ATP, and later, using an integrated experimental screening and molecular modeling approach, the peptide KAIHPMR-NH 2 was demonstrated to form a stable, induced loop upon recognition of UTP . Peptide sequences selected using phage display were refined computationally and correlated with experimental K D values down to sub-mM.…”