Probing the Dynamics of a Protein Hydrophobic Core by Deuteron Solid-State Nuclear Magnetic Resonance Spectroscopy

Vugmeyster, Liliya; Ostrovsky, Dmitry; Ford, Jennifer B.; Burton, Sarah D.; Lipton, Andrew S.; Hoatson, Gina L.; Vold, Robert L.

doi:10.1021/ja902977u

Cited by 49 publications

(124 citation statements)

References 79 publications

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“…(42, 47-50) The core has exhibited flexibility on multiple time scales and showed the presence of glassy behavior characterized by non-Arrhenius relaxation with non-exponential magnetization build-up curves at low temperatures. The 2 H line shapes measurements indicated extensive μs-ms time scale motions at room temperatures which were quenched by either lowering the temperature or by dehydrating the protein.…”

Section: Resultsmentioning

confidence: 99%

15N CSA tensors and 15N–1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

Vugmeyster

Ostrovsky

2015

Journal of Magnetic Resonance

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In this work, we assess the usefulness of static 15N NMR techniques for the determination of the 15N chemical shift anisotropy (CSA) tensor parameters and 15N-1H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone 15N CSA tensors at two temperatures, 22 and –35°C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22°C, while the values of the asymmetry were in the 0.32–0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the 15N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the 15N CSA parameters, a more advanced approach based on the “magic sandwich” SAMMY pulse sequence (Nevzorov & Opella, J. Magn. Reson. (2003) 164, 182-186) was employed for the determination of the 15N-1H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

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Section: Resultsmentioning

confidence: 99%

15N CSA tensors and 15N–1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

Vugmeyster

Ostrovsky

2015

Journal of Magnetic Resonance

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“…We note that the additional librations inside the rotameric well, which manifest themselves as an effective asymmetry, were not visible across the entire temperature range and, therefore, were not included in the model for the hydrophobic core methyl groups in A␤. In contrast, in the hydrophobic core of the globular villin headpiece protein the asymmetry was evident at temperatures below 260 -240 K (56,62).…”

Section: Computational Modeling Of the Data Indicates Rotameric Jumpsmentioning

confidence: 92%

“…The need for such a mode is evident from low temperature spectra, which display an additional asymmetry. Based on our previous work on globular proteins (62), this type of motion is modeled well by diffusion of the methyl axes along an arc (Fig. 4).…”

Section: Computational Modeling Of the Data Indicates Rotameric Jumpsmentioning

confidence: 99%

Flexibility and Solvation of Amyloid-β Hydrophobic Core

Vugmeyster

Falconer

Ostrovsky

et al. 2016

Journal of Biological Chemistry

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150

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One of the characteristics of Alzheimer disease is the presence of neurotoxic deposits in brain tissue, which are largely made up of a short, 39 -42-amino acid-long peptide referred to as amyloid ␤ (A␤).2 〈␤ peptide plays a major role in Alzheimer disease pathogenesis (1). The deposits (plaques) are an active subject of investigation in many research centers in an attempt to design preventative and therapeutic approaches to the disease (2-14). The molecular structures and morphologies of the fibrils comprising the plaques have been studied at various levels with a variety of imaging and spectroscopic techniques including neutron diffraction, atomic force microscopy, cryoelectronmicroscopy,magneticresonancespectroscopy,andfluorescence (8,(11)(12)(13)(15)(16)(17)(18)(19)(20)(21)(22).A typical characteristic of the fibrils is the presence of ribbon-like ␤-sheets with the strands close to perpendicular to the axis of the fibril, whereas the hydrogen bonds between different strands run parallel to the axis. In vitro studies of the full-length fibrils (that comprise 40 -42-residue peptides) demonstrate multiple morphological possibilities for fibril structures that are very much dependent on the details of the growth conditions (23-25). However, the characteristics of molecular structures are largely preserved (11). For example, in the wild-type sequence, only structures that contain parallel ␤-sheets are observed ( Fig. 1) (9, 24 -28). By contrast, antiparallel ␤-sheet structures can found in the D23N (Iowa) mutant (6,13,29,30), which is associated with an early onset of the neurodegeneration process (6). The polymorphs of D23N with the antiparallel ␤-sheet structures are "protofibrils"; i.e. they are relatively short and curved fibril-like intermediates. They are metastable and eventually convert to mature D23N fibrils, which have parallel ␤-sheet structures that are very similar to wild-type A␤ fibrils (13,22,29).Although both parallel and antiparallel structures can display cytotoxicity (13), the level of toxicity varies greatly depending on the morphological form (11,31). These polymorphs are often viewed as twisted or parallel shapes using transmission electron microscopy (11,25,32,33). The antiparallel ␤-sheet structure represents perhaps the most extreme variability in morphology among polymorphs identified up to date. Effective drug development has not been achieved so far, and one of the possible reasons is the complexity of the polymorphs and interconversions between them as well as the presence of conformational diversity within each polymorph.The intrinsic conformational diversity of the A␤ monomer is well known. In solution, A␤ lacks regular ␣-helical or ␤-stranded structure and is recognized as an intrinsically disordered protein (33-36). However, studies of dynamics in the fibril forms at site-specific level are relatively sparse (37). The most common view is that the hydrophobic core of the fibrils is rigid, complemented by other relative flexible regions (33, 38 -40). The flexibility of non-core re...

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“…There are nine possible conformations corresponding to three rotational isomers each for the C α -C β and C β -C γ bonds. In the absence of any other motions of the side chain, four of these conformations are structurally unique (47). Models for the motion of leucine side chains are usually based on the assumption that exchange occurs between a subset of these bond rotational isomers.…”

mentioning

confidence: 99%

“…Experimental line shapes were closely simulated with this model assuming exchange between side chain conformers with a rate constant of k ¼ 1 × 10 5 s −1 . A recent study of methyl-deuterated side chain (47) assumed exchange between all four unique side chain conformers, with additional modulation of the 2 H line shape attributed to diffusion on the arc of a cone of half angle 70.5°. The dynamic model we adopted and show in Fig.…”

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confidence: 99%

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

Weidner

Breen

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

131

221

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The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately.protein | surface | isotope labels | solid-liquid interface

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Probing the Dynamics of a Protein Hydrophobic Core by Deuteron Solid-State Nuclear Magnetic Resonance Spectroscopy

Cited by 49 publications

References 79 publications

15N CSA tensors and 15N–1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

15N CSA tensors and 15N–1H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

Flexibility and Solvation of Amyloid-β Hydrophobic Core

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

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