¹³C Spin Dilution for Simplified and Complete Solid-State NMR Resonance Assignment of Insoluble Biological Assemblies

Abstract

A strategy for simplified and complete resonance assignment of insoluble and noncrystalline proteins by solid-state NMR (ssNMR) spectroscopy is presented. Proteins produced with [1-13 C]-or [2-13 C]glucose are very sparsely labeled, and the resulting 2D ssNMR spectra exhibit smaller line widths (by a factor of ∼2 relative to uniformly labeled proteins) and contain a reduced number of crosspeaks. This allows for an accelerated and straightforward resonance assignment without the necessity of time-consuming 3D spectroscopy or sophisticated pulse sequences. The strategy aims at complete backbone and side-chain resonance assignments based on bidirectional sequential walks. The approach was successfully demonstrated with the de novo assignment of the Type Three Secretion System PrgI needle protein. Using a limited set of simple 2D experiments, we report a 97% complete resonance assignment of the backbone and side-chain 13 C atoms.R ecent developments in magic-angle-spinning (MAS) solidstate NMR (ssNMR) methodology, 1À4 isotope labeling schemes, 5,6 structure calculation protocols, 7,8 and access to highfield instrumentation have allowed details at atomic resolution and, in the most favorable cases, high-resolution structures of microcrystalline proteins, 6À11 fibrillar aggregates, 12À17 oligomeric complexes, 18À22 and membrane proteins in nativelike environments 23À26 to be obtained. However, achieving a sufficient (and if possible, nearly complete) assignment of the NMR signals still remains as a major obstacle in obtaining site-specific structural information. The lack of resolution and the spectral overlap observed in uniformly ([U-13 C]glucose) labeled proteins requires the use of several 2D experiments 27 and, in the case of remaining assignment ambiguities, 3D or 4D spectroscopy. This renders the assignment step extremely time-consuming and demanding in terms of instrument performance and access to high-field spectrometers. An alternative to uniform labeling is the use of 13 C alternate labeling schemes, 5,28,29 which reduce spectral crowding and facilitate the assignment and the collection of distance restraints, as previously demonstrated 5,6 with glycerolbased labeling schemes.We recently reported 30 the use of mixtures of [1-13 C]-5 and [2-13 C]glucose (Glc) 29 for ssNMR studies of supramolecular protein interfaces. The high spectral quality observed for [1-13 C]-and [2-13 C]Glc-labeled R-synuclein already suggested that this labeling scheme could be useful for resonance assignments. Here we demonstrate that [1-13

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

“…S1). The quality of the data was comparable to that obtained for benchmarks in ssNMR spectral quality, such as well-structured microcrystalline proteins (27,28), β-helical HET-s(218-289) prion fibrils (29), or the type III secretion system needles (30,31). Because the CC and NCA experiments were based on through-space dipolar couplings, which can be averaged out by dynamics, the observed peaks had to represent the rigid core of the protein.…”

Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

“…The H iÀ1 CA iÀ1 CO iÀ1 spectrum provides the H iÀ1 frequency and the H i N i CA i spectrum yields the N iÀ1 frequency. The high quality of the set of five 3D spectra allowed for the unambiguous and reliable assignment of all 1 H, 13 CA, 13 We found only slight chemical shift differences between earlier studied protonated [39] samples and the currently studied deuterated sample, which are completely explainable by the deuterium isotope effect [53]. The …”

“…Expression, purification and polymerization of perdeuterated 15 N-and 13 C-labeled wild-type PrgI protein was performed as described before [3,38,39]. A low protonation degree in the samples was achieved according to the approach described earlier by Reif and coworkers [4].…”

Structure d’une nanomachine bactérienne

“…Cette rotation rapide compense l'absence de réo-rientation moléculaire en phase solide et permet d'observer à haute résolution un signal par atome de carbone ou d'azote. Notre équipe a développé une méthode exploitant la dilution des isotopes de 13 C [10] qui améliore la résolution de ces signaux. Ainsi, les spectres de l'aiguille du T3SS constituent, à l'heure actuelle, la référence en termes de qualité spectroscopique pour la RMN du solide.…”