Recommendations for the presentation of NMR structures of proteins and nucleic acids

Markley, John L.; Bax, Ad; Arata, Yoji; Hilbers, C. W.; Kaptein, Robert; Sykes, Brian D.; Wright, Peter E.; Wüthrich, Kurt

doi:10.1046/j.1432-1327.1998.2560001.x

Cited by 242 publications

(261 citation statements)

References 29 publications

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“…Side chain carbon and hydrogen assignments (84% absolute, not discounting proline residues) were obtained using three-dimensional H(CC)(CO)NH-TOCSY and (H)CC(CO)NH-TOCSY experiments, each collected at 2 different mixing times (12 and 20 ms). Assignments were referenced to 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS), directly for protons and indirectly for nitrogen and carbon (14).…”

Section: Methodsmentioning

confidence: 99%

Defining the Apoptotic Trigger

O’Brien¹,

Nucci²,

Fuglestad

et al. 2015

Journal of Biological Chemistry

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Section: Methodsmentioning

confidence: 99%

Defining the Apoptotic Trigger

O’Brien¹,

Nucci²,

Fuglestad

et al. 2015

Journal of Biological Chemistry

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“…Spectra are referenced to 2,2-dimethyl-2-silapentane sulfonic acid. 13 C chemical shifts are indirectly referenced using a scal-ing factor of 0.251449530 (27). Spectra were processed with Topspin (Bruker) and analyzed with Sparky (46).…”

Section: Methodsmentioning

confidence: 99%

Substrate Specificity of Cytoplasmic N-Glycosyltransferase

Naegeli

Michaud

Schubert

et al. 2014

Journal of Biological Chemistry

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Background: N-Glycosyltransferases represent a novel class of N-glycosylation-catalyzing enzymes. Results: A quantitative activity assay allowed us to determine substrate specificities of N-glycosyltransferase. Conclusion: N-Glycosyltransferase exhibits a relaxed sugar substrate specificity and a peptide specificity strikingly similar to that of oligosaccharyltransferase. Significance: This study highlights the convergent evolution of two N-glycosylation systems and might lay the basis for a novel route for glycoengineering in bacteria.

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“…Spectral analysis was performed using the programs XEASY (34) and CARA (R. Keller et al, unpublished). Chemical shifts were referenced to 2,2-dimethyl-2 silapentane-5-sulfonate sodium salt (DSS) (35).…”

Section: Nmr Spectroscopymentioning

confidence: 99%

NMR-Derived Dynamic Aspects of N-Type Inactivation of a Kv Channel Suggest a Transient Interaction with the T1 Domain

et al. 2006

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Some eukaryotic Kv channels contain an N-terminal inactivation peptide (IP), which mediates a fast inactivation process that limits channel function during membrane depolarization and thus shapes the action potential. We obtained sequence-specific NMR assignments for the polypeptide backbone of a tetrameric N-terminal fragment (amino acids 1-181) of the Aplysia Kv1.1 channel.Additional NMR measurements show that the T1 domain has the same globular structure in solution as previously determined by crystallography, and that the IP (residues 1-20) and the Linker (residues 21-65) are in a flexibly disordered, predominantly extended conformation. A potential contact site between the T1 domain and the flexible tail (residues 1-65) has been identified based upon chemical shift changes of individual T1 domain amino acids, which maps to the T1 surface near the interface between adjacent subunits. Paramagnetic perturbation experiments further indicate that in the ensemble of solution conformers, there is at least a small population of species with the IP localized in close proximity to the proposed interacting residues of the T1 tetramer. Electrophysiological measurements show that all three mutations in this pocket we tested slow the rate of inactivation and speed up recovery, as predicted from the preinactivation site model. These results suggest that specific, short-lived transient interactions between the T1 domain and the IP or the Linker segment may play a role in defining the regulatory kinetics of fast channel inactivation.Cytoplasmic domains of voltage-gated K + (Kv) channels regulate channel assembly, trafficking and function, and control cytoplasmic access to the ion conduction pathway (1-7). Inactivation of Kv channels is a critical biological timing mechanism that limits the duration of channel activity in response to depolarization, as well as suppressing further channel activity for a period of time following depolarization. Thus, the ability to inactivate is an essential property of a variety of channels involved in shaping and regulating the excitability of the cell (2). A particular form of rapid inactivation of Kv channels, called Ntype inactivation, is mediated by an inactivation peptide (IP) segment of approximately 20 amino acids located at the N-terminal end of the α-subunits or of certain associating β-subunits. Results from experiments with free synthetic IP's, which restore inactivation to IPfree Kv channels (3,8,9), support the idea that a single IP can function by physically Because of the presence of the bulky tetrameric T1 assembly located between the IP and the central IP-binding site (12)(13)(14), and since the central cavity of the T1 domain is not part of the ion conduction pathway (15), it has been hypothesized that there must exist a pathway that allows the IP to move around the intervening T1 domain to reach its target site within the transmembrane (TM) pore of the channel, and that the lateral "side-windows" formed between T1 and the TM domains most likely provide this route (...

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Recommendations for the presentation of NMR structures of proteins and nucleic acids

Cited by 242 publications

References 29 publications

Defining the Apoptotic Trigger

Defining the Apoptotic Trigger

Substrate Specificity of Cytoplasmic N-Glycosyltransferase

NMR-Derived Dynamic Aspects of N-Type Inactivation of a Kv Channel Suggest a Transient Interaction with the T1 Domain

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