Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Coiled coils 9-to-5: rational de novo design of α-helical barrels with tunable oligomeric states† † Electronic supplementary information (ESI) available: Methods and ESI data. See DOI: 10.1039/d1sc00460c

ABSTRACT: The rational design of linear peptides that assemble controllably and predictably in water is challenging. Short sequences must encode unique target structures and avoid alternative states. However, the non-covalent forces that stabilize and discriminate between states are weak. Nonetheless, for α-helical coiled-coil assemblies considerable progress has been made in rational de novo design. In these, sequence repeats of nominally hydrophobic (h) and polar (p) residues, hpphppp, direct the assembly of amphipathic helices into dimeric to tetrameric bundles. Expanding this pattern to hpphhph can produce larger α-helical barrels. Here, we show that pentameric to nonameric barrels are accessed by varying the residue at one of the h sites. In peptides with four L/I–K–E–I–A–x–Z repeats, decreasing the size of Z from threonine to serine to alanine to glycine gives progressively larger oligomers. X-ray crystal structures of the resulting α-helical barrels rationalize this: side chains at Z point directly into the helical interfaces, and smaller residues allow closer helix contacts and larger assemblies. Systematic de novo design of peptides that form α-helical barrels with functionalisable central channels with a range of internal diameters.

SUBMITTER: Dawson W

PROVIDER: S-EPMC8503928 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Carbon/ZrO2 aerogel composite microtube superfoam† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d4ra00109e

Project description: Not available

| S-EPMC10906140 | biostudies-literature

Antiferromagnetic skyrmion-based high speed diode† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d2na00748g

Project description:Antiferromagnetic (AFM) skyrmions are favored over ferromagnetic (FM) skyrmions as they can be driven parallel to in-plane driving currents and eventually prevent the annihilation at the edges of nanotrack. In this study, an AFM skyrmion-based diode is proposed to realize the one-way skyrmion motion that is crucial for data processing in nanoelectronic and spintronic devices. The skyrmion transport is controlled by exploiting the staircase notch region in the middle of the nanotrack. By virtue of this, the micromagnetic interaction energy between the skyrmion and the notch edges generates a potential gradient that further gives rise to repulsive forces on the skyrmion. The resultant of the forces from the driving current and edge repulsions make the skyrmion move along the notch region to overcome the device window and reach the detection region. The notch is designed in such a way that it prevents the movement of the skyrmion in the reverse direction, thereby achieving diode functionality. The proposed device offers processing speed in the order of 103 m s−1, hence paving the way for the development of energy-efficient and high-speed devices in antiferromagnetic spintronics. An AFM skyrmion based diode is designed using a staircase notch region at the middle of the nanotrack. The notch region induces the change in potential energy and acts as a barrier, thus allowing the unidirectional motion of the skyrmion.

| S-EPMC9846466 | biostudies-literature

Nα-arylsulfonyl histamines as selective β-glucosidase inhibitors† † Electronic supplementary information (ESI) available. See DOI: 10.1039/c8ra06625f

Project description:Nα-benzenesulfonylhistamine, a new semi-synthetic β-glucosidase inhibitor, was obtained by bioactivity-guided isolation from a chemically engineered extract of Urtica urens L. prepared by reaction with benzenesulfonyl chloride. In order to identify better β-glucosidase inhibitors, a new series of Nα,Nτ-di-arylsulfonyl and Nα-arylsulfonyl histamine derivatives was prepared. Biological studies revealed that the β-glucosidase inhibition was in a micromolar range for several Nα-arylsulfonyl histamine compounds of the series, Nα-4-fluorobenzenesulfonyl histamine being the most powerful compound. Besides, this reversible and competitive inhibitor presented a good selectivity for β-glucosidase with respect to other target enzymes including α-glucosidase. A selective β-glucosidase inhibitor was discovered using the chemically engineered extracts approach.

| S-EPMC9088825 | biostudies-literature

Lipoic acid-based vitrimer-like elastomer† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3py00883e

Project description: Not available

| S-EPMC10644234 | biostudies-literature

Trimethylaluminum-mediated one-pot peptide elongation† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3sc00208j

Project description:Efficient and straightforward peptide bond formation of N-, and C-terminal unprotected amino acids was successfully achieved by using trimethylaluminum. The coupling reaction was accomplished by pre-reaction of N-, and C-terminal unprotected amino acids and trimethylaluminum to form a five-membered ring that smoothly reacted with nucleophilic amino acid esters. This simple and highly efficient reaction system allows one-pot tripeptide synthesis without the need for expensive coupling reagents. Furthermore, peptide bond formation can be effectively achieved even for amino acids with bulky substituents at the side chain to afford the corresponding tripeptides in high yields in a one-pot manner. In addition, the reaction can be applied for further peptide elongation by the subsequent addition of amino acids and trimethylaluminum. We anticipate that this cost-effective, straightforward, and efficient protocol will be useful for the synthesis of a wide variety of peptides. Efficient and straightforward peptide bond formation of N-, and C-terminal unprotected amino acids was successfully achieved by using trimethylaluminum.

| S-EPMC10231425 | biostudies-literature

New fluorene-based bipolar charge transporting materials† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3ra07583d

Project description: Not available

| S-EPMC10794882 | biostudies-literature

Mechanochemically assisted morphing of shape shifting polymers† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3sc02404k

Project description:Morphing in creatures has inspired various synthetic polymer materials that are capable of shape shifting. The morphing of polymers generally relies on stimuli-active (typically heat and light active) units that fix the shape after a mechanical load-based shape programming. Herein, we report a strategy that uses a mechanochemically active 2,2′-bis(2-phenylindan-1,3-dione) (BPID) mechanophore as a switching unit for mechanochemical morphing. The mechanical load on the polymer triggers the dissociation of the BPID moiety into stable 2-phenylindan-1,3-dione (PID) radicals, whose subsequent spontaneous dimerization regenerates BPID and fixes the temporary shapes that can be effectively recovered to the permanent shapes by heating. A greater extent of BPID activation, through a higher BPID content or mechanical load, leads to higher mechanochemical shape fixity. By contrast, a relatively mechanochemically less active hexaarylbiimidazole (HABI) mechanophore shows a lower fixing efficiency when subjected to the same programing conditions. Another control system without a mechanophore shows a low fixing efficiency comparable to the HABI system. Additionally, the introduction of the BPID moiety also manifests remarkable mechanochromic behavior during the shape programing process, offering a visualizable indicator for the pre-evaluation of morphing efficiency. Unlike conventional mechanical mechanisms that simultaneously induce morphing, such as strain-induced plastic deformation or crystallization, our mechanochemical method allows for shape programming after the mechanical treatment. Our concept has potential for the design of mechanochemically programmable and mechanoresponsive shape shifting polymers. A 2,2′-bis(2-phenylindan-1,3-dione) (BPID) mechanophore is applied as a switching unit for mechanochemical morphing of polymers. Mechancial force activates the BPID into stable PID radicals, whose subsequent dimerization fixes the temporary shapes.

| S-EPMC10466301 | biostudies-literature

Engineering the interface in mechanically responsive graphene-based films† † Electronic supplementary information (ESI) available. See DOI: 10.1039/c8ra07974a

Project description:Due to their extraordinary mechanical properties, nanocarbon materials (e.g. carbon nanotube and graphene) are attracting great interests in the field of nanocomposites. One unique feature in nanocarbon-based nanocomposites is their intrinsically rich interface, allowing them to adapt the microstructures in response to external loading and, in turn, to stiffen themselves. This mechanical behavior, called responsive stiffening, was usually observed in biological materials such as bones and muscles. The mechanically responsive behaviors of nanocarbon-based materials are particularly exciting because the nanocarbon-enabled huge interface area offers opportunities to tune such stiffening performance while this interface advantage is not fully exploited yet. Here, we demonstrate stiffening behaviors in graphene oxide (GO)-based film materials in response to dynamic oscillations. Through a facile method of polymer content alteration and alkali treatment, the microstructure and interlayer interaction of GO films are modified, along with the resulted responsively stiffening performance. Based on polarized Raman spectra characterizations, we attribute the stiffening mechanism to the microstructural evolution of GO films during dynamic tension as well as the polymer chains alignment. Finally, we highlight the significantly improved static mechanical properties of GO film after a simple stiffening process. Our results not only aid in the development of biomimetic, adaptive materials, but provide a mechanical way for the design of high-performance nanocarbon-based nanocomposites. Engineering interface and microstructures to improve mechanical performance of graphene-based films via a “mechanical” way.

| S-EPMC9088400 | biostudies-literature

Evaluating Riboglow-FLIM probes for RNA sensing† † Electronic supplementary information (ESI) available. See DOI: https://doi.org/10.1039/d3cb00197k

Project description: Not available

| S-EPMC10849122 | biostudies-literature

Contributions to cytochrome c inner- and outer-sphere reorganization energy† † Electronic supplementary information (ESI) available. See DOI: 10.1039/d1sc02865k

Project description:Cytochromes c are small water-soluble proteins that catalyze electron transfer in metabolism and energy conversion processes. Hydrogenobacter thermophilus cytochrome c552 presents a curious case in displaying fluxionality of its heme axial methionine ligand; this behavior is altered by single point mutation of the Q64 residue to N64 or V64, which fixes the ligand in a single configuration. The reorganization energy (λ) of these cytochrome c552 variants is experimentally determined using a combination of rotating disc electrochemistry, chronoamperometry and cyclic voltammetry. The differences between the λ determined from these complementary techniques helps to deconvolute the contribution of the active site and its immediate environment to the overall λ (λTotal). The experimentally determined λ values in conjunction with DFT calculations indicate that the differences in λ among the protein variants are mainly due to the differences in contributions from the protein environment and not just inner-sphere λ. DFT calculations indicate that the position of residue 64, responsible for the orientation of the axial methionine, determines the geometric relaxation of the redox active molecular orbital (RAMO). The orientation of the RAMO with respect to the heme is key to determining electron transfer coupling (HAB) which results in higher ET rates in the wild-type protein relative to the Q64V mutant despite a 150 mV higher λTotal in the former. Efficient delocalization of the redox-active molecular orbital (RAMO) in HtWT results in an increase in HAB value which in turn accelerates the electron transfer (ET) rate in spite of the higher reorganization energy (λ) than the HtQ64V mutant.

| S-EPMC8442690 | 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