Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2.

ABSTRACT: The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles.

SUBMITTER: Gattin Z

PROVIDER: S-EPMC5653203 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2.

Gattin Zrinka Z Schneider Robert R Laukat Yvonne Y Giller Karin K Maier Elke E Zweckstetter Markus M Griesinger Christian C Benz Roland R Becker Stefan S Lange Adam A

Journal of biomolecular NMR 20141116 3-4

The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investiga ...[more]

PMID: 25399320

Similar Datasets

Characterization of stratum corneum molecular dynamics by natural-abundance ¹³C solid-state NMR.

Project description:Despite the enormous potential for pharmaceutical applications, there is still a lack of understanding of the molecular details that can contribute to increased permeability of the stratum corneum (SC). To investigate the influence of hydration and heating on the SC, we record the natural-abundance (13)C signal of SC using polarization transfer solid-state NMR methods. Resonance lines from all major SC components are assigned. Comparison of the signal intensities obtained with the INEPT and CP pulse sequences gives information on the molecular dynamics of SC components. The majority of the lipids are rigid at 32°C, and those lipids co-exist with a small pool of mobile lipids. The ratio between mobile and rigid lipids increases with hydration. An abrupt change of keratin filament dynamics occurs at RH?=?80-85%, from completely rigid to a structure with rigid backbone and mobile protruding terminals. Heating has a strong effect on the lipid mobility, but only a weak influence on the keratin filaments. The results provide novel molecular insight into how the SC constituents are affected by hydration and heating, and improve the understanding of enhanced SC permeability, which is associated with elevated temperatures and SC hydration.

| S-EPMC3633950 | biostudies-literature

Integrated solid-state NMR and molecular dynamics modeling determines membrane insertion of human ?-defensin analog.

Project description:Human ?-defensins (hBD) play central roles in antimicrobial activities against various microorganisms and in immune-regulation. These peptides perturb phospholipid membranes for function, but it is not well understood how defensins approach, insert and finally disrupt membranes on the molecular level. Here we show that hBD-3 analogs interact with lipid bilayers through a conserved surface that is formed by two adjacent loops in the solution structure. By integrating a collection of 13C, 1H and 31P solid-state NMR methods with long-term molecular dynamic simulations, we reveal that membrane-binding rigidifies the peptide, enhances structural polymorphism, and promotes ?-strand conformation. The peptide colocalizes with negatively charged lipids, confines the headgroup motion, and deforms membrane into smaller, ellipsoidal vesicles. This study designates the residue-specific, membrane-bound topology of hBD-3 analogs, serves as the basis for further elucidating the function-relevant structure and dynamics of other defensins, and facilitates the development of defensin-mimetic antibiotics, antifungals, and anti-inflammatories.

| S-EPMC6825183 | biostudies-literature

Use of Solid-State NMR Spectroscopy for the Characterization of Molecular Structure and Dynamics in Solid Polymer and Hybrid Electrolytes.

Project description:Solid-state NMR spectroscopy is an established experimental technique which is used for the characterization of structural and dynamic properties of materials in their native state. Many types of solid-state NMR experiments have been used to characterize both lithium-based and sodium-based solid polymer and polymer-ceramic hybrid electrolyte materials. This review describes several solid-state NMR experiments that are commonly employed in the analysis of these systems: pulse field gradient NMR, electrophoretic NMR, variable temperature T1 relaxation, T2 relaxation and linewidth analysis, exchange spectroscopy, cross polarization, Rotational Echo Double Resonance, and isotope enrichment. In this review, each technique is introduced with a short description of the pulse sequence, and examples of experiments that have been performed in real solid-state polymer and/or hybrid electrolyte systems are provided. The results and conclusions of these experiments are discussed to inform readers of the strengths and weaknesses of each technique when applied to polymer and hybrid electrolyte systems. It is anticipated that this review may be used to aid in the selection of solid-state NMR experiments for the analysis of these systems.

| S-EPMC8068304 | biostudies-literature

Characterization of Phosphorus Species in Human Dentin by Solid-State NMR.

Project description:The rat has been considered as an appropriate animal model for the study of the mineralization process in humans. In this work, we found that the phosphorus species in human dentin characterized by solid-state NMR spectroscopy consist mainly of orthophosphate and hydrogen phosphate. Some orthophosphates are found in a disordered phase, where the phosphate ions are hydrogen-bonded to structural water, some present a stoichiometric apatite structure, and some a hydroxyl-depleted apatite structure. The results of this study are largely the same as those previously obtained for rat dentin. However, the relative amounts of the various phosphorus species in human and rat dentin are dramatically different. In particular, stoichiometric apatite is more abundant in human dentin than in rat dentin, whereas the converse is true for disordered-phase orthophosphates. Furthermore, spatial proximity among all phosphorus species in human dentin is identical within experimental error, in contrast to what observed for rat dentin. Although it is not clear how these spectroscopic data could relate to the hierarchical structure or the mechanical properties of teeth, our data reveal that the molecular structures of human and rat dentin at different growth stages are not exactly the same.

| S-EPMC6983145 | biostudies-literature

Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR.

Project description:Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from 240 copies of the Cp149 core protein. We measure both T 1 and T 1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.

| S-EPMC8762115 | biostudies-literature

Characterization of H/D exchange in type 1 pili by proton-detected solid-state NMR and molecular dynamics simulations.

Project description:Uropathogenic Escherichia coli invades and colonizes hosts by attaching to cells using adhesive pili on the bacterial surface. Although many biophysical techniques have been used to study the structure and mechanical properties of pili, many important details are still unknown. Here we use proton-detected solid-state NMR experiments to investigate solvent accessibility and structural dynamics. Deuterium back-exchange at labile sites of the perdeuterated, fully proton back-exchanged pili was conducted to investigate hydrogen/deuterium (H/D) exchange patterns of backbone amide protons in pre-assembled pili. We found distinct H/D exchange patterns in lateral and axial intermolecular interfaces in pili. Amide protons protected from H/D exchange in pili are mainly located in the core region of the monomeric subunit and in the lateral intermolecular interface, whereas the axial intermolecular interface and the exterior region of pili are highly exposed to H/D exchange. Additionally, we performed molecular dynamics simulations of the type 1 pilus rod and estimated the probability of H/D exchange based on hydrogen bond dynamics. The comparison of the experimental observables and simulation data provides insights into stability and mechanical properties of pili.

| S-EPMC6692446 | biostudies-literature

Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes.

Project description:Little direct information is available regarding the influence of membrane environment on transmembrane (TM) G-protein-coupled receptor (GPCR) conformation and dynamics. The human CB1 cannabinoid receptor (hCB1) is a prominent GPCR pharmacotherapeutic target in which helix 7 appears critical to ligand recognition. We have chemically synthesized a hCB1 peptide corresponding to a segment of TM helix 7 and the entire contiguous helix 8 domain (fourth cytoplasmic loop) and reconstituted it in defined phospholipid-bilayer model membranes. Using an NMR-based strategy combined with molecular dynamics simulations, we provide the first direct experimental description of the orientation of hCB1 helix 7 in phospholipid membranes of varying thickness and the mechanism by which helix-7 conformation adjusts to avoid hydrophobic mismatch. Solid-state (15)N NMR data show that hCB1 helices 7 and 8 reconstituted into phospholipid bilayers are oriented in a TM and in-plane (i.e., parallel to the phospholipid membrane surface) fashion, respectively. TM helix orientation is influenced by the thickness of the hydrophobic membrane bilayer as well as the interaction of helix 8 with phospholipid polar headgroups. Molecular dynamics simulations show that a decrease in phospholipid chain-length induces a kink at P394 in TM helix 7 to avoid hydrophobic mismatch. Thus, the NP(X)nY motif found in hCB1 and highly conserved throughout the GPCR superfamily is important for flexing helix 7 to accommodate bilayer thickness. Dynamic modulation of hCB1-receptor TM helix conformation by its membrane environment may have general relevance to GPCR structure and function.

| S-EPMC3712639 | biostudies-literature

Unravelling Guest Dynamics in Crystalline Molecular Organics Using <sup>2</sup>H Solid-State NMR and Molecular Dynamics Simulation.

Project description:2H solid-state NMR and atomistic molecular dynamics (MD) simulations are used to understand the disorder of guest solvent molecules in two cocrystal solvates of the pharmaceutical furosemide. Traditional approaches to interpreting the NMR data fail to provide a coherent model of molecular behavior and indeed give misleading kinetic data. In contrast, the direct prediction of the NMR properties from MD simulation trajectories allows the NMR data to be correctly interpreted in terms of combined jump-type and libration-type motions. Time-independent component analysis of the MD trajectories provides additional insights, particularly for motions that are invisible to NMR. This allows a coherent picture of the dynamics of molecules restricted in molecular-sized cavities to be determined.

| S-EPMC11240262 | biostudies-literature

Dynamics of amyloid ? fibrils revealed by solid-state NMR.

Project description:We have investigated the site-specific backbone dynamics of mature amyloid ? (A?) fibrils using solid-state NMR spectroscopy. Overall, the known ?-sheet segments and the turn linking these two ?-strands exhibit high order parameters between 0.8 and 0.95, suggesting low conformational flexibility. The first approximately eight N-terminal and the last C-terminal residues exhibit lower order parameters between ?0.4 and 0.8. Interestingly, the order parameters increase again for the first two residues, Asp(1) and Ala(2), suggesting that the N terminus could carry some structural importance.

| S-EPMC3265881 | biostudies-other

Solid-state NMR characterization of gas vesicle structure.

Project description:Gas vesicles are gas-filled buoyancy organelles with walls that consist almost exclusively of gas vesicle protein A (GvpA). Intact, collapsed gas vesicles from the cyanobacterium Anabaena flos-aquae were studied by solid-state NMR spectroscopy, and most of the GvpA sequence was assigned. Chemical shift analysis indicates a coil-?-?-?-?-coil peptide backbone, consistent with secondary-structure-prediction algorithms, and complementary information about mobility and solvent exposure yields a picture of the overall topology of the vesicle subunit that is consistent with its role in stabilizing an air-water interface.

| S-EPMC2941023 | 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