Rapid identification of protein–protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements

Kodama, Yuya; Reese, Michael L.; Shimba, Nobuhisa; Ono, Katsuki; Kanamori, Eiji; Dötsch, Volker; Noguchi, Shuji; Fukunishi, Yoshifumi; Suzuki, E; Shimada, Ichio; Takahashi, Hideo

doi:10.1016/j.jsb.2011.04.001

Cited by 5 publications

(11 citation statements)

References 66 publications

(74 reference statements)

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“…Kodama et al [130] used time-sharing NMR measurements as a rapid, effective and unbiased approach for the identification of a protein-protein interface without resonance assignments. Only a single protein 15 N-and 13 C-labelled sample was required for the analysis.…”

Section: Structural Analysis Of Peptides and Proteinsmentioning

confidence: 99%

NMR Spectroscopy for Studying Interactions of Bioactive Molecules

Novak¹,

Jednačak²

2012

Physico-Chemical Methods in Drug Discovery and Development

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Section: Structural Analysis Of Peptides and Proteinsmentioning

confidence: 99%

NMR Spectroscopy for Studying Interactions of Bioactive Molecules

Novak¹,

Jednačak²

2012

Physico-Chemical Methods in Drug Discovery and Development

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“…Single in vitro expression reactions typically yielded 0.2–0.3 mM NMR samples. NMR spectra with correlated 1 H– 13 C and 1 H– 15 N, and sufficient S/N ratios for most resonances were obtained after 2–3 h in time-shared NMR experiments . To observe weaker signals with sufficient S/N ratios, the experiment was performed for 16 h, and 98% of expected resonances were identified .…”

Section: Resultsmentioning

confidence: 99%

“…All NMR spectra were recorded at 303 K on a Bruker AVANCE-600 instrument equipped with a cryo-cooled probe (Bruker BioSpin GmbH; Karlsruhe, Germany). 1 H– 15 N and 1 H– 13 C shift correlations were simultaneously obtained in time-shared NMR experiments . The experiment was implemented using TROSY type coherence transfer in indirect dimension for backbone 1 H– 15 N and aromatic 1 H– 13 C shift correlations.…”

Section: Methodsmentioning

confidence: 99%

“…Here, we present an alternative assignment-free approach for rapid identification of compound-binding sites by using NMR. Although it shares basic concepts with our previous assignmentfree approach for protein−protein interactions, 4 extensive modifications of the procedure accommodate smaller binding interfaces of low-molecular-weight compounds. The key feature of this approach is an elaborate labeling scheme that utilizes single-site 13 C-or 15 N-labeled amino acids in combination with newly developed computational protocols that are suitable for small molecule interactions.…”

Section: ■ Introductionmentioning

confidence: 99%

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Rapid Identification of Ligand-Binding Sites by Using an Assignment-Free NMR Approach

et al. 2013

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In this study, we developed an assignment-free approach for rapid identification of ligand-binding sites in target proteins by using NMR. With a sophisticated cell-free stable isotope-labeling procedure that introduces (15)N- or (13)C-labels to specific atoms of target proteins, this approach requires only a single series of ligand titrations with labeled targets. Using titration data, ligand-binding sites in the target protein can be identified without time-consuming assignment procedures. We demonstrated the feasibility of this approach by using structurally well-characterized interactions between mitogen-activated protein (MAP) kinase p38α and its inhibitor 2-amino-3-benzyloxypyridine. Furthermore, we confirmed the recently proposed fatty acid binding to p38α and confirmed the fatty acid-binding site in the MAP kinase insert region.

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“…98 Besides providing a route to structure determination, methyl-TROSY-based data can provide powerful insight into protein-protein interactions 99 , protein-ligand interactions, protein dynamics 91 , and protein-DNA interaction. 86 …”

Section: Methyl Trosy Nmr Allows Nmr To Probe Structural and Mechanismentioning

confidence: 99%

The Quiet Renaissance of Protein Nuclear Magnetic Resonance

et al. 2013

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From roughly 1985 through the start of the new millennium, the cutting edge of solution protein nuclear magnetic resonance (NMR) spectroscopy was to a significant extent driven by the aspiration to determine structures. Here we survey recent advances in protein NMR that herald a renaissance in which a number of its most important applications reflect the broad problem-solving capability displayed by this method during its classical era during the 1970s and early 80s. “Without receivers fitted and kept in order, the air may tingle and thrill with the message, but it will not reach my spirit and consciousness.” Mary Slessor, Calabar, circa 1910

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Rapid identification of protein–protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements

Cited by 5 publications

References 66 publications

NMR Spectroscopy for Studying Interactions of Bioactive Molecules

NMR Spectroscopy for Studying Interactions of Bioactive Molecules

Rapid Identification of Ligand-Binding Sites by Using an Assignment-Free NMR Approach

The Quiet Renaissance of Protein Nuclear Magnetic Resonance

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