Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Abb S

PROVIDER: S-EPMC4729956 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Self-assembly of phenylalanine oligopeptides: insights from experiments and simulations.

Project description:Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into discrete, hollow, well ordered nanotubes, and its derivatives form nanoassemblies of various morphologies. Here we demonstrate for the first time, to our knowledge, the formation of planar nanostructures with beta-sheet content by the triphenylalanine peptide (FFF). We characterize these structures using various microscopy and spectroscopy techniques. We also obtain insights into the interactions and structural properties of the FF and FFF nanostructures by 0.4-micros, implicit-solvent, replica-exchange, molecular-dynamics simulations of aqueous FF and FFF solutions. In the simulations the peptides form aggregates, which often contain open or ring-like peptide networks, as well as elementary and network-containing structures with beta-sheet characteristics. The networks are stabilized by polar and nonpolar interactions, and by the surrounding aggregate. In particular, the charged termini of neighbor peptides are involved in hydrogen-bonding interactions and their aromatic side chains form "T-shaped" contacts, as in three-dimensional FF crystals. These interactions may assist the FF and FFF self-assembly at the early stage, and may also stabilize the mature nanostructures. The FFF peptides have higher network propensities and increased aggregate stabilities with respect to FF, which can be interpreted energetically.

| S-EPMC2712050 | biostudies-literature

Septipyridines as conformationally controlled substitutes for inaccessible bis(terpyridine)-derived oligopyridines in two-dimensional self-assembly.

Project description:The position of the peripheral nitrogen atoms in bis(terpyridine)-derived oligopyridines (BTPs) has a strong impact on their self-assembly behavior at the liquid/HOPG (highly oriented pyrolytic graphite) interface. The intermolecular hydrogen bonding interactions in these peripheral pyridine units show specific 2D structures for each BTP isomer. From nine possible constitutional isomers only four have been described in the literature. The synthesis and self-assembling behavior of an additional isomer is presented here, but the remaining four members of the series are synthetically inaccessible. The self-assembling properties of three of the missing four BTP isomers can be mimicked by making use of the energetically preferred N-C-C-N transoid conformation between 2,2'-bipyridine subunits in a new class of so-called septipyridines. The structures are investigated by scanning tunneling microscopy (STM) and a combination of force-field and first-principles electronic structure calculations.

| S-EPMC3190612 | biostudies-literature

Two-Dimensional Band Structure in Honeycomb Metal-Organic Frameworks.

Project description:Two-dimensional (2D) metal-organic frameworks (MOFs) have been recently proposed as a flexible material platform for realizing exotic quantum phases including topological and anomalous quantum Hall insulators. Experimentally, direct synthesis of 2D MOFs has been essentially confined to metal substrates, where the strong interaction with the substrate masks the intrinsic electronic properties of the MOF. In addition to electronic decoupling from the underlying metal support, synthesis on weakly interacting substrates (e.g., graphene) would enable direct realization of heterostructures of 2D MOFs with inorganic 2D materials. Here, we demonstrate synthesis of 2D honeycomb MOFs on epitaxial graphene substrate. Using low-temperature scanning tunneling microscopy (STM) and atomic force microscopy (AFM) complemented by density-functional theory (DFT) calculations, we show the formation of a 2D band structure in the MOF decoupled from the substrate. These results open the experimental path toward MOF-based designer electronic materials with complex, engineered electronic structures.

| S-EPMC6179349 | biostudies-literature

Self-assembly of rationally designed peptides under two-dimensional confinement.

Project description:The rational design of interfacially confined biomolecules offers a unique opportunity to explore the cooperative relationship among self-assembly, nucleation, and growth processes. This article highlights the role of electrostatics in the self-assembly of β-sheet-forming peptides at the air-water interface. We characterize the phase behavior of a periodically sequenced sheet-forming peptide by using Langmuir techniques, Brewster angle microscopy, attenuated total reflection Fourier transform infrared spectroscopy, and circular dichroism spectroscopy. We find that peptides with an alternating binary sequence transition at high pressures from discrete circular domains to fibrous domains. The qualitative behavior is independent of surface pressure but dependent on molecular areas. In addition, thermodynamic models are employed to specifically quantify differences in electrostatics by obtaining parameters for the critical aggregation area, the limiting molecular area, and the dimensionless ratio of line tension/dipole density. Using these parameters, we are able to relate localized charge distribution to phase transitions, which will allow us to apply these molecules to examine how the dynamics of self-assembly can be directly coupled to the formation of composite nanostructures in biology.

| S-EPMC2965942 | biostudies-literature

Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals.

Project description:Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge and an active area of development. More challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamic behaviour in porous three-dimensional (3D) crystalline solids has been exploited for stimuli-responsive functions and adaptive behaviour. As in such 3D materials, integrating flexibility and adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns using a readily accessible design strategy. Three single- or double-point mutants of the C4-symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single-disulfide, double-disulfide and metal-coordination) into crystalline 2D arrays. Owing to the flexibility of the single-disulfide interactions, the lattices of one of the variants ((C98)RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. (C98)RhuA lattices display a Poisson's ratio of -1-the lowest thermodynamically possible value for an isotropic material-making them auxetic.

| S-EPMC4991361 | biostudies-literature

Layer-by-layer self-assembly of pillared two-dimensional multilayers.

Project description:We report Layer-by-Layer (LbL) self-assembly of pillared two-dimensional (2D) multilayers, from water, onto a wide range of substrates. This LbL method uses a small molecule, tris(2-aminoethyl) amine (TAEA), and a colloidal dispersion of Ti3C2Tx MXene to LbL self-assemble (MXene/TAEA)n multilayers, where n denotes the number of bilayers. Assembly with TAEA results in highly ordered (MXene/TAEA)n multilayers where the TAEA expands the interlayer spacing of MXene flakes by only ~ 1 Å and reinforces the interconnection between them. The TAEA-pillared MXene multilayers show the highest electronic conductivity of 7.3 × 104 S m-1 compared with all reported MXene multilayers fabricated by LbL technique. The (MXene/TAEA)n multilayers could be used as electrodes for flexible all-solid-state supercapacitors delivering a high volumetric capacitance of 583 F cm-3 and high energy and power densities of 3.0 Wh L-1 and 4400 W L-1, respectively. This strategy enables large-scale fabrication of highly conductive pillared MXene multilayers, and potentially fabrication of other 2D heterostructures.

| S-EPMC6560128 | biostudies-literature

Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures.

Project description:Self-assembly is a ubiquitous approach to the design and fabrication of novel supermolecular architectures. Here we report a strategy termed 'lipid-bilayer-assisted self-assembly' that is used to assemble DNA origami nanostructures into two-dimensional lattices. DNA origami structures are electrostatically adsorbed onto a mica-supported zwitterionic lipid bilayer in the presence of divalent cations. We demonstrate that the bilayer-adsorbed origami units are mobile on the surface and self-assembled into large micrometre-sized lattices in their lateral dimensions. Using high-speed atomic force microscopy imaging, a variety of dynamic processes involved in the formation of the lattice, such as fusion, reorganization and defect filling, are successfully visualized. The surface modifiability of the assembled lattice is also demonstrated by in situ decoration with streptavidin molecules. Our approach provides a new strategy for preparing versatile scaffolds for nanofabrication and paves the way for organizing functional nanodevices in a micrometer space.

| S-EPMC4560778 | biostudies-literature

Candidate quantum spin liquid due to dimensional reduction of a two-dimensional honeycomb lattice.

Project description:As with quantum spin liquids based on two-dimensional triangular and kagome lattices, the two-dimensional honeycomb lattice with either a strong spin-orbital coupling or a frustrating second-nearest-neighbor coupling is expected to be a source of candidate quantum spin liquids. An ammonium salt [(C3H7)3NH]2[Cu2(C2O4)3](H2O)2.2 containing hexagonal layers of Cu(2+) was obtained from solution. No structural transition or long-range magnetic ordering was observed from 290 K to 2 K from single crystal X-ray diffraction, specific heat and susceptibility measurements. The anionic layers are separated by sheets of ammonium and H2O with distance of 3.5 Å and no significant interaction between anionic layers. The two-dimensional honeycomb lattice is constructed from Jahn-Teller distorted Cu(2+) and oxalate anions, showing a strong antiferromagnetic interaction between S = 1/2 metal atoms with θ = -120 (1) K. Orbital analysis of the Cu(2+) interactions through the oxalate-bridges suggests a stripe mode pattern of coupling with weak ferromagnetic interaction along the b axis, and strong antiferromagnetic interaction along the a axis. Analysis of the magnetic susceptibility shows that it is dominated by a quasi-one-dimensional contribution with spin chains that are at least as well isolated as those of well-known quasi-one-dimensional spin liquids.

| S-EPMC5377320 | biostudies-literature

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

Project description: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.

| S-EPMC5310974 | biostudies-literature

Controlled molecular self-assembly of complex three-dimensional structures in soft materials.

Project description:Many applications in tissue engineering, flexible electronics, and soft robotics call for approaches that are capable of producing complex 3D architectures in soft materials. Here we present a method using molecular self-assembly to generate hydrogel-based 3D architectures that resembles the appealing features of the bottom-up process in morphogenesis of living tissues. Our strategy effectively utilizes the three essential components dictating living tissue morphogenesis to produce complex 3D architectures: modulation of local chemistry, material transport, and mechanics, which can be engineered by controlling the local distribution of polymerization inhibitor (i.e., oxygen), diffusion of monomers/cross-linkers through the porous structures of cross-linked polymer network, and mechanical constraints, respectively. We show that oxygen plays a role in hydrogel polymerization which is mechanistically similar to the role of growth factors in tissue growth, and the continued growth of hydrogel enabled by diffusion of monomers/cross-linkers into the porous hydrogel similar to the mechanisms of tissue growth enabled by material transport. The capability and versatility of our strategy are demonstrated through biomimetics of tissue morphogenesis for both plants and animals, and its application to generate other complex 3D architectures. Our technique opens avenues to studying many growth phenomena found in nature and generating complex 3D structures to benefit diverse applications.

| S-EPMC5776829 | biostudies-other

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