Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints

Milikisiyants, Sergey; Wang, Shenlin; Munro, Rachel; Donohue, Matthew P.; Ward, Meaghan E.; Bolton, David R.; Brown, Leonid S.; Smirnova, Tatyana I.; Ladizhansky, Vladimir; Smirnov, Alex I.

doi:10.1016/j.jmb.2017.05.005

Cited by 45 publications

(42 citation statements)

References 99 publications

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“…This was demonstrated for the oligomeric structure of sensory rhodopsin reconstituted into lipid bilayers [62]. A combination of solid-state PRE and DEER restraints ruled out dimer formation, whereas analysis of DEER modulation depth ruled out higher oligomers than trimers.…”

Section: Integrative Modellingmentioning

confidence: 89%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

111

133

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron-electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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Section: Integrative Modellingmentioning

confidence: 89%

The contribution of modern EPR to structural biology

Jeschke

2018

Emerging Topics in Life Sciences

111

133

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“…For the large toolbox of SPs and SLs, 17 currently not commercially available PD-x (x = 13, 14,16,34,35,36,37,38,42,[52][53][54][55][56][57][58]62; see Schemes S2, S6, S8, S10 and S12-S14), were Figure 11) were obtained in good to very good yields (73-93 %) depending on the type of Steglich esterification and the reaction time (3 h-24 h) using mild reaction conditions (0°C-RT). For further conclusions, Figure 12 summarizes all water solubilities in one graph, which makes direct comparisons easier.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…Spin probing and spin labeling of supramolecular systems are well established methods in applied magnetic resonance (MR) techniques such as electron paramagnetic resonance (EPR) and in some nuclear magnetic resonance (NMR) methods (e. g. DNP-NMR, PRE-NMR). [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16] Starting more than 50 years ago with the work of Lebedev et al (1960) and Neiman et al (1964), [17,18] nitroxide radicals, especially the tetramethylpiperidine-N-oxyl radical, TEMPO, are well-studied compounds with a wide range of applications, e. g. in biophysics, modern physical and advanced organic/pharmaceutical chemistry, polymer science, molecular biology and medicine. [1,[19][20][21][22][23][24][25][26][27][28][29] It should be noted that probably the first relatively stable nitroxide radical, the potassium salt of nitrosodisulfonate, was synthesized by pivotal 19 th century chemist Edmond Frémy and is still often called "Frémy's salt".…”

Section: Introductionmentioning

confidence: 99%

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A Platform of Phenol‐Based Nitroxide Radicals as an “EPR Toolbox” in Supramolecular and Click Chemistry

Hauenschild

Hinderberger

2018

ChemPlusChem

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A large number (63) of well‐defined nitroxide radicals, all phenol‐based TEMPO and PROXYL esters, were synthesized using different strategies based on well‐established Steglich esterifications. All of these radicals can be used as spin probes (SPs) and spin labels (SLs) for electron paramagnetic resonance (EPR) spectroscopy of supramolecular systems. Depending on the nature of the functional group(s) on each SP/SL, the synthesized nitroxide radicals serve as polyphilic molecular “toolbox” for the EPR‐spectroscopic detection and characterization of specific types of interactions, e. g. π–π interactions, sulfur‐sulfur interactions, hydrogen bonding, electrostatic and dipole‐dipole interactions, and van der Waals and hydrophobic interactions, in the presence of the selected supramolecular systems of interest (e. g. proteins, peptides). For each synthesized SP/SL the water solubility was gravimetrically determined for use in aqueous solution at pH 7.

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“…Data from other sources can be readily included into this integrated approach. The distance restraints obtained here from solution-state and MAS NMR may be complemented or replaced by distance information obtained from co-evolution data 29–31 , cross-linking experiments, 32 Förster resonance energy transfer, 33 DEER electron paramagnetic resonance 34–36 , or NMR-detected paramagnetic relaxation enhancement (PRE) data. 37 The secondary structure information obtained here from NMR chemical-shift assignments may be complemented with prediction algorithms in case of missing NMR assignments.…”

Section: Discussionmentioning

confidence: 99%

Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex

Gauto

Estrozi

Schwieters

et al. 2018

Preprint

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Atomic-resolution structure determination is the key requirement for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enabled determination of the high-resolution structure of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and specifically labelled methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution (up to 8 Å) cryo-EM data are available, thus paving avenues for the structure determination of challenging biological assemblies.

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Oligomeric Structure of Anabaena Sensory Rhodopsin in a Lipid Bilayer Environment by Combining Solid-State NMR and Long-range DEER Constraints

Cited by 45 publications

References 99 publications

The contribution of modern EPR to structural biology

The contribution of modern EPR to structural biology

A Platform of Phenol‐Based Nitroxide Radicals as an “EPR Toolbox” in Supramolecular and Click Chemistry

Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex

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