Investigation of slow molecular dynamics using R-CODEX

Li, Wenbo; McDermott, Ann E.

doi:10.1016/j.jmr.2012.05.019

Cited by 11 publications

(17 citation statements)

References 43 publications

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“…the transfer of polarization from 1 H to 15 N or 13 C is, in the form of the steady-state NOE, a commonly measured parameter in liquid-state NMR. Saturating the I spins before the start of the experiment will lead to a change in the steady-state value of the S spins which is given by (39) with the cross-relaxation rate constant given by (40) If the T 1 times of the S-spin are known, the cross-relaxation rate constant can be back calculated from the steady state NOE value η. Figure 12a) and b) shows a plot of the steady state NOE η as a function of the order parameter and the correlation time which shows that the NOE does not give any additional information about the order parameter compared to the T 1 time.…”

Section: Heteronuclear Cross Relaxation (Noe)-mentioning

confidence: 99%

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

Schanda

Ernst

2016

Progress in Nuclear Magnetic Resonance Spectroscopy

193

295

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Magic-angle spinning solid-state NMR spectroscopy is an important technique to study molecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecular sciences. Here we provide an overview of experimental approaches to study molecular dynamics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin relaxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Experimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct information about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their application, we close by discussing a small number of recent dynamics studies, where the dynamic properties of proteins in crystals are compared to those in solution.

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Section: Heteronuclear Cross Relaxation (Noe)-mentioning

confidence: 99%

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

Schanda

Ernst

2016

Progress in Nuclear Magnetic Resonance Spectroscopy

193

295

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“…However, most of these techniques yield only relatively short intermolecular distances (up to~5 Å ). Alternatively, one can use the centerband-only detection of exchange (CODEX) pulse sequence, which was originally designed to probe slow molecular reorientations on a timescale of R1 ms (36,37). Due to fast MAS, such experiments were initially used to reveal many heteroatomic sites with high resolution and sensitivity, and to determine their correlation times and function as well as motional amplitudes at ambient temperatures (36).…”

Section: Introductionmentioning

confidence: 99%

Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR

Salnikov

Raya

Zotti

et al. 2016

Biophysical Journal

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Alamethicins (ALMs) are antimicrobial peptides of fungal origin. Their sequences are rich in hydrophobic amino acids and strongly interact with lipid membranes, where they cause a well-defined increase in conductivity. Therefore, the peptides are thought to form transmembrane helical bundles in which the more hydrophilic residues line a water-filled pore. Whereas the peptide has been well characterized in terms of secondary structure, membrane topology, and interactions, much fewer data are available regarding the quaternary arrangement of the helices within lipid bilayers. A new, to our knowledge, fluorine-labeled ALM derivative was prepared and characterized when reconstituted into phospholipid bilayers. As a part of these studies, C 19 F 3 -labeled compounds were characterized and calibrated for the first time, to our knowledge, for 19 F solid-state NMR distance and oligomerization measurements by centerband-only detection of exchange (CODEX) experiments, which opens up a large range of potential labeling schemes. The 19 F-19 F CODEX solid-state NMR experiments performed with ALM in POPC lipid bilayers and at peptide/lipid ratios of 1:13 are in excellent agreement with molecular-dynamics calculations of dynamic pentameric assemblies. When the peptide/lipid ratio was lowered to 1:30, ALM was found in the dimeric form, indicating that the supramolecular organization is tuned by equilibria that can be shifted by changes in environmental conditions.

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“…Generally, however, there is interest in characterizing molecular reorientation even in the absence of a detectible isotropic chemical shift difference. The R‐CODEX (27) experiment uses dipolar couplings to sense motion. This method does not require chemical shift differences, and any motion that appreciably alters the direction of a dipolar coupling can be characterized.…”

Section: Resultsmentioning

confidence: 99%

“…While these measurements have been very useful, it is likely that the ability to determine hop angle and motional mechanism would be more powerful if a uniaxial interaction such as the dipolar coupling were used instead of the chemical shift interaction. Several dipolar‐based CODEX experiments have been reported recently (24, 25), including a variation called R‐CODEX (27).…”

Section: Introductionmentioning

confidence: 99%

From the Editor

Bredillet¹

2012

Project Management Journal

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New methods for probing dynamical properties of biological macromolecules on the millisecond timescale will enable a better understanding of the structure–function relationship. In this article, three solid‐state NMR detection methods, line‐shape analysis, two‐dimensional exchange experiments, and a variant of the center‐band only detection of exchange (CODEX) experiment called R‐CODEX, are used to characterize a crystalline amino acid that serves as a model for motions in solid proteins, L‐phenylalanine hydrochloride. The millisecond ring flip motion of the aromatic ring in L‐phenylalanine hydrochloride is characterized in detail for the first time. Limitations of these experiments for processes involving submillisecond timescales are also discussed. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 14–22, 2013.

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Investigation of slow molecular dynamics using R-CODEX

Cited by 11 publications

References 43 publications

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

Studying dynamics by magic-angle spinning solid-state NMR spectroscopy: Principles and applications to biomolecules

Alamethicin Supramolecular Organization in Lipid Membranes from 19F Solid-State NMR

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