Modeling a Ryanodine Receptor N-terminal Domain Connecting the Central Vestibule and the Corner Clamp Region

Zhu, Li; Zhong, Xiaowei; Chen, S.R. Wayne; Banavali, Nilesh K.; Liu, Zheng

doi:10.1074/jbc.m112.429670

Cited by 10 publications

(19 citation statements)

References 64 publications

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“…Most of our cryo-EM mappings using this method are consistent with other studies. For instance, 3D localization of Tyr2801 in the phosphorylation domain (Meng et al, 2007) is consistent with the docking models from two groups in which a crystal structure of RyR fragments containing the phosphorylated reside was fitted into a RyR cryo-EM structure (Sharma et al, 2012;Yuchi et al, 2012); 3D localization of Tyr846 (Wang et al, 2011) is consistent with a docking model based on a pseudo-atomic structure of the Nterminal fragment (Zhu et al, 2013); and 3D localization of Arg626 in the FK506-binding protein (FKBP)-adjoining domain by combining FRET and cryo-EM studies (Wang et al, 2011) is consistent with binding assays that implicate this region in the RyR-FKBP interaction (Girgenrath et al, 2013). However, a shortcoming of the long linkers is that they may allow GFP to move away from the target sites.…”

Section: Resultssupporting

confidence: 52%

“…The proposed RyR2 CaM-binding sequence 263-615 (Balshaw et al, 2001) is incompatible with the EM data of Wang et al and the Xray crystallography/molecular docking results from Tung et al (Wang et al, 2007;Tung et al, 2010). The predicted CaMbinding sequence 921-1173 in RyR1 (Chen and MacLennan, 1994) is also incompatible with experimental and modeling studies on a fragment that overlaps this sequence (Zhu et al, 2013). Proposed CaM-binding sequences in the vicinity of 2724-3016 in RyR2 (Balshaw et al, 2001) and 2804-2930 in RyR1 (Chen and MacLennan, 1994) contain a phosphorylation site Fig.…”

Section: Sequences Not Directly Involved In Cam Bindingmentioning

confidence: 43%

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Two potential calmodulin-binding sequences in the ryanodine receptor contribute to a mobile, intra-subunit calmodulin-binding domain

Huang

Liu

Wang

et al. 2013

Journal of Cell Science

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SummaryCalmodulin (CaM), a 16 kDa ubiquitous calcium-sensing protein, is known to bind tightly to the calcium release channel/ryanodine receptor (RyR), and modulate RyR function. CaM binding studies using RyR fragments or synthetic peptides have revealed the presence of multiple, potential CaM-binding regions in the primary sequence of RyR. In the present study, we inserted GFP into two of these proposed CaM-binding sequences and mapped them onto the three-dimensional structure of intact cardiac RyR2 by cryo-electron microscopy. Interestingly, we found that the two potential CaM-binding regions encompassing, Arg3595 and Lys4269, respectively, are in close proximity and are adjacent to the previously mapped CaM-binding sites. To monitor the conformational dynamics of these CaM-binding regions, we generated a fluorescence resonance energy transfer (FRET) pair, a dual CFP-and YFP-labeled RyR2 (RyR2 R3595-CFP/K4269-YFP ) with CFP inserted after Arg3595 and YFP inserted after Lys4269. We transfected HEK293 cells with the RyR2 R3595-CFP/K4269-YFP cDNA, and examined their FRET signal in live cells. We detected significant FRET signals in transfected cells that are sensitive to the channel activator caffeine, suggesting that caffeine is able to induce conformational changes in these CaMbinding regions. Importantly, no significant FRET signals were detected in cells co-transfected with cDNAs encoding the single CFP (RyR2 R3595-CFP ) and single YFP (RyR2 K4269-YFP ) insertions, indicating that the FRET signal stemmed from the interaction between R3595-CFP and K4269-YFP that are in the same RyR subunit. These observations suggest that multiple regions in the RyR2 sequence may contribute to an intra-subunit CaM-binding pocket that undergoes conformational changes during channel gating.

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Section: Resultssupporting

confidence: 52%

Section: Sequences Not Directly Involved In Cam Bindingmentioning

confidence: 43%

Two potential calmodulin-binding sequences in the ryanodine receptor contribute to a mobile, intra-subunit calmodulin-binding domain

Huang

Liu

Wang

et al. 2013

Journal of Cell Science

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“…(3-Chloropyridin-2-yl)hydrazine (2) was synthesized by refluxing 2,3-dichloropyridine (1) and 80 % hydrazine hydrate in ethanol. 1-(3-Chloropyridin-2-yl)-3-pyrazolidinone-5-carboxylate (3) was prepared by reaction between compound 2 and diethyl maleate in the presence of an appropriate amount of sodium ethoxide.…”

Section: Resultsmentioning

confidence: 99%

“…[1,2] These receptors are the major cellular mediators of calcium ion release from the sarcoplasmic and endoplasmic reticulum, [2,3] an essential step in muscle excitation-contraction coupling (ECC). [2][3][4][5] Diamide insecticides have emerged as one of the most promising new compound classes in insecticide chemistry owing to their excellent insecticidal efficacy and high levels of mammalian safety. [6] Cyantraniliprole, [7] chlorantraniliprole, [8] and flubendiamide, [9] the first three insecticides developed from this class, demonstrate exceptional broad-spectrum activity against Lepidoptera.…”

Section: Introductionmentioning

confidence: 99%

Novel Anthranilic Diamide Insecticides: Design, Synthesis, and Insecticidal Evaluation

Hua¹,

Mao²,

Fan³

et al. 2014

Aust. J. Chem.

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Three series of new anthranilic diamide derivatives containing sulfide, N-cyanomethylsulfilimine, and N-cyanomethylsulfoximine groups were designed and synthesized by coupling the active substructures of anthranilic diamides and sulfoxaflor. The structures of the synthesized compounds were confirmed by infrared spectroscopy, 1 H and 13 C NMR, and elemental analysis. Several unique structural characteristics were revealed via the crystal structure analysis of compoundBioassay results indicated that most of the synthesized compounds showed superior insecticidal activities against Mythimna separata and Plutella xylostella when compared with the positive control cyantraniliprole. In particular, N- (2-(2-methyl-2-(N-cyanomethylsulfideimino)propylcarbamoyl)-4-chloro-6-methylphenyl)-3-bromo-1-(3-chloropyridin-2-yl)-1H-pyrazole-5-carboxamide 17e showed excellent insecticidal activity against Mythimna separata, with a mortality rate of 100 % at a concentration of 1 mg mL À1 . These results indicated that sulfide, N-cyanomethylsulfilimine, and N-cyanomethylsulfoximine moieties, as important active substructures, could improve or maintain the activity of the anthranilic diamide and promote novel pesticide development.

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“…Thus far, some of these structural elements have been deduced based on computational secondary structure prediction (7,8) and docking of partial atomic structures into the cryo-EM map (9)(10)(11). Significant research efforts are currently devoted to locating channel regulatory sites in the RyR three-dimensional map (12).…”

Section: Introductionmentioning

confidence: 99%

FRET-Based Trilateration of Probes Bound within Functional Ryanodine Receptors

Svensson

Oda

Nitu

et al. 2014

Biophysical Journal

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To locate the biosensor peptide DPc10 bound to ryanodine receptor (RyR) Ca(2+) channels, we developed an approach that combines fluorescence resonance energy transfer (FRET), simulated-annealing, cryo-electron microscopy, and crystallographic data. DPc10 is identical to the 2460-2495 segment within the cardiac muscle RyR isoform (RyR2) central domain. DPc10 binding to RyR2 results in a pathologically elevated Ca(2+) leak by destabilizing key interactions between the RyR2 N-terminal and central domains (unzipping). To localize the DPc10 binding site within RyR2, we measured FRET between five single-cysteine variants of the FK506-binding protein (FKBP) labeled with a donor probe, and DPc10 labeled with an acceptor probe (A-DPc10). Effective donor positions were calculated from simulated-annealing constrained by both the RyR cryo-EM map and the FKBP atomic structure docked to the RyR. FRET to A-DPc10 was measured in permeabilized cardiomyocytes via confocal microscopy, converted to distances, and used to trilaterate the acceptor locus within RyR. Additional FRET measurements between donor-labeled calmodulin and A-DPc10 were used to constrain the trilaterations. Results locate the DPc10 probe within RyR domain 3, ?35 Å from the previously docked N-terminal domain crystal structure. This multiscale approach may be useful in mapping other RyR sites of mechanistic interest within FRET range of FKBP.

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Modeling a Ryanodine Receptor N-terminal Domain Connecting the Central Vestibule and the Corner Clamp Region

Cited by 10 publications

References 64 publications

Two potential calmodulin-binding sequences in the ryanodine receptor contribute to a mobile, intra-subunit calmodulin-binding domain

Two potential calmodulin-binding sequences in the ryanodine receptor contribute to a mobile, intra-subunit calmodulin-binding domain

Novel Anthranilic Diamide Insecticides: Design, Synthesis, and Insecticidal Evaluation

FRET-Based Trilateration of Probes Bound within Functional Ryanodine Receptors

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