Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A remote prolyl isomerization controls domain assembly via a hydrogen bonding network.

ABSTRACT: Prolyl cis/trans isomerizations determine the rates of protein folding reactions and can serve as molecular switches and timers. In the gene-3-protein of filamentous phage, Pro-213 trans --> cis isomerization in a hinge region controls the assembly of the 2 domains N1 and N2 and, in reverse, the activation of the phage for infection. We elucidated the structural and energetic basis of this proline-limited domain assembly at the level of individual residues by real-time 2D NMR. A local cluster of inter-domain hydrogen bonds, remote from Pro-213, is stabilized up to 3,000-fold by trans --> cis isomerization. This network of hydrogen bonds mediates domain assembly and is connected with Pro-213 by rigid backbone segments. Thus, proline cis/trans switching is propagated in a specific and directional fashion to change the protein structure and stability at a distant position.

SUBMITTER: Weininger U

PROVIDER: S-EPMC2718393 | biostudies-other | 2009 Jul

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

A remote prolyl isomerization controls domain assembly via a hydrogen bonding network.

Weininger Ulrich U Jakob Roman P RP Eckert Barbara B Schweimer Kristian K Schmid Franz X FX Balbach Jochen J

Proceedings of the National Academy of Sciences of the United States of America 20090715 30

Prolyl cis/trans isomerizations determine the rates of protein folding reactions and can serve as molecular switches and timers. In the gene-3-protein of filamentous phage, Pro-213 trans --> cis isomerization in a hinge region controls the assembly of the 2 domains N1 and N2 and, in reverse, the activation of the phage for infection. We elucidated the structural and energetic basis of this proline-limited domain assembly at the level of individual residues by real-time 2D NMR. A local cluster of ...[more]

PMID: 19617535

Similar Datasets

A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase.

Project description:Cholesterol oxidase is a flavoenzyme that catalyzes the oxidation and isomerization of 3beta-hydroxysteroids. Structural and mutagenesis studies have shown that Asn485 plays a key role in substrate oxidation. The side chain makes an NH...pi interaction with the reduced form of the flavin cofactor. A N485D mutant was constructed to further test the role of the amide group in catalysis. The mutation resulted in a 1800-fold drop in the overall k(cat). Atomic resolution structures were determined for both the N485L and N485D mutants. The structure of the N485D mutant enzyme (at 1.0 A resolution) reveals significant perturbations in the active site. As predicted, Asp485 is oriented away from the flavin moiety, such that any stabilizing interaction with the reduced flavin is abolished. Met122 and Glu361 form unusual hydrogen bonds to the functional group of Asp485 and are displaced from the positions they occupy in the wild-type active site. The overall effect is to disrupt the stabilization of the reduced FAD cofactor during catalysis. Furthermore, a narrow transient channel that is shown to form when the wild-type Asn485 forms the NH...pi interaction with FAD and that has been proposed to function as an access route of molecular oxygen, is not observed in either of the mutant structures, suggesting that the dynamics of the active site are altered.

| S-EPMC3089011 | biostudies-literature

Control of Assembly of Dihydropyridyl and Pyridyl Molecules via Directed Hydrogen Bonding.

Project description:The crystallization of two dihydropyridyl molecules, 1,4-bis(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)benzene ([C40H24N10]·2DMF, 1·2DMF; DMF = dimethylformamide) and 1,4-bis(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)phenylbenzene ([C46H28N10]·2DMF, 3·2DMF), and their respective oxidized pyridyl analogues, 1,4-bis(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene ([C40H20N10], 2) and 1,4-bis(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)phenylbenzene ([C46H24N10]·DMF, 4·DMF), has been achieved under solvothermal conditions. The dihydropyridyl molecules are converted to their pyridyl products via in situ oxidative dehydrogenation in solution. The structures of the four molecules have been fully characterized by single crystal and powder X-ray diffraction. The oxidized pyridyl products, 2 and 4, are more elongated due to aromatization of the dihydropyridyl rings at each end of their parent molecules 1 and 3, respectively. The solid-state supramolecular structures of the pyridyl molecules are distinct from the dihydropyridyl molecules in terms of their hierarchical assembly via hydrogen bonding due to the loss of primary N-H hydrogen bond donors in the two electron oxidized tectons. Overall, the geometrically shorter molecules 1 and 3 display close-packed structures, whereas the more extended 2 and 4 assemble into more open supramolecular systems.

| S-EPMC4583071 | biostudies-literature

Prolyl isomerization controls activation kinetics of a cyclic nucleotide-gated ion channel.

Project description:SthK, a cyclic nucleotide-modulated ion channel from Spirochaeta thermophila, activates slowly upon cAMP increase. This is reminiscent of the slow, cAMP-induced activation reported for the hyperpolarization-activated and cyclic nucleotide-gated channel HCN2 in the family of so-called pacemaker channels. Here, we investigate slow cAMP-induced activation in purified SthK channels using stopped-flow assays, mutagenesis, enzymatic catalysis and inhibition assays revealing that the cis/trans conformation of a conserved proline in the cyclic nucleotide-binding domain determines the activation kinetics of SthK. We propose that SthK exists in two forms: trans Pro300 SthK with high ligand binding affinity and fast activation, and cis Pro300 SthK with low affinity and slow activation. Following channel activation, the cis/trans equilibrium, catalyzed by prolyl isomerases, is shifted towards trans, while steady-state channel activity is unaffected. Our results reveal prolyl isomerization as a regulatory mechanism for SthK, and potentially eukaryotic HCN channels. This mechanism could contribute to electrical rhythmicity in cells.

| S-EPMC7744796 | biostudies-literature

Calcineurin Undergoes a Conformational Switch Evoked via Peptidyl-Prolyl Isomerization.

Project description:A limited repertoire of PPP family of serine/threonine phosphatases with a highly conserved catalytic domain acts on thousands of protein targets to orchestrate myriad central biological roles. A major structural reorganization of human calcineurin, a ubiquitous Ser/Thr PPP regulated by calcium and calmodulin and targeted by immunosuppressant drugs cyclosporin A and FK506, is unveiled here. The new conformation involves trans- to cis-isomerization of proline in the SAPNY sequence, highly conserved across PPPs, and remodels the main regulatory site where NFATc transcription factors bind. Transitions between cis- and trans-conformations may involve peptidyl prolyl isomerases such as cyclophilin A and FKBP12, which are known to physically interact with and modulate calcineurin even in the absence of immunosuppressant drugs. Alternative conformations in PPPs provide a new perspective on interactions with substrates and other protein partners and may foster development of more specific inhibitors as drug candidates.

| S-EPMC4527731 | biostudies-literature

Asymmetric allylic substitution-isomerization to axially chiral enamides <i>via</i> hydrogen-bonding assisted central-to-axial chirality transfer.

Project description:Axially chiral enamides bearing a N-C axis have been recently studied and were proposed to be valuable chiral building blocks, but a stereoselective synthesis has not been achieved. Here, we report the first enantioselective synthesis of axially chiral enamides via a highly efficient, catalytic approach. In this approach, C(sp2)-N bond formation is achieved through an iridium-catalyzed asymmetric allylation, and then in situ isomerization of the initial products through an organic base promoted 1,3-H transfer, leading to the enamide products with excellent central-to-axial transfer of chirality. Computational and experimental studies revealed that the 1,3-H transfer occurs via a stepwise deprotonation/re-protonation pathway with a chiral ion-pair intermediate. Hydrogen bonding interactions with the enamide carbonyl play a significant role in promoting both the reactivity and stereospecificity of the stepwise 1,3-H transfer. The mild and operationally simple formal N-vinylation reaction delivered a series of configurationally stable axially chiral enamides with good to excellent yields and enantioselectivities.

| S-EPMC8162293 | biostudies-literature

Supramolecular polymers with tunable topologies via hierarchical coordination-driven self-assembly and hydrogen bonding interfaces.

Project description:A powerful strategy to obtain complex supramolecular materials is the bottom-up construction of noncovalently bound materials by hierarchical self-assembly. This assembly process involves stepwise, uniform increases to the architectural complexity of a substrate, starting from discrete precursors and growing in dimensionality through controlled reactivity to a final product. Herein, two orthogonal processes are exploited: coordination-driven self-assembly and hydrogen bonding. The former relies on the predictable formation of metal-ligand bonds wherein the directionalities of the rigid precursors used determines the structural outcome. The latter uses 2-ureido-4-pyrimidinone interfaces that are structurally robust by virtue of the quadruple hydrogen bonding that can occur between subunits. By combining these two processes into a single system, it is possible to generate hierarchical materials that preserve the attractive tunability associated with discrete supramolecular coordination complexes. For instance, the synthesis of a one-dimensional chain comprising linked metalla-rhomboids is readily adapted to a 2D cross-linked hexagonal network by simply selecting a different metal acceptor precursor as an assembly component. The specific interactions between subunits, in this case platinum(II)-pyridyl bonds and the quadruple H-bonding of ureidopyrimidinone, are unchanged, establishing a unique strategy to obtain supramolecular polymers with marked topological differences with minimal synthetic redesign. In addition, the structural rigidity imposed by the inclusion of the platinum metallacycles serves to minimize the formation of cyclic oligomers, increasing the efficacy of formation and improving the properties of the resultant materials. Furthermore, this study taps the potential of organoplatinum(II) metallacycles in materials science.

| S-EPMC3785758 | biostudies-literature

Hydrogen-Bonding-Driven 3D Supramolecular Assembly of Peptidomimetic Zipper.

Project description:Hydrogen-bonding-driven three-dimensional (3D) assembly of a peptidomimetic zipper has been established for the first time by using an α/AApeptide zipper that assembles into a de novo lattice arrangement through two layers of hydrogen-bonded linker-directed interactions. Via a covalently bridged 1D 413-helix, drastic enhancement in stability has been achieved in the formed 3D crystalline supramolecular architecture as evidenced by gas-sorption studies. As the first example of an unnatural peptidic zipper, the dimensional augmentation of the zipper differs from metal-coordinated strategies, and may have general implications for the preparation of peptidic functional materials for a variety of future applications.

| S-EPMC10866394 | biostudies-literature

Spontaneous Isomerization of a Hydroxynaphthalene-Containing Spiropyran in Polar Solvents Enhanced by Hydrogen Bonding Interactions.

Project description:The synthesis of spiropyran dyes exhibiting solvent-driven isomerization even in the dark condition is an important subject for the design of optical materials. A conventional synthesis strategy involves the conjugation of indoline moieties with electron-deficient aromatic moieties. Herein, we report that a spiropyran conjugated with a hydroxynaphthalene moiety (1) is a new member exhibiting solvent-driven isomerization, even bearing an electron-donating -OH moiety. The dye exists as a colorless spirocyclic (SP) form in nonpolar media. It, however, shows a blue color in polar media, especially in aqueous media, due to the formation of ring-opened merocyanine (MC) forms, where the isomerization terminates in 10 s even at room temperature. The spontaneous SP → MC isomerization originates from the MC forms stabilized by the highly delocalized π-electrons on the hydroxynaphthalene moiety. The solvation in polar media and the hydrogen bonding interaction with water molecules decrease the ground-state energy of the MC forms, triggering spontaneous isomerization. The dye exhibits two MC absorption bands assigned to the trans-trans-cis (TTC) and cis-trans-cis (CTC) isomers. The absorbance of the CTC band increases more significantly with an increase in the water content, and the increase exhibits a linear relationship with a hydrogen-bond donor acidity of solvents. The phenolate oxygen of the CTC form has larger hydrogen-bond acceptor basicity, resulting in stronger stabilization by the water molecule.

| S-EPMC8717586 | biostudies-literature

Asymmetric remote C-H borylation of internal alkenes via alkene isomerization.

Project description:Recent years have witnessed the growing interest in the remote functionalization of alkenes for it offers a strategy to activate the challenging C-H bonds distant from the initiation point via alkene isomerization/functionalization. However, the catalytic enantioselective isomerization/functionalization with one single transition metal catalyst remains rare. Here we report a highly regio- and enantioselective cobalt-catalyzed remote C-H bond borylation of internal alkenes via sequential alkene isomerization/hydroboration. A chiral ligand featured twisted pincer, anionic, and non-rigid characters is designed and used for this transformation. This methodology, which is operationally simple using low catalyst loading without additional activator, shows excellent enantioselectivity and can be used to convert various internal alkenes with regio- and stereoisomers to valuable chiral secondary organoboronates with good functional group tolerance.

| S-EPMC6158179 | biostudies-literature

High-fidelity self-assembly pathways for hydrogen-bonding molecular semiconductors.

Project description:The design of molecular systems with high-fidelity self-assembly pathways that include several levels of hierarchy is of primary importance for the understanding of structure-function relationships, as well as for controlling the functionality of organic materials. Reported herein is a high-fidelity self-assembly system that comprises two hydrogen-bonding molecular semiconductors with regioisomerically attached short alkyl chains. Despite the availability of both discrete cyclic and polymeric linear hydrogen-bonding motifs, the two regioisomers select one of the two motifs in homogeneous solution as well as at the 2D-confined liquid-solid interface. This selectivity arises from the high directionality of the involved hydrogen-bonding interactions, which renders rerouting to other self-assembly pathways difficult. In thin films and in the bulk, the resulting hydrogen-bonded assemblies further organize into the expected columnar and lamellar higher-order architectures via solution processing. The contrasting organized structures of these regioisomers are reflected in their notably different miscibility with soluble fullerene derivatives in the solid state. Thus, electron donor-acceptor blend films deliver a distinctly different photovoltaic performance, despite their virtually identical intrinsic optoelectronic properties. Currently, we attribute this high-fidelity control via self-assembly pathways to the molecular design of these supramolecular semiconductors, which lacks structure-determining long aliphatic chains.

| S-EPMC5320534 | 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