Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallization of a potassium ion channel and X-ray and neutron data collection.

ABSTRACT: The mechanism by which potassium ions are transported through ion channels is currently being investigated by several groups using many different techniques. Clarification of the location of water molecules during transport is central to understanding how these integral membrane proteins function. Neutrons have a unique sensitivity to both hydrogen and potassium, rendering neutron crystallography capable of distinguishing waters from K+ ions. Here, the collection of a complete neutron data set from a potassium ion channel to a resolution of 3.55?Å using the Macromolecular Neutron Diffractometer (MaNDi) is reported. A room-temperature X-ray data set was also collected from the same crystal to a resolution of 2.50?Å. Upon further refinement, these results will help to further clarify the ion/water population within the selectivity filter of potassium ion channels.

SUBMITTER: Langan PS

PROVIDER: S-EPMC6572099 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallization of a potassium ion channel and X-ray and neutron data collection.

Langan Patricia S PS Vandavasi Venu Gopal VG Sullivan Brendan B Harp Joel J Weiss Kevin K Coates Leighton L

Acta crystallographica. Section F, Structural biology communications 20190521 Pt 6

The mechanism by which potassium ions are transported through ion channels is currently being investigated by several groups using many different techniques. Clarification of the location of water molecules during transport is central to understanding how these integral membrane proteins function. Neutrons have a unique sensitivity to both hydrogen and potassium, rendering neutron crystallography capable of distinguishing waters from K<sup>+</sup> ions. Here, the collection of a complete neutron ...[more]

PMID: 31204690

Similar Datasets

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase.

Project description:Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1-3 mm(3)) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space group P212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.

| S-EPMC4631597 | biostudies-literature

Expression, purification, crystallization and X-ray data collection for RAS and its mutants.

Project description:This article expands on crystal structure data for human H-RAS with mutations at position Y137, briefly described in a paper on the effects of phosphorylation of Y137 by ABL kinases (Tyrosine phosphorylation of RAS by ABL allosterically enhances effector binding, published in the FASEB Journal [1]). The crystal structures of the Y137E mutant (phosphorylation mimic) and of the Y137F mutant (without the hydroxyl group where phosphorylation occurs) were deposited in the Protein Data Bank with PDB codes 4XVQ (H-RAS(Y137E)) and 4XVR (H-RAS(Y137F)). This article includes details for expression and purification of RAS and its mutants with no affinity tags, in vitro exchange of guanine nucleotides, protein crystallization, X-ray data collection and structure refinement.

| S-EPMC4710794 | biostudies-literature

Ion conduction through the hERG potassium channel.

Project description:The inward rectifier voltage-gated potassium channel hERG is of primary importance for the regulation of the membrane potential of cardiomyocytes. Unlike most voltage-gated K(+)-channels, hERG shows a low elementary conductance at physiological voltage and potassium concentration. To investigate the molecular features underlying this unusual behavior, we simulated the ion conduction through the selectivity filter at a fully atomistic level by means of molecular dynamics-based methods, using a homology-derived model. According to our calculations, permeation of potassium ions can occur along two pathways, one involving site vacancies inside the filter (showing an energy barrier of about 6 kcal mol(-1)), and the other characterized by the presence of a knock-on intermediate (about 8 kcal mol(-1)). These barriers are indeed in accordance with a low conductance behavior, and can be explained in terms of a series of distinctive structural features displayed by the hERG ion permeation pathway.

| S-EPMC3487835 | biostudies-literature

Crystallization and X-ray diffraction data collection of topoisomerase IV ParE subunit from Xanthomonas oryzae pv. oryzae.

Project description:Topoisomerase IV is involved in topological changes in the bacterial genome using the free energy from ATP hydrolysis. Its functions are the decatenation of daughter chromosomes following replication by DNA relaxation and double-strand DNA breakage. In this study, the N-terminal fragment of the topoisomerase IV ParE subunit from Xanthomonas oryzae pv. oryzae was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.15 A resolution using a synchrotron-radiation source. The crystal belonged to space group P4(2)2(1)2, with unit-cell parameters a = b = 105.30, c = 133.76 A. The asymmetric unit contains one molecule, with a corresponding V(M) of 4.21 A(3) Da(-1) and a solvent content of 69.6%.

| S-EPMC2688423 | biostudies-literature

Crystallization and preliminary X-ray crystallographic characterization of a cyclic nucleotide-binding homology domain from the mouse EAG potassium channel.

Project description:The members of the family of voltage-gated KCNH potassium channels play important roles in cardiac and neuronal repolarization, tumour proliferation and hormone secretion. These channels have a C-terminal cytoplasmic domain which is homologous to cyclic nucleotide-binding domains (CNB-homology domains), but it has been demonstrated that channel function is not affected by cyclic nucleotides and that the domain does not bind nucleotides in vitro. Here, the crystallization and preliminary crystallographic analysis of a CNB-homology domain from a member of the KCNH family, the mouse EAG channel, is reported. X-ray diffraction data were collected to 2.2 Å resolution and the crystal belonged to the hexagonal space group P3(1)21.

| S-EPMC3310546 | biostudies-literature

Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions.

Project description:Lytic polysaccharide monooxygenases (LPMOs) are copper-center enzymes that are involved in the oxidative cleavage of the glycosidic bond in crystalline cellulose and other polysaccharides. The LPMO reaction is initiated by the addition of a reductant and oxygen to ultimately form an unknown activated copper-oxygen species that is responsible for polysaccharide-substrate H-atom abstraction. Given the sensitivity of metalloproteins to radiation damage, neutron protein crystallography provides a nondestructive technique for structural characterization while also informing on the positions of H atoms. Neutron cryo-crystallography permits the trapping of catalytic intermediates, thereby providing insight into the protonation states and chemical nature of otherwise short-lived species in the reaction mechanism. To characterize the reaction-mechanism intermediates of LPMO9D from Neurospora crassa, a cryo-neutron diffraction data set was collected from an ascorbate-reduced crystal. A second neutron diffraction data set was collected at room temperature from an LPMO9D crystal exposed to low-pH conditions to probe the protonation states of ionizable groups involved in catalysis under acidic conditions.

| S-EPMC8034432 | biostudies-literature

Crystallization and preliminary X-ray data collection of the L27(PATJ)-(L27N,L27C)(Pals1)-L27(MALS) tripartite complex.

Project description:The L27 (LIN-2/LIN-7) domain is a protein-protein interaction module capable of assembling proteins into biologically important complexes. Pals1 contains two L27 domains: the first, L27N, interacts with PATJ, and the second, L27C, interacts with MALS, forming a tripartite complex that plays a crucial role in the establishment and maintenance of cell polarity. To provide a better understanding of the mechanism of assembly of this tripartite complex, four different L27(PATJ)-(L27N,L27C)(Pals1)-L27(MALS) constructs were cloned, expressed, purified and crystallized. Crystals of tripartite complex 1 of L27(PATJ)-(L27N,L27C)(Pals1)-L27(MALS) diffracted to 2.05 Å resolution. These crystals belonged to either space group P6(1)22 or P6(5)22, with unit-cell parameters a = b = 145.2, c = 202.5 Å. Assuming the presence of four molecules in the asymmetric unit, a Matthews coefficient of 2.69 Å(3) Da(-1) was calculated, corresponding to a solvent content of 54.25%.

| S-EPMC3212472 | biostudies-literature

Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase.

Project description:Carbohydrate-binding modules (CBMs) are discrete parts of carbohydrate-hydrolyzing enzymes that bind specific types of carbohydrates. Ultra high-resolution X-ray crystallographic studies of CBMs have helped to decipher the basis for specificity in carbohydrate-protein interactions. However, additional studies are needed to better understand which structural determinants confer which carbohydrate-binding properties. To address these issues, neutron crystallographic studies were initiated on one experimentally engineered CBM derived from a xylanase, X-2 L110F, a protein that is able to bind several different plant carbohydrates such as xylan, β-glucan and xyloglucan. This protein evolved from a CBM present in xylanase Xyn10A of Rhodothermus marinus. The protein was complexed with a branched xyloglucan heptasaccharide. Large single crystals of hydrogenous protein (∼1.6 mm(3)) were grown at room temperature and subjected to H/D exchange. Both neutron and X-ray diffraction data sets were collected to 1.6 Å resolution. Joint neutron and X-ray refinement using phenix.refine showed significant density for residues involved in carbohydrate binding and revealed the details of a hydrogen-bonded water network around the binding site. This is the first report of a neutron structure of a CBM and will add to the understanding of protein-carbohydrate binding interactions.

| S-EPMC4528944 | biostudies-literature

Ion concentration-dependent ion conduction mechanism of a voltage-sensitive potassium channel.

Project description:Voltage-sensitive potassium ion channels are essential for life, but the molecular basis of their ion conduction is not well understood. In particular, the impact of ion concentration on ion conduction has not been fully studied. We performed several micro-second molecular dynamics simulations of the pore domain of the Kv1.2 potassium channel in KCl solution at four different ion concentrations, and scrutinized each of the conduction events, based on graphical representations of the simulation trajectories. As a result, we observed that the conduction mechanism switched with different ion concentrations: at high ion concentrations, potassium conduction occurred by Hodgkin and Keynes' knock-on mechanism, where the association of an incoming ion with the channel is tightly coupled with the dissociation of an outgoing ion, in a one-step manner. On the other hand, at low ion concentrations, ions mainly permeated by a two-step association/dissociation mechanism, in which the association and dissociation of ions were not coupled, and occurred in two distinct steps. We also found that this switch was triggered by the facilitated association of an ion from the intracellular side within the channel pore and by the delayed dissociation of the outermost ion, as the ion concentration increased.

| S-EPMC3572011 | biostudies-literature

X-CHIP: an integrated platform for high-throughput protein crystallization and on-the-chip X-ray diffraction data collection.

Project description:The X-CHIP (X-ray Crystallization High-throughput Integrated Platform) is a novel microchip that has been developed to combine multiple steps of the crystallographic pipeline from crystallization to diffraction data collection on a single device to streamline the entire process. The system has been designed for crystallization condition screening, visual crystal inspection, initial X-ray screening and data collection in a high-throughput fashion. X-ray diffraction data acquisition can be performed directly on-the-chip at room temperature using an in situ approach. The capabilities of the chip eliminate the necessity for manual crystal handling and cryoprotection of crystal samples, while allowing data collection from multiple crystals in the same drop. This technology would be especially beneficial for projects with large volumes of data, such as protein-complex studies and fragment-based screening. The platform employs hydrophilic and hydrophobic concentric ring surfaces on a miniature plate transparent to visible light and X-rays to create a well defined and stable microbatch crystallization environment. The results of crystallization and data-collection experiments demonstrate that high-quality well diffracting crystals can be grown and high-resolution diffraction data sets can be collected using this technology. Furthermore, the quality of a single-wavelength anomalous dispersion data set collected with the X-CHIP at room temperature was sufficient to generate interpretable electron-density maps. This technology is highly resource-efficient owing to the use of nanolitre-scale drop volumes. It does not require any modification for most in-house and synchrotron beamline systems and offers a promising opportunity for full automation of the X-ray structure-determination process.

| S-EPMC3107051 | 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