Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequence-Selective Binding of Oligopeptides in Water through Hydrophobic Coding.

ABSTRACT: A general method for sequence-specific binding of peptides remains elusive despite decades of research. By creating an array of "hydrophobically coded dimples" on the surface of surface-core doubly cross-linked micelles, we synthesized water-soluble nanoparticle receptors to recognize peptides by the location, number, and nature of their hydrophobic side chains. Minute differences in the side chains could be distinguished, and affinities up to 20 nM were obtained for biologically active oligopeptides in water.

SUBMITTER: Awino JK

PROVIDER: S-EPMC5310974 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sequence-Selective Binding of Oligopeptides in Water through Hydrophobic Coding.

Awino Joseph K JK Gunasekara Roshan W RW Zhao Yan Y

Journal of the American Chemical Society 20170131 6

A general method for sequence-specific binding of peptides remains elusive despite decades of research. By creating an array of "hydrophobically coded dimples" on the surface of surface-core doubly cross-linked micelles, we synthesized water-soluble nanoparticle receptors to recognize peptides by the location, number, and nature of their hydrophobic side chains. Minute differences in the side chains could be distinguished, and affinities up to 20 nM were obtained for biologically active oligopep ...[more]

PMID: 28128940

Similar Datasets

Two-dimensional honeycomb network through sequence-controlled self-assembly of oligopeptides.

Project description:The sequence of a peptide programs its self-assembly and hence the expression of specific properties through non-covalent interactions. A large variety of peptide nanostructures has been designed employing different aspects of these non-covalent interactions, such as dispersive interactions, hydrogen bonding or ionic interactions. Here we demonstrate the sequence-controlled fabrication of molecular nanostructures using peptides as bio-organic building blocks for two-dimensional (2D) self-assembly. Scanning tunnelling microscopy reveals changes from compact or linear assemblies (angiotensin I) to long-range ordered, chiral honeycomb networks (angiotensin II) as a result of removal of steric hindrance by sequence modification. Guided by our observations, molecular dynamic simulations yield atomistic models for the elucidation of interpeptide-binding motifs. This new approach to 2D self-assembly on surfaces grants insight at the atomic level that will enable the use of oligo- and polypeptides as large, multi-functional bio-organic building blocks, and opens a new route towards rationally designed, bio-inspired surfaces.

| S-EPMC4729956 | biostudies-literature

Achieving Selective Wettability Surface through Aerosol Jet Hydrophobic Line Printing.

Project description:Selective wettability surface patterning, involving the combination of wetting and nonwetting surface features in an alternating manner, has emerged as a key surface control technique with broad applications in cell microarrays, microfluidics, and drop placement. However, traditional approaches to creating such patterns often suffer material waste and rely on masking substrate surfaces with predesigned templates, resulting in elevated costs. Here, we present an approach to achieve selective wettability surface patterning using aerosol jet printing that offers a solution to these challenges. Our method involves the precise deposition of atomized, hydrophobic silica nanoparticle droplets onto substrate surfaces. By directing these atomized droplets, we created well-defined hydrophobic lines. The individual lines have an average width of 60 μm and a thickness of 1.32 μm, which, when overlaid, form a complete superhydrophobic surface with a water contact angle of 154°. The implications of these findings are substantial for various applications. We accordingly show the applicability of our method for confining drops and demonstrate on-target waterproofing of electronic circuit lines.

| S-EPMC10851364 | biostudies-literature

Highly Hydrophobic Polydimethylsiloxane-Coated Expanded Vermiculite Sorbents for Selective Oil Removal from Water.

Project description:Naturally abundant vermiculite clay was expanded by using an aqueous solution of H2O2 and its surface was modified with ultra-thin polydimethylsiloxane (PDMS) using facile thermal vapor deposition to prepare an ecologically friendly, low-cost oil sorbent that plays an important role in oil spillage remediation. The resulting PDMS-coated expanded vermiculite (eVMT@PDMS) particles exhibited adequate hydrophobicity and oleophilicity for oil/water separation, with numerous conical slit pores (a size of 0.1-100 μm) providing a great sorption capacity and an efficient capillarity-driven flow pathway for oil collection. Simply with using a physically-packed eVMT@PDMS tube (or pouch), selective oil removals were demonstrated above and beneath the surface of the water. Furthermore, these sorbents were successfully integrated and then applied to the advanced oil-collecting devices such as a barrel-shaped oil skimmer and a self-primed oil pump.

| S-EPMC7912906 | biostudies-literature

Water-Soluble Molecularly Imprinted Nanoparticle Receptors with Hydrogen-Bond-Assisted Hydrophobic Binding.

Project description:Molecularly imprinted nanoparticles (MINPs) were prepared when surfactants with a tripropargylammonium headgroup and a methacrylate-functionalized hydrophobic tail were cross-linked in the micelle form on the surface and in the core in the presence of hydrophobic template molecules. With the surfactants containing an amide bond near the headgroup, the MINPs had a layer of hydrogen-bonding groups in the interior that strongly influenced their molecular recognition. Templates/guests with strong hydrogen-bonding groups in the midsection of the molecule benefited most, especially if the hydrophobe of the template could penetrate the amide layer to reach the hydrophobic core of the cross-linked micelles. The location and the orientation of the hydrophilic groups were also important, as they determined how the template interacted with the surfactant micelles and, ultimately, with the MINP receptors.

| S-EPMC5010460 | biostudies-literature

Artificial water channels enable fast and selective water permeation through water-wire networks.

Project description:Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for a rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport >109 water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability-selectivity trade-off curve. PAH[4]'s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production and barrier applications.

| S-EPMC7008941 | biostudies-literature

LingZhi oligopeptides amino acid sequence analysis and anticancer potency evaluation.

Project description:LingZhi (Ganoderma lucidum) has been used as a therapeutic agent for decades, but the antitumor potency of LingZhi oligopeptides (LZOs) was not well explored. In current study, ten novel LZO amino acid sequences were identified, and anticancer potency was evaluated. We found that LZO-3 [EGHGF] significantly triggered A549 cell apoptosis via mitochondrial dysregulation, as evidenced by caspases activation, mitochondrial membrane potential collapse, Bcl-2/Bax ratio alteration, and cytochrome c release. Further, the down-regulation of Trx/TrxR reductase and the improvement of the MDM2/p53 state also contributed to the LZO-3-induced cell apoptosis. Notably, our findings provide evidence for the novel potency of LZOs, which could be developed as promising chemotherapeutic agents against lung cancer.

| S-EPMC9049989 | biostudies-literature

Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity.

Project description:We demonstrate phage-display screening on self-assembled ligands that enables the identification of oligopeptides that selectively bind dynamic supramolecular targets over their unassembled counterparts. The concept is demonstrated through panning of a phage-display oligopeptide library against supramolecular tyrosine-phosphate ligands using 9-fluorenylmethoxycarbonyl-phenylalanine-tyrosine-phosphate (Fmoc-FpY) micellar aggregates as targets. The 14 selected peptides showed no sequence consensus but were enriched in cationic and proline residues. The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with K D = 74 ± 3 μM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY through the KVYF terminus and this binding event disrupts the assembled structure. In absence of the target micellar aggregate, P7 was further found to dynamically alternate between multiple conformations, with a preferred hairpin-like conformation that was shown to contribute to supramolecular ligand binding. Three identified phages presented appreciable binding, and two showed to catalyze the hydrolysis of a model para-nitro phenol phosphate substrate, with P7 demonstrating conformation-dependent activity with a modest k cat/K M = 4 ± 0.3 × 10-4 M-1 s-1.

| S-EPMC8694286 | biostudies-literature

Synthetic lectins for selective binding of glycoproteins in water.

Project description:Although synthetic mimics of lectins can be extremely useful in biological and biomedical research, molecular recognition of carbohydrates has been hampered by their strong solvation in water and subtle structural differences among analogues. Molecularly imprinted nanoparticle receptors were prepared with glycans directly cleaved from glycoproteins. Functionalized with boroxole groups in the binding sites, these water-soluble synthetic lectins bound the parent glycoproteins selectively in water with an association constant of Ka = 104-105 M-1. The strong binding enabled the receptors to protect the targeted glycans from enzymatic cleavage. When clicked onto magnetic nanoparticles, the receptors enabled facile isolation of glycoproteins from a mixture.

| S-EPMC7484035 | biostudies-literature

Tuning of protease resistance in oligopeptides through N-alkylation.

Project description:N-Methylation of amino acids is an effective way to create protease resistance in both natural and synthetic peptides. However, alkyl substituents other than N-methyl have not been extensively studied. Here, we prepare and examine a series of N-substituted peptides in which the size and length of the alkyl group is modulated. These design insights provide a unique and modular handle for tuning proteolysis in oligopeptides.

| S-EPMC6141190 | biostudies-literature

Site-selective aqueous C-H acylation of tyrosine-containing oligopeptides with aldehydes.

Project description:The development of useful synthetic tools to label amino acids within a peptide framework for the ultimate modification of proteins in a late-stage fashion is a challenging task of utmost importance within chemical biology. Herein, we report the first Pd-catalyzed C-H acylation of a collection of Tyr-containing peptides with aldehydes. This water-compatible tagging technique is distinguished by its site-specificity, scalability and full tolerance of sensitive functional groups. Remarkably, it provides straightforward access to a high number of oligopeptides with altered side-chain topology including mimetics of endomorphin-2 and neuromedin N, thus illustrating its promising perspectives toward the diversification of structurally complex peptides and chemical ligation.

| S-EPMC8162766 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data