Specific Electrostatic Molecular Recognition in Water

Abstract

The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide-peptide interactions could conveniently be observed by clustering of the small, fluorescently labeled target beads on the surface of larger ligand-containing beads. Sequences of isolated hits were determined by MS/MS. The interactions of the complex showing the highest affinity were investigated by a novel single-bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured.

Design and Combinatorial Development of Shield-1 Peptide Mimetics Binding to Destabilized FKBP12

“…To distinguish and verify the potency among the structures of the solid-supported hit compounds, a well-based on-bead binding assay was employed . Guided by the results from the library screen, a set of immobilized substrates were resynthesized on PEGA 1900 beads (125–200 μm).…”

“…To distinguish and verify the potency among the structures of the solidsupported hit compounds, a well-based on-bead binding assay was employed. 34 Guided by the results from the library screen, a set of immobilized substrates were resynthesized on PEGA 1900 beads (125−200 μm). The beads were singly sorted into a 96-well plate using a COMPAS bead sorter (Union Biometrica) and subjected to a dilution series of MBP-DD-(ROX).…”

Computational Evolution of Threonine-Rich β-Hairpin Peptides Mimicking Specificity and Affinity of Antibodies

“…We investigated the binding of GFP to 1 in an on-bead binding assay, making use of an adapted version of the method we recently reported. 49 Equally sized PEGA beads with β-body 1 were distributed in triplicates at three beads per individual well in a 96-well microtiter plate, and incubated with solutions containing increasing amounts of GFP. Binding was allowed to reach the point of equilibration by overnight incubation at room temperature, permitting enough time for the protein molecules to diffuse to the interior of the PEGA beads.…”

Bottom-Up Design Approach for OBOC Peptide Libraries

“…This paper, written for the special issue Peptides and Peptide Technologies: A Themed Issue in Honor of Professor Morten Meldal on the Occasion of His Citation Laureates, wants to pay tribute to his pioneering work on one-bead-one-compound (OBOC) peptide libraries [ 1 , 2 , 3 , 4 , 5 , 6 ] and development of advanced synthetic methodologies on solid supports [ 7 , 8 , 9 , 10 , 11 ].…”