Solid-state NMR studies of proteins: the view from static &lt;sup&gt;2&lt;/sup&gt;H NMR experiments

Siminovitch, D.

doi:10.1139/bcb-76-2-3-411

Cited by 22 publications

(10 citation statements)

References 64 publications

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“…Deuterium NMR spectroscopy and molecular dynamics simulations have both contributed a large body of data to characterizing the molecular structure and dynamics of biological samples, including in particular lipid membranes with bound peptides or associated proteins (13,23,(63)(64)(65)(66)(67)(68)(69). Sample deuteration of lipids or peptides is directly accomplished by chemical synthesis, and one-dimensional solid-state 2 H NMR spectra are relatively straightforward to acquire.…”

Section: Discussionmentioning

confidence: 99%

Flexibility of Ras Lipid Modifications Studied by 2H Solid-State NMR and Molecular Dynamics Simulations

Vogel

Tan

Waldmann

et al. 2007

Biophysical Journal

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Human posttranslationally modified N-ras oncogenes are known to be implicated in numerous human cancers. Here, we applied a combination of experimental and computational techniques to determine structural and dynamical details of the lipid chain modifications of an N-ras heptapeptide in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes. Experimentally, 2H NMR spectroscopy was used to study oriented membranes that incorporated ras heptapeptides with two covalently attached perdeuterated hexadecyl chains. Atomistic molecular dynamics simulations of the same system were carried out over 100 ns including 60 DMPC and 4 ras molecules. Several structural and dynamical experimental parameters could be directly compared to the simulation. Experimental and simulated 2H NMR order parameters for the methylene groups of the ras lipid chains exhibited a systematic difference attributable to the absence of collective motions in the simulation and to geometrical effects. In contrast, experimental 2H NMR spin-lattice relaxation rates for Zeeman order were well reproduced in the simulation. The lack of slower collective motions in the simulation did not appreciably influence the relaxation rates at a Larmor frequency of 115.1 MHz. The experimental angular dependence of the 2H NMR relaxation rates with respect to the external magnetic field was also relatively well simulated. These relaxation rates showed a weak angular dependence, suggesting that the lipid modifications of ras are very flexible and highly mobile in agreement with the low order parameters. To quantify these results, the angular dependence of the 2H relaxation rates was calculated by an analytical model considering both molecular and collective motions. Peptide dynamics in the membrane could be modeled by an anisotropic diffusion tensor with principal values of Dparallel=2.1x10(9) s(-1) and Dperpendicular=4.5x10(5) s(-1). A viscoelastic fitting parameter describing the membrane elasticity, viscosity, and temperature was found to be relatively similar for the ras peptide and the DMPC host matrix. Large motional amplitudes and relatively short correlation times facilitate mixing and dispersal with the lipid bilayer matrix, with implications for the role of the full-length ras protein in signal transduction and oncogenesis.

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Section: Discussionmentioning

confidence: 99%

Flexibility of Ras Lipid Modifications Studied by 2H Solid-State NMR and Molecular Dynamics Simulations

Vogel

Tan

Waldmann

et al. 2007

Biophysical Journal

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“…In most cases the parameters describing both the magnitude and the orientation of the anisotropic parts of these tensors relative to the peptide plane (i.e., Ω P E ) exhibit only relatively small dependency on the residue type and the local structure [28][29][30]. While these minor variations may be very important probes for structure determination, the variation is sufficiently small that the typical values in almost any case will be sufficiently precise for simulation and optimization of pulse sequences for application on real structures.…”

Section: Tensor Representationmentioning

confidence: 99%

Specification and Visualization of Anisotropic Interaction Tensors in Polypeptides and Numerical Simulations in Biological Solid-State NMR

Bak

Schultz

Vosegaard

et al. 2002

Journal of Magnetic Resonance

106

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“…One alternative for studying membrane-bound proteins is solid-state NMR spectroscopy. 2 H NMR spectroscopic methods can be used to investigate the dynamic properties of synthetic hydrophobic peptides at specific residues and, therefore, determine their location with respect to the lipid bilayer (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40). By selectively labeling amino acids with 2 H, the locations and dynamic properties of side chains can be drawn from the results.…”

Section: Introductionmentioning

confidence: 99%

Solid-State NMR Studies of a Diverged Microsomal Amino-Proximate Δ12 Desaturase Peptide Reveal Causes of Stability in Bilayer: Tyrosine Anchoring and Arginine Snorkeling

Gibbons

Karp

Cellar

et al. 2006

Biophysical Journal

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This study reports the solid-state NMR spectroscopic characterization of the amino-proximate transmembrane domain (TM-A) of a diverged microsomal delta12-desaturase (CREP-1) in a phospholipid bilayer. A series of TM-A peptides were synthesized with 2H-labeled side chains (Ala-53, -56, and -63, Leu-62, Val-50), and their dynamic properties were studied in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) bilayers at various temperatures. At 6 mol % peptide to lipid, 31P NMR spectra indicated that the peptides did not significantly disrupt the phospholipid bilayer in the L(alpha) phase. The 2H NMR spectra from Ala-53 and Ala-56 samples revealed broad Pake patterns with quadrupolar splittings of 16.9 kHz and 13.3 kHz, respectively, indicating restricted motion confined within the hydrocarbon core of the phospholipid bilayer. Conversely, the deuterated Ala-63 sample revealed a peak centered at 0 kHz with a linewidth of 1.9 kHz, indicating increased side-chain motion and solvent exposure relative to the spectra of the other Ala residues. Val-50 and Leu-62 showed Pake patterns, with quadrupolar splittings of 3.5 kHz and 3.7 kHz, respectively, intermediate to Ala-53/Ala-56 and Ala-63. This indicates partial motional averaging and supports a model with the Val and Leu residues embedded inside the lipid bilayer. Solid-state NMR spectroscopy performed on the 2H-labeled Ala-56 TM-A peptide incorporated into magnetically aligned phospholipid bilayers indicated that the peptide is tilted 8 degrees with respect to the membrane normal of the lipid bilayer. Snorkeling and anchoring interactions of Arg-44 and Tyr-60, respectively, with the polar region or polar hydrophobic interface of the lipid bilayer are suggested as control elements for insertional depth and orientation of the helix in the lipid matrix. Thus, this study defines the location of key residues in TM-A with respect to the lipid bilayer, describes the conformation of TM-A in a biomembrane mimic, presents a peptide-bilayer model useful in the consideration of local protein folding in the microsomal desaturases, and presents a model of arginine and tyrosine control of transmembrane protein stability and insertion.

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Solid-state NMR studies of proteins: the view from static <sup>2</sup>H NMR experiments

Cited by 22 publications

References 64 publications

Flexibility of Ras Lipid Modifications Studied by 2H Solid-State NMR and Molecular Dynamics Simulations

Flexibility of Ras Lipid Modifications Studied by 2H Solid-State NMR and Molecular Dynamics Simulations

Specification and Visualization of Anisotropic Interaction Tensors in Polypeptides and Numerical Simulations in Biological Solid-State NMR

Solid-State NMR Studies of a Diverged Microsomal Amino-Proximate Δ12 Desaturase Peptide Reveal Causes of Stability in Bilayer: Tyrosine Anchoring and Arginine Snorkeling

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