Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Principles of self-assembly of helical pores from dendritic dipeptides.

ABSTRACT: The self-assembly of the dendritic dipeptides (4-3,4-3,5)nG2-CH2-Boc-L-Tyr-L-Ala-OMe and their achiral dendritic alcohol (4-3,4-3,5)nG2-CH2OH precursors, both with n = 1-16, where n represents the number of methylenic units in the alkyl groups of the dendron, are reported. All chiral dendritic dipeptides and achiral dendritic alcohols self-assemble into helical porous columns that are stable in both solution and solid state. The pore diameter (D(pore)) of the columns self-assembled from dendritic dipeptides is approximately 10 A larger than that of structures assembled from dendritic alcohols. The increase of the D(pore) at the transition from dendritic alcohol to dendritic dipeptide is accompanied by a decreased solid angle of the building block. This trend is in agreement with previous pore size-solid angle dependences observed with different protective groups of the dipeptide and primary structures of the dendron. However, within the series of dendritic alcohols and dendritic dipeptides with various n, the D(pore) increases when the solid angle increases. The results of these investigations together with those of previous studies on the role of dipeptide stereochemistry and protective groups on this self-assembly process provide the molecular principles required to program the construction of supramolecular helical pores with diameter controlled at the A level from a single dendritic dipeptide architecture. These principles are expected to be valid for libraries of dendritic dipeptides based on dendrons and dipeptides with various primary structures.

SUBMITTER: Percec V

PROVIDER: S-EPMC1413792 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Self-Assembly and Enzyme Responsiveness of Amphiphilic Linear-Dendritic Block Copolymers Based on Poly(<i>N</i>-vinylpyrrolidone) and Dendritic Phenylalanyl-lysine Dipeptides.

Project description:In this study, we present the synthesis, self-assembly, and enzyme responsive nature of a unique class of well-defined amphiphilic linear-dendritic block copolymers (PNVP-b-dendr(Phe-Lys)n, n = 1-3) based on linear poly(N-vinylpyrrolidone) (PNVP) and dendritic phenylalanyl-lysine (Phe-Lys) dipeptides. The copolymers were prepared via a combination ofreversible addition-fragmentation chain transfer (RAFT) /xanthates (MADIX) polymerization of N-vinylpyrrolidone and stepwise peptide chemistry. The results of fluorescence spectroscopy, 1H NMR analyses, transmission electron microscopy (TEM), and particle size analysis demonstrated that the copolymers self-assemble in aqueous solution into micellar nanocontainers that can disassemble and release encapsulated anticancer drug doxorubicin or hydrophobic dye Nile red by trigger of a serine protease trypsin under physiological conditions. The disassembly of the formed micelles and release rates of the drug or dye can be adjusted by changing the generation of dendrons in PNVP-b-dendr(Phe-Lys)n. Furthermore, the cytocompatibility of the copolymers have been confirmed using human lung epithelial cells (BEAS-2B) and human liver cancer cells (SMMC-7721). Due to the fact of their enzyme responsive properties and good biocompatibility, the copolymers may have potential applicability in smart controlled release systems capable of site-specific response.

| S-EPMC6836210 | biostudies-literature

Design principles for nonequilibrium self-assembly.

Project description:We consider an important class of self-assembly problems, and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the set of configurations that can be obtained under nonequilibrium conditions. Our central result provides intuition for how equilibrium self-assembly landscapes are modified under finite nonequilibrium drive.

| S-EPMC5167149 | biostudies-literature

Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs.

Project description:Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.

| S-EPMC6642399 | biostudies-literature

Self-Assembly of Block Heterochiral Peptides into Helical Tapes.

Project description:Patterned substitution of d-amino acids into the primary sequences of self-assembling peptides influences molecular-level packing and supramolecular morphology. We report that block heterochiral analogs of the model amphipathic peptide KFE8 (Ac-FKFEFKFE-NH2), composed of two FKFE repeat motifs with opposite chirality, assemble into helical tapes with dimensions greatly exceeding those of their fibrillar homochiral counterparts. At sufficient concentrations, these tapes form hydrogels with reduced storage moduli but retain the shear-thinning behavior and consistent mechanical recovery of the homochiral analogs. Varying the identity of charged residues (FRFEFRFE and FRFDFRFD) produced similarly sized nonhelical tapes, while a peptide with nonenantiomeric l- and d-blocks (FKFEFRFD) formed helical tapes closely resembling those of the heterochiral KFE8 analogs. A proposed energy-minimized model suggests that a kink at the interface between l- and d-blocks leads to the assembly of flat monolayers with nonidentical surfaces that display alternating stacks of hydrophobic and charged groups.

| S-EPMC7606833 | biostudies-literature

Constructing helical nanowires <i>via</i> polymerization-induced self-assembly.

Project description:While reliable strategies for constructing block copolymer (BCP) nanowires have been developed, helical nanowires are rarely reported in polymerization-induced self-assembly (PISA). Herein, in this work, a new strategy for constructing helical nanowires was developed via PISA mediated by a fluorinated stabilizer block. Ultralong nanowires with helical structure can be readily produced in a wide range of block compositions. In addition, the generality of this strategy was well testified by expanding monomer types. The achiral BCP nano-objects underwent a morphology transition from spheres to helical nanowires during aging. We believe this work will provide a general strategy for producing helical nanowires through PISA of achiral BCPs.

| S-EPMC8695331 | biostudies-literature

Principles Governing the Self-Assembly of Coiled-Coil Protein Nanoparticles.

Project description:Self-assembly refers to the spontaneous organization of individual building blocks into higher order structures. It occurs in biological systems such as spherical viruses, which utilize icosahedral symmetry as a guiding principle for the assembly of coat proteins into a capsid shell. In this study, we characterize the self-assembling protein nanoparticle (SAPN) system, which was inspired by such viruses. To facilitate self-assembly, monomeric building blocks have been designed to contain two oligomerization domains. An N-terminal pentameric coiled-coil domain is linked to a C-terminal coiled-coil trimer by two glycine residues. By combining monomers with inherent propensity to form five- and threefold symmetries in higher order agglomerates, the supposition is that nanoparticles will form that exhibit local and global symmetry axes of order 3 and 5. This article explores the principles that govern the assembly of such a system. Specifically, we show that the system predominantly forms according to a spherical core-shell morphology using a combination of scanning transmission electron microscopy and small angle neutron scattering. We introduce a mathematical toolkit to provide a specific description of the possible SAPN morphologies, and we apply it to characterize all particles with maximal symmetry. In particular, we present schematics that define the relative positions of all individual chains in the symmetric SAPN particles, and provide a guide of how this approach can be generalized to nonspherical morphologies, hence providing unprecedented insights into their geometries that can be exploited in future applications.

| S-EPMC4744166 | biostudies-literature

Synthesis and Self-Assembly of Bundle-Forming ?-Helical Peptide-Dendron Hybrids.

Project description:Dendronized helix bundle assemblies combine the sequence diversity and folding properties of proteins with the tailored physical properties of dendrimers. Assembly of peptide-dendron hybrids into ?-helical bundles encapsulates the helix bundle motif in a dendritic sheath that will allow the functional, protein-like domain to be transplanted to nonbiological environments. A bioorthogonal graft-to synthetic strategy for preparing helix bundle-forming peptide-dendron hybrids is described herein for hybrids 1a, 1b, and 2. Titration experiments monitored by circular dichroism spectroscopy support our self-assembly model for how the peptide-dendron hybrids self-assemble into ?-helical bundles with the dendrons on outside of the bundle.

| S-EPMC4710556 | biostudies-literature

Synthesis, optical properties, and helical self-assembly of a bivaline-containing tetraphenylethene.

Project description:A chiral tetraphenylethene derivative with two valine-containing attachments (TPE-DVAL), was synthesized by Cu(I)-catalyzed azide-alkyne "click" reaction. The optical properties and self-assembling behaviours of TPE-DVAL were investigated. The molecule is non-emissive and circular dichroism (CD)-silent in solution, but shows strong fluorescence and Cotton effects in the aggregation state, demonstrating aggregation-induced emission (AIE) and CD (AICD) characteristics. TPE-DVAL exhibits good circularly polarized luminescence (CPL) when depositing on the surface of quartz to allow the evaporation of its 1,2-dichloroethane solution. SEM and TEM images of the molecule show that the molecule readily self-assembles into right-handed helical nanofibers upon the evaporation of its solvent of DCE. The molecular alignments and interactions in assembling process are further explored through XRD analysis and computational simulation. The driving forces for the formation of the helical fibers were from the cooperative effects of intermolecular hydrogen bonding, π-π interactions and steric effect.

| S-EPMC4725923 | biostudies-literature

Macroscopic ordering of helical pores for arraying guest molecules noncentrosymmetrically.

Project description:Helical nanostructures have attracted continuous attention, not only as media for chiral recognition and synthesis, but also as motifs for studying intriguing physical phenomena that never occur in centrosymmetric systems. To improve the quality of signals from these phenomena, which is a key issue for their further exploration, the most straightforward is the macroscopic orientation of helices. Here as a versatile scaffold to rationally construct this hardly accessible structure, we report a polymer framework with helical pores that unidirectionally orient over a large area (?10?cm(2)). The framework, prepared by crosslinking a supramolecular liquid crystal preorganized in a magnetic field, is chemically robust, functionalized with carboxyl groups and capable of incorporating various basic or cationic guest molecules. When a nonlinear optical chromophore is incorporated in the framework, the resultant complex displays a markedly efficient nonlinear optical output, owing to the coherence of signals ensured by the macroscopically oriented helical structure.

| S-EPMC4598726 | biostudies-literature

Self-Assembly of a Functional Oligo(Aniline)-Based Amphiphile into Helical Conductive Nanowires.

Project description:A tetra(aniline)-based cationic amphiphile, TANI-NHC(O)C5H10N(CH3)3(+)Br(-) (TANI-PTAB) was synthesized, and its emeraldine base (EB) state was found to self-assemble into nanowires in aqueous solution. The observed self-assembly is described by an isodesmic model, as shown by temperature-dependent UV-vis investigations. Linear dichroism (LD) studies, combined with computational modeling using time-dependent density functional theory (TD-DFT), suggests that TANI-PTAB molecules are ordered in an antiparallel arrangement within nanowires, with the long axis of TANI-PTAB arranged perpendicular to the nanowire long axis. Addition of either S- or R- camphorsulfonic acid (CSA) to TANI-PTAB converted TANI to the emeraldine salt (ES), which retained the ability to form nanowires. Acid doping of TANI-PTAB had a profound effect on the nanowire morphology, as the CSA counterions' chirality translated into helical twisting of the nanowires, as observed by circular dichroism (CD). Finally, the electrical conductivity of CSA-doped helical nanowire thin films processed from aqueous solution was 2.7 mS cm(-1). The conductivity, control over self-assembled 1D structure and water-solubility demonstrate these materials' promise as processable and addressable functional materials for molecular electronics, redox-controlled materials and sensing.

| S-EPMC4694622 | 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