scholarly journals Segmental order parameters in a nonionic surfactant lamellar phase studied with 1H–13C solid-state NMR

2008 ◽  
Vol 10 (39) ◽  
pp. 6033 ◽  
Author(s):  
Tiago Mendes Ferreira ◽  
Bruno Medronho ◽  
Rachel W. Martin ◽  
Daniel Topgaard
Keyword(s):  
Solid State ◽  
Nonionic Surfactant ◽  
Solid State Nmr ◽  
Order Parameters ◽  
Lamellar Phase

Determination of methyl order parameters using solid state NMR under off magic angle spinning

2019 ◽  
Vol 73 (8-9) ◽  
pp. 471-475 ◽  
Author(s):  
Kai Xue ◽  
Salvatore Mamone ◽  
Benita Koch ◽  
Riddhiman Sarkar ◽  
Bernd Reif
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Magic Angle Spinning ◽  
Order Parameters ◽  
Magic Angle ◽  
Angle Spinning

scholarly journals The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5489
Author(s):  
Alexander Vogel ◽  
Mathias Bosse ◽  
Marcel Gauglitz ◽  
Sarah Wistuba ◽  
Peter Schmidt ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Solid State ◽  
Neuropeptide Y ◽  
Solid State Nmr ◽  
Bound State ◽  
Receptor Activation ◽  
Order Parameters ◽  
Dynamics Simulation ◽  
15N Nmr

We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were studied using 15N-NMR and quantitative determination of 1H-13C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. Order parameters reporting the amplitudes of the molecular motions of the C-H bond vectors of Y1R in DMPC membranes are 0.57 for the Cα sites and lower in the side chains (0.37 for the CH2 and 0.18 for the CH3 groups). Different NMR excitation schemes identify relatively rigid and also dynamic segments of the molecule. In monounsaturated membranes composed of longer lipid chains, Y1R is more rigid, attributed to a higher hydrophobic thickness of the lipid membrane. The presence of an antagonist or NPY has little influence on the amplitude of motions, whereas the addition of agonist and arrestin led to a pronounced rigidization. To investigate Y1R dynamics with site resolution, we conducted extensive all-atom MD simulations of the apo and antagonist-bound state. In each state, three replicas with a length of 20 μs (with one exception, where the trajectory length was 10 μs) were conducted. In these simulations, order parameters of each residue were determined and showed high values in the transmembrane helices, whereas the loops and termini exhibit much lower order. The extracellular helix segments undergo larger amplitude motions than their intracellular counterparts, whereas the opposite is observed for the loops, Helix 8, and termini. Only minor differences in order were observed between the apo and antagonist-bound state, whereas the time scale of the motions is shorter for the apo state. Although these relatively fast motions occurring with correlation times of ns up to a few µs have no direct relevance for receptor activation, it is believed that they represent the prerequisite for larger conformational transitions in proteins.

scholarly journals Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor

2020 ◽  
Vol 11 ◽  
Author(s):  
Emelyne M. Pacull ◽  
Franziska Sendker ◽  
Frank Bernhard ◽  
Holger A. Scheidt ◽  
Peter Schmidt ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Solid State ◽  
Solid State Nmr ◽  
Magic Angle Spinning ◽  
Order Parameters ◽  
Free Expression ◽  
Magic Angle ◽  
Growth Hormone Secretagogue Receptor ◽  
Growth Hormone Secretagogue ◽  
C Terminus

Cell-free expression represents an attractive method to produce large quantities of selectively labeled protein for NMR applications. Here, cell-free expression was used to label specific regions of the growth hormone secretagogue receptor (GHSR) with NMR-active isotopes. The GHSR is a member of the class A family of G protein-coupled receptors. A cell-free expression system was established to produce the GHSR in the precipitated form. The solubilized receptor was refolded in vitro and reconstituted into DMPC lipid membranes. Methionines, arginines, and histidines were chosen for 13C-labeling as they are representative for the transmembrane domains, the loops and flanking regions of the transmembrane α-helices, and the C-terminus of the receptor, respectively. The dynamics of the isotopically labeled residues was characterized by solid-state NMR measuring motionally averaged 1H-13C dipolar couplings, which were converted into molecular order parameters. Separated local field DIPSHIFT experiments under magic-angle spinning conditions using either varying cross polarization contact times or direct excitation provided order parameters for these residues showing that the C-terminus was the segment with the highest motional amplitude. The loop regions and helix ends as well as the transmembrane regions of the GHSR represent relatively rigid segments in the overall very flexible receptor molecule. Although no site resolution could be achieved in the experiments, the previously reported highly dynamic character of the receptor concluded from uniformly 13C labeled receptor samples could be further specified by this segmental labeling approach, leading to a more diversified understanding of the receptor dynamics under equilibrium conditions.

scholarly journals Accessing Methyl Groups in Proteins via 1H-detected MAS Solid-state NMR Spectroscopy Employing Random Protonation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sam Asami ◽  
Bernd Reif
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Cost Effective ◽  
Order Parameters ◽  
Side Chain ◽  
Methyl Groups ◽  
Glucose Carbon ◽  
Distance Restraints ◽  
Asymmetry Parameters ◽  
Labelling Scheme

Abstract We recently introduced RAP (reduced adjoining protonation) labelling as an easy to implement and cost-effective strategy to yield selectively methyl protonated protein samples. We show here that even though the amount of H2O employed in the bacterial growth medium is rather low, the intensities obtained in MAS solid-state NMR 1H,13C correlation spectra are comparable to spectra obtained for samples in which α-ketoisovalerate was employed as precursor. In addition to correlations for Leu and Val residues, RAP labelled samples yield also resonances for all methyl containing side chains. The labelling scheme has been employed to quantify order parameters, together with the respective asymmetry parameters. We obtain a very good correlation between the order parameters measured using a GlcRAP (glucose carbon source) and a α-ketoisovalerate labelled sample. The labelling scheme holds the potential to be very useful for the collection of long-range distance restraints among side chain atoms. Experiments are demonstrated using RAP and α-ketoisovalerate labelled samples of the α-spectrin SH3 domain, and are applied to fibrils formed from the Alzheimer’s disease Aβ1-40 peptide.

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