Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-stackable molecules assemble into porous crystals displaying concerted cavity-changing motions† † Electronic supplementary information (ESI) available: Experimental procedures and additional data (1H and 13C NMR spectra, FT-IR spectra, HR-MS) of the newly synthesized compounds. CCDC 1980363–1980368, 2048700, and 2048701. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/d1sc01163d

ABSTRACT: With small molecules, it is not easy to create large void spaces. Flat aromatics stack tightly, while flexible chains fold to fill the cavities. As an intuitive design to make open channels inside molecularly constructed solids, we employed propeller-shaped bicyclic triazoles to prepare a series of aromatic-rich three-dimensional (3D) building blocks. This modular approach has no previous example, but is readily applicable to build linear, bent, and branched arrays of non-stackable architectural motifs from existing flat aromatics by single-pot reactions. A letter H-shaped molecule thus prepared self-assembles into porous crystals, the highly unusual stepwise gas sorption behaviour of which prompted in-depth studies. A combination of single-crystal and powder X-ray diffraction analysis revealed multiple polymorphs, and sterically allowed pathways for their reversible interconversions that open and close the pores in response to external stimuli. Like non-collapsible open voids within stacks of steel H-beams, a non-covalent assembly of three-dimensional aromatics produces porous crystals. Concerted motions of the molecular H-beams open and close the cavities in response to external stimuli.

SUBMITTER: Kang T

PROVIDER: S-EPMC8115244 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.

Project description:Contacts with neighboring molecules in protein crystals inevitably restrict the internal motions of intrinsically flexible proteins. The resultant clear electron densities permit model building, as crystallographic snapshot structures. Although these still images are informative, they could provide biased pictures of the protein motions. If the mobile parts are located at a site lacking direct contacts in rationally designed crystals, then the amplitude of the movements can be experimentally analyzed. We propose a fusion protein method, to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts in the CCFS. Conventional model building fails when large amplitude motions exist. In this study, the mobile parts appear as smeared electron densities in the CCFS, by suitable processing of the X-ray diffraction data. We applied the CCFS method to a highly mobile presequence peptide bound to the mitochondrial import receptor, Tom20, and a catalytically relevant flexible segment in the oligosaccharyltransferase, AglB. These two examples demonstrated the general applicability of the CCFS method to the analysis of the spatial distribution of motions within protein molecules.

| S-EPMC4815401 | biostudies-literature

Protein concerted motions in the DNA-human topoisomerase I complex.

Project description:The collective motions of the core and C-terminal domains of human topoisomerase I (topo I) have been analysed by molecular dynamics simulation of the protein in covalent complex with a 22 bp DNA duplex. The analysis evidenced a great number of correlated movements of core subdomain I and II residues, and a central role for helix 5 in the protein-DNA communication, in particular with the scissile strand downstream of the cleavage site. The flow of information between these core subdomains and DNA suggests that subdomains I and II play an essential role in the DNA relaxation process. In core subdomain III the majority of DNA contacting residues do not communicate with protein regions far from DNA, suggesting that they have a structural role. However, selected core subdomain III residues, involved in the orientation of the active site region, show correlated movements with residues distant from DNA, indicating that the information concerning the catalytic event is also transmitted. The flexibility of two loops formed by residues 519-520 and 580-584 seems indispensable to the dynamic participation of core subdomain III to the DNA cleavage and religation steps. The motion of specific residues has also been found to explain the effect of single point mutations that make topo I resistant to the anticancer drug camptothecin.

| S-EPMC149835 | biostudies-literature

Non-equilibrium Model for Nanofluid Free Convection Inside a Porous Cavity Considering Lorentz Forces.

Project description:In current article, transportation of CuO nanoparticles through a porous enclosure is demonstrated. The enclosure has complex shaped hot wall. Porous media has been simulated via two temperature equations. Magnetic force impact on nanofluid treatment was considered. Control volume based finite element method has been described to solve current article in vorticity stream function form. Single phase model was chosen for nanofluid. Nanofluid characteristics are predicted via KKL model. Roles of solid-nanofluid interface heat transfer parameter (Nhs), porosity, Hartmann and Rayleigh numbers have been illustrated. Outputs illustrated that conduction mode reduces with augment of Ra. Increasing magnetic forces make nanofluid motion to decrease. Temperature gradient of nanofluid decreases with augment of Nhs. Reducing porosity leads to enhance in Nusselt number.

| S-EPMC6237777 | biostudies-literature

Ordered Lipid Domains Assemble via Concerted Recruitment of Constituents from Both Membrane Leaflets.

Project description:Lipid rafts serve as anchoring platforms for membrane proteins. Thus far they escaped direct observation by light microscopy due to their small size. Here we used differently colored dyes as reporters for the registration of both ordered and disordered lipids from the two leaves of a freestanding bilayer. Photoswitchable lipids dissolved or reformed the domains. Measurements of domain mobility indicated the presence of 120 nm wide ordered and 40 nm wide disordered domains. These sizes are in line with the predicted roles of line tension and membrane undulation as driving forces for alignment.

| S-EPMC7115998 | biostudies-literature

Segmental motions, not a two-state concerted switch, underlie allostery in CheY.

Project description:The switch between an inactive and active conformation is an important transition for signaling proteins, yet the mechanisms underlying such switches are not clearly understood. Escherichia coli CheY, a response regulator protein from the two-component signal transduction system that regulates bacterial chemotaxis, is an ideal protein for the study of allosteric mechanisms. By using 15N CPMG relaxation dispersion experiments, we monitored the inherent dynamic switching of unphosphorylated CheY. We show that CheY does not undergo a two-state concerted switch between the inactive and active conformations. Interestingly, partial saturation of Mg2+ enhances the intrinsic allosteric motions. Taken together with chemical shift perturbations, these data indicate that the ?s-ms timescale motions underlying CheY allostery are segmental in nature. We propose an expanded allosteric network of residues, including W58, that undergo asynchronous, local switching between inactive and active-like conformations as the primary basis for the allosteric mechanism.

| S-EPMC3552614 | biostudies-literature

Control of the conductance of engineered protein nanopores through concerted loop motions.

Project description:Protein nanopores have attracted much interest for nucleic acid sequencing, chemical sensing, and protein folding at the single molecule level. The outer membrane protein OmpG from E. coli stands out because it forms a nanopore from a single polypeptide chain. This property allows the separate engineering of each of the seven extracellular loops that control access to the pore. The longest of these loops, loop?6, has been recognized as the main gating loop that closes the pore at low pH values and opens it at high pH values. A method was devised to pin each of the loops to the embedding membrane and measure the single-pore conductances of the resulting constructs. The electrophysiological and complementary NMR measurements show that the pinning of individual loops alters the structure and dynamics of neighboring and distant loops in a correlated fashion. Pinning loop?6 generates a constitutively open pore and patterns of concerted loop motions control access to the OmpG nanopore.

| S-EPMC4091679 | biostudies-literature

Structural variability and concerted motions of the T cell receptor - CD3 complex.

Project description:We investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) - CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined by Dong et al., 2019. We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15° to 55°. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR - CD3 complex, in particular in the EC interactions of the Cβ FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR - CD3 complex revealed in our simulations provide atomistic insights on conformational changes of the complex in response to tilt-inducing forces on antigen-bound TCRs.

| S-EPMC8504971 | biostudies-literature

Detection of long-range concerted motions in protein by a distance covariance.

Project description:We asses the ability of a distance correlation coefficient (DiCC), calculated from distance covariance, for detecting long-range concerted motion in proteins. We establish a set of criteria for ideal correlation coefficient values based on the coefficient of determination in multi-dimension, R2. We compare in detail DiCC and conventional coefficients against these criteria. We demonstrate that in contrast to conventional correlation coefficients, which capture long-distance correlation adequately only with certain restrictions in multi-dimension, DiCC reflects appropriate correlation in both one- and multi-dimension. Finally we demonstrate the usefulness of DiCC for assessing long-distance correlated fluctuation in protein dynamics.

| S-EPMC3630994 | biostudies-literature

The consistency of large concerted motions in proteins in molecular dynamics simulations.

Project description:A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the simulation parameters in each simulation. Parameters studied included temperature, bond constraints, cut-off radius for electrostatic interactions, and initial placement of hydrogen atoms. The essential dynamics technique was used to reveal dynamic differences between the simulations. Similar essential dynamics properties were found for all simulations, indicating that the large concerted motions found in the simulations are not particularly sensitive to small changes in the force field. A thorough investigation into the stability of the essential dynamics properties as derived from a molecular dynamics simulation of a few hundred picoseconds is provided. Although the definition of the essential modes of motion has not fully converged in these short simulations, the subspace in which these modes are confined is found to be reproducible.

| S-EPMC1233640 | biostudies-other

Engineering crystals of dendritic molecules.

Project description:A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal.

| S-EPMC2708701 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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