BSH-CP based 3D solid-state NMR experiments for protein resonance assignment

Shi, Chaowei; Fasshuber, Hannes; Chevelkov, Veniamin; Xiang, ShengQi; Habenstein, Birgit; Vasa, Suresh K.; Becker, Stefan; Lange, Adam

doi:10.1007/s10858-014-9820-8

Cited by 23 publications

(41 citation statements)

References 36 publications

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“…With CitApc embedded in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes, we were able to track structural changes in PASp in context of the TM environment. Solid-state NMR samples of wild-type CitApc and CitApc (R93A) with and without citrate were assigned using a combination of chemical shift-matching based on liquid-state data and de novo assignment using two-and three-dimensional solidstate NMR spectra (36). Peak positions in solid-state spectra [2D proton-driven spin diffusion (PDSD), 3D NCACB, NCOCA, and NCOCACB] were in a first step predicted from liquid-state NMR assignments and, where possible, transferred to solid-state peaks.…”

Section: Resultsmentioning

confidence: 99%

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Salvi

Schomburg

Giller

et al. 2017

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

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Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid-and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) domain of HK CitA are identical for the isolated domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS domain, which is well characterized for the isolated domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core domain.transmembrane receptors | solid-state NMR spectroscopy | transmembrane signaling | integrated structural biology | histidine sensor kinase H istidine kinases (HKs) are key players in prokaryotic signaling and the primary means of processing extracellular stimuli (1-6). Due to their modular organization, HKs can relay a multitude of different input stimuli, including sensing of nutrients, light, physicochemical parameters (e.g., metal ions, ions gradient), temperature, oxygen, and molecules reporting cell density, to accomplish diverse responses. Over the last decade, various structures have been solved for the cytosolic kinase core and a number of signaling domains and more recently even for the complete cytoplasmic region (7-13), but the transmembrane (TM) signaling mechanism itself remains challenging to decipher. Structural information on individual stimulus-receiving domains therefore provides an important tool to identify TM signal transduction schemes.Because extracytoplasmic receiver domains are generally directly connected to TM helices, structural rearrangements within these motifs can be correlated with the TM-signaling mechanism. Different receiver domains have been characterized with and without their ligands and reveal structural differences between the two states that impose restraints on possible motions of the TM helices. Based on such structures, a symmetry-to-asymmetry switch has been postulated for KinB (14), TorT/TorS (15), and LuxPQ (16), implying a possible tilt of TM helices (17). For chemotaxis sensor Tar and for HK NarX a piston movement of the second TM helix has been postulated as a consequence of receiver domain motions (9,(18)(19)(20).Among receiver domains, PAS domains stand out by being able to process diverse input signals, which is reflected by...

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Section: Resultsmentioning

confidence: 99%

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Salvi

Schomburg

Giller

et al. 2017

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

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“…S3). The latter experiment and also the 3D NCACO and NCOCA experiments benefitted from efficient CO-CA transfer, which was achieved by using band-selective homonuclear cross-polarization (CP) (33)(34)(35). For illustration, a sequential walk from Ala128 to Ala123 is shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

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

Vasa¹,

Lin

Shi

et al. 2014

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

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Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by highresolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.solid-state NMR | cytoskeleton | protein structure | filaments

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“…An overview over the restraints used in this calculation and the restraint statistics is given in Table S2. : Sequential ssNMR resonance assignment strategy [14] used to assign FimA in pili. The determination of the ssNMR resonances was performed using a 3D sequential assignment strategy, illustrated with the stretch Q102-N98.…”

Section: Classification Of Ssnmr Restraintsmentioning

confidence: 99%

Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli

et al. 2015

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Type 1 pili are filamentous protein assemblies on the surface of Gram‐negative bacteria that mediate adhesion to host cells during the infection process. The molecular structure of type 1 pili remains elusive on the atomic scale owing to their insolubility and noncrystallinity. Herein we describe an approach for hybrid‐structure determination that is based on data from solution‐state NMR spectroscopy on the soluble subunit and solid‐state NMR spectroscopy and STEM data on the assembled pilus. Our approach is based on iterative modeling driven by structural information extracted from different sources and provides a general tool to access pseudo atomic structures of protein assemblies with complex subunit folds. By using this methodology, we determined the local conformation of the FimA pilus subunit in the context of the assembled type 1 pilus, determined the exact helical pilus architecture, and elucidated the intermolecular interfaces contributing to pilus assembly and stability with atomic detail.

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BSH-CP based 3D solid-state NMR experiments for protein resonance assignment

Cited by 23 publications

References 36 publications

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor

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

Hybrid Structure of the Type 1 Pilus of Uropathogenic Escherichia coli

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