A Chemical Biology Primer for NMR Spectroscopists

Clark, Evan T.; Sievers, Elanor E.; Debelouchina, Galia T.

doi:10.1016/j.jmro.2022.100044

Cited by 4 publications

(3 citation statements)

References 116 publications

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“…Any deviations of the experimental spectra from the expected peak shapes for a completely disordered region would indicate preferred or disfavored conformations. Better approaches for analyzing peak shapes in terms of structure combined with new technologies (Berruyer et al, 2020 ; Chaudhari et al, 2016 ; Wang et al, 2020 ) and biochemical approaches to sample preparation, such as the segmental or specific isotopic labeling of proteins (Clark et al, 2022 ; Ghosh et al, 2020 ), open up the possibility of examining one, or a few sites, in the context of a full‐length protein.…”

Section: Introductionmentioning

confidence: 99%

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

et al. 2023

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Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α‐synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.

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Section: Introductionmentioning

confidence: 99%

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

et al. 2023

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“…A wide range of technologies for site-specic labeling have been demonstrated, and many of these approaches are applicable to IDPs. [33][34][35] Here we review the applications of cysteine chemistry, unnatural amino acid incorporation through genetic means (amber suppression), inteins, and sortase, with a particular emphasis on the unique challenges presented by IDPs and LLPS. We focus primarily on the installation of small chemical probes such as uorescent labels, rather than the use of large fusion uorescent proteins, as these approaches may be less familiar to the reader and may have distinct advantages in certain applications.…”

Section: Introduction Of Chemical Probes For Imaging and Spectroscopi...mentioning

confidence: 99%

Chemical tools for study and modulation of biomolecular phase transitions

Berkeley

Debelouchina

2022

Chem. Sci.

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“…Any deviations of the experimental spectra from the expected peak shapes for a completely disordered region indicate conformations that are preferred or disfavored. Better approaches for analyzing peak shapes in terms of structure combined with new technologies [31][32][33] and biochemical approaches to sample preparation, such as the segmental or specific isotopic labeling of proteins [34,35] opens up the possibility of examining one, or a few sites, in the context of a full-length protein.…”

Section: Introductionmentioning

confidence: 99%

The conformational ensemble of an intrinsically disordered protein explains peak shapes under DNP conditions

Kragelj

Dumarieh

Xiao

et al. 2022

Preprint

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Elucidating the conformational preferences of regions of intrinsic disorder in biologically relevant contexts represents a frontier of structural biology. The sensitivity enhancements conferred by DNP enable structural studies of proteins in native contexts by MAS NMR. However, DNP requires low temperatures which results in broad peaks, particularly for for regions of intrinsic disorder. We describe an approach to predict and interpret peak shapes for frozen regions of intrinsic disorder in terms of dihedral angle populations. We demonstrate the method using the protein a-synuclein. This approach can be used to obtain experimental structural restraints for regions of intrinsic disorder in both simplified and biological settings, providing information that eludes characterization by diffraction-based methods as well as solution-state NMR spectroscopy and molecular dynamics due to molecular size limitations.

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A Chemical Biology Primer for NMR Spectroscopists

Cited by 4 publications

References 116 publications

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

Chemical tools for study and modulation of biomolecular phase transitions

The conformational ensemble of an intrinsically disordered protein explains peak shapes under DNP conditions

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