Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solid-state packing dictates the unexpected solubility of aromatic peptides.

ABSTRACT: The understanding and prediction of the solubility of biomolecules, even of the simplest ones, reflect an open question and unmet need. Short aromatic tripeptides are among the most highly aggregative biomolecules. However, in marked contrast, Ala-Phe-Ala (AFA) was surprisingly found to be non-aggregative and could be solubilized at millimolar concentrations. Here, aiming to uncover the underlying molecular basis of its high solubility, we explore in detail the solubility, aggregation propensity, and atomic-level structure of the tripeptide. We demonstrate an unexpectedly high water solubility of AFA reaching 672 mM, two orders of magnitude higher than reported previously. The single crystal structure reveals an anti-parallel β sheet conformation devoid of any aromatic interactions. This study provides clear mechanistic insight into the structural basis of solubility and suggests a simple and feasible tool for its estimation, bearing implications for design of peptide drugs, peptides materials, and advancement of peptide nanotechnology.

SUBMITTER: Bera S

PROVIDER: S-EPMC8063180 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Unexpected organic hydrate luminogens in the solid state.

Project description:Developing organic photoluminescent materials with high emission efficiencies in the solid state under a water atmosphere is important for practical applications. Herein, we report the formation of both intra- and intermolecular hydrogen bonds in three tautomerizable Schiff-base molecules which comprise active hydrogen atoms that act as proton donors and acceptors, simultaneously hindering emission properties. The intercalation of water molecules into their crystal lattices leads to structural rearrangement and organic hydrate luminogen formation in the crystalline phase, triggering significantly enhanced fluorescence emission. By suppressing hydrogen atom shuttling between two nitrogen atoms in the benzimidazole ring, water molecules act as hydrogen bond donors to alter the electronic transition of the molecular keto form from nπ* to lower-energy ππ* in the excited state, leading to enhancing emission from the keto form. Furthermore, the keto-state emission can be enhanced using deuterium oxide (D2O) owing to isotope effects, providing a new opportunity for detecting and quantifying D2O.

| S-EPMC8058042 | biostudies-literature

Harnessing solid-state packing for selective detection of chloride in a macrocyclic anionophore.

Project description:We report the synthesis of an inherently fluorescent macrocyclic receptor for chloride. The use of a disulphide tether provides for an excellent yield in the macrocyclization step. This compound binds chloride in the solution and solid state, and while unstable over time in aqueous solution, shows a selective response toward chloride over other anions in the solid state due to intermolecular interactions between fluorophore backbones. Surprisingly, the optoelectronic response to anions differs in solution and the films, with a distinct colorimetric response observed only in the film.

| S-EPMC4973467 | biostudies-literature

Polymorph crystal packing effects on charge transfer emission in the solid state.

Project description:Condensation of 1,8-naphthalic anhydride with N,N-(dimethylamino)aniline produced the donor-acceptor compound DMIM, which crystallised from a chloroform-diethyl ether mixture to afford two different coloured crystal polymorphs. Crystals for one polymorph are small and green, whereas the other crystals are orange and needle-like. X-ray crystal structures for both polymorphs were determined. The donor N,N-dimethylaniline and acceptor naphthalimide groups are twisted with respect to each other; the degree of twist is marginally different for the two structures. The orange crystal polymorph crystallises in the monoclinic space group C2/c and contains two slightly different molecular conformers in the unit cell (calculated density is 1.410 g cm-3). The green crystal polymorph crystallises in the triclinic space group P1 and contains only one type of molecule in the unit cell (calculated density is 1.401 g cm-3). The crystal packing motifs for the two polymorphs are subtly different, explaining the small variance in the observed densities. Very weak room temperature emission was observed for DMIM in a CHCl3 solution, but crystals deposited on a glass slide glowed when irradiated at 488 nm using a fluorescence microscope. Disparate solid-state emission spectra and lifetimes for the two polymorphic crystal forms are observed for the dyad. The emission is assigned to charge recombination fluorescence from a charge transfer state.

| S-EPMC5814771 | biostudies-other

Solid state forms of 4-aminoquinaldine - From void structures with and without solvent inclusion to close packing.

Project description:Polymorphs of 4-aminoquinaldine (4-AQ) have been predicted in silico and experimentally identified and characterised. The two metastable forms, AH (anhydrate) II and AH III, crystallise in the trigonal space group [Formula: see text] and are less densely packed than the thermodynamically most stable phase AH I° (P21/c ). AH II can crystallise and exist both, as a solvent inclusion compound and as an unsolvated phase. The third polymorph, AH III, is exclusively obtained by desolvation of a carbon tetrachloride solvate. Theoretical calculations correctly estimated the experimental 0K stability order, confirmed that AH II can exist without solvents, gave access to the AH III structure, and identified that there exists a subtle balance between close packing and number of hydrogen bonding interactions in the solid state of anhydrous 4-AQ. Furthermore, the prevalence of void space and solvent inclusion in [Formula: see text] structures is discussed.

| S-EPMC4693969 | biostudies-literature

Fluorescence Emission of Self-assembling Amyloid-like Peptides: Solution versus Solid State.

Project description:Analysis of the intrinsic UV-visible fluorescence exhibited by self-assembling amyloid-like peptides in solution and in solid the state highlights that their physical state has a profound impact on the optical properties. In the solid state, a linear dependence of the fluorescence emission peaks as a function of excitation wavelength is detected. On the contrary, an excitation-independent emission is observed in solution. The present findings constitute a valuable benchmark for current and future explanations of the fluorescence emission by amyloids.

| S-EPMC8597038 | biostudies-literature

Bridged Aromatic Oxo- and Thioethers with Intense Emission in Solution and the Solid State.

Project description:In this contribution, we report on a class of emitters based on bridged oxo- and/or thioethers revealing striking photoluminescence properties in fluid solution and in the solid state. In total, nine compounds were investigated concerning their photophysical properties, which were interpreted by quantum chemical calculations. To our delight, we discovered compounds possessing nearly identical photoluminescence quantum yields (ΦF ) in solution and in the solid state, which has been rarely reported so far. Besides these efforts, we shed light on the influence of polymorphism and solvent polarity on the emission properties. In addition, an in-depth X-ray diffractometric analysis was conducted to correlate molecular packing in the crystal with differences in the photophysical properties.

| S-EPMC8456941 | biostudies-literature

The influence of solid state information and descriptor selection on statistical models of temperature dependent aqueous solubility.

Project description:Predicting the equilibrium solubility of organic, crystalline materials at all relevant temperatures is crucial to the digital design of manufacturing unit operations in the chemical industries. The work reported in our current publication builds upon the limited number of recently published quantitative structure-property relationship studies which modelled the temperature dependence of aqueous solubility. One set of models was built to directly predict temperature dependent solubility, including for materials with no solubility data at any temperature. We propose that a modified cross-validation protocol is required to evaluate these models. Another set of models was built to predict the related enthalpy of solution term, which can be used to estimate solubility at one temperature based upon solubility data for the same material at another temperature. We investigated whether various kinds of solid state descriptors improved the models obtained with a variety of molecular descriptor combinations: lattice energies or 3D descriptors calculated from crystal structures or melting point data. We found that none of these greatly improved the best direct predictions of temperature dependent solubility or the related enthalpy of solution endpoint. This finding is surprising because the importance of the solid state contribution to both endpoints is clear. We suggest our findings may, in part, reflect limitations in the descriptors calculated from crystal structures and, more generally, the limited availability of polymorph specific data. We present curated temperature dependent solubility and enthalpy of solution datasets, integrated with molecular and crystal structures, for future investigations.

| S-EPMC6115327 | biostudies-literature

Scalable synthesis of 5,11-diethynylated indeno[1,2-b]fluorene-6,12-diones and exploration of their solid state packing.

Project description:We report a new synthetic route to 5,11-disubstituted indeno[1,2-b]fluorene-6,12-diones that is amenable to larger scale reactions, allowing for the preparation of gram amounts of material. With this new methodology, we explored the effects on crystal packing morphology for the indeno[1,2-b]fluorene-6,12-diones by varying the substituents on the silylethynyl groups.

| S-EPMC4168888 | biostudies-literature

Shape-persistent macrocyclic aromatic tetrasulfonamides: Molecules with nanosized cavities and their nanotubular assemblies in solid state.

Project description:Alkoxy side-chain-flanked diarylsulfonamide serves as a reliable structural motif for constructing macrocyclic aromatic tetrasulfonamides. This 90 degrees structural motif is persistent both in solution and in the solid state, which allows the one-step formation of tetrasulfonamide macrocycles. These macrocycles adopt a cone-shaped conformation in solution and in the solid state. For each molecule, an interior cavity surrounded by the aromatic residues is formed. The cavity sizes of the macrocycles can be tuned by incorporating aromatic residues of proper sizes. Guest (solvent) molecules are found in the cavities and bound by side chains. In solution, 1H NMR shows that the cone conformations undergo rapid interconversion at room temperature. The alkoxy side chains are found to be indispensable for maintaining the cone conformation. In addition, these porous molecules self-assemble into hollow tubular structures in the solid state. A variety of host molecules and building blocks for constructing nanoporous solid-state structures can be expected from these molecules.

| S-EPMC1544137 | biostudies-literature

Structural and energetic basis of carbohydrate-aromatic packing interactions in proteins.

Project description:Carbohydrate-aromatic interactions mediate many biological processes. However, the structure-energy relationships underpinning direct carbohydrate-aromatic packing interactions in aqueous solution have been difficult to assess experimentally and remain elusive. Here, we determine the structures and folding energetics of chemically synthesized glycoproteins to quantify the contributions of the hydrophobic effect and CH-? interactions to carbohydrate-aromatic packing interactions in proteins. We find that the hydrophobic effect contributes significantly to protein-carbohydrate interactions. Interactions between carbohydrates and aromatic amino acid side chains, however, are supplemented by CH-? interactions. The strengths of experimentally determined carbohydrate CH-? interactions do not correlate with the electrostatic properties of the involved aromatic residues, suggesting that the electrostatic component of CH-? interactions in aqueous solution is small. Thus, tight binding of carbohydrates and aromatic residues is driven by the hydrophobic effect and CH-? interactions featuring a dominating dispersive component.

| S-EPMC3715148 | 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