Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
J Struct Biol. 2011 Apr 9;
Authors: Kodama Y, Reese ML, Shimba N, Ono K, Kanamori E, Dötsch V, Noguchi S, Fukunishi Y, Suzuki EI, Shimada I, Takahashi H
Protein-protein interactions are necessary for various cellular processes, and therefore, information related to protein-protein interactions and structural information of complexes is invaluable. To identify protein-protein interfaces using NMR, resonance assignments are generally necessary to analyze the data; however, they are time consuming to collect, especially for large proteins. In this paper, we present a rapid, effective, and unbiased approach for the identification of a protein-protein interface without resonance assignments. This approach requires only a single set of 2D titration experiments of a single protein sample, labeled with a unique combination of an (15)N-labeled amino acid and several amino acids (13)C-labeled on specific atoms. To rapidly obtain high resolution data, we applied a new pulse sequence for time-shared NMR measurements that allowed simultaneous detection of a ?(1)-TROSY-type backbone (1)H-(15)N and aromatic (1)H-(13)C shift correlations together with single quantum methyl (1)H-(13)C shift correlations. We developed a structure-based computational approach, that uses our experimental data to search the protein surfaces in an unbiased manner to identify the residues involved in the protein-protein interface. Finally, we demonstrated that the obtained information of the molecular interface could be directly leveraged to support protein-protein docking studies. Such rapid construction of a complex model provides valuable information and enables more efficient biochemical characterization of a protein-protein complex, for instance, as the first step in structure-guided drug development.
PMID: 21501688 [PubMed - as supplied by publisher]
Identification of Cryptic Products of the Gliotoxin Gene Cluster Using NMR-Based Comparative Metabolomics and a Model for Gliotoxin Biosynthesis
Identification of Cryptic Products of the Gliotoxin Gene Cluster Using NMR-Based Comparative Metabolomics and a Model for Gliotoxin Biosynthesis
Ry R. Forseth, Ellen M. Fox, DaWoon Chung, Barbara J. Howlett, Nancy P. Keller and Frank C. Schroeder
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2029987/aop/images/medium/ja-2011-029987_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja2029987
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/kET0fe1YTXQ
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[NMR paper] Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors.
Strategies for the NMR-based identification and optimization of allosteric protein kinase inhibitors.
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Chembiochem. 2005 Sep;6(9):1607-10
Authors: Jahnke W, Blommers MJ, Fernández C, Zwingelstein C, Amstutz R
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[NMR paper] High-throughput inference of protein-protein interfaces from unassigned NMR data.
High-throughput inference of protein-protein interfaces from unassigned NMR data.
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Bioinformatics. 2005 Jun;21 Suppl 1:i292-301
Authors: Mettu RR, Lilien RH, Donald BR
SUMMARY: We cast the problem of identifying protein-protein interfaces, using only unassigned NMR spectra, into a geometric clustering problem. Identifying protein-protein interfaces is critical to understanding inter- and intra-cellular communication, and NMR allows the study of...
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[NMR paper] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
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Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
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11-24-2010 09:16 PM
[NMR paper] Micromixer-based time-resolved NMR: applications to ubiquitin protein conformation.
Micromixer-based time-resolved NMR: applications to ubiquitin protein conformation.
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Anal Chem. 2003 Feb 15;75(4):956-60
Authors: Kakuta M, Jayawickrama DA, Wolters AM, Manz A, Sweedler JV
Time-resolved NMR spectroscopy is used to studychanges in protein conformation based on the elapsed time after a change in the solvent composition of a protein solution. The use of a micromixer and a continuous-flow method is described where the contents of...
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[NMR paper] Probability-based protein secondary structure identification using combined NMR chemi
Probability-based protein secondary structure identification using combined NMR chemical-shift data.
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Protein Sci. 2002 Apr;11(4):852-61
Authors: Wang Y, Jardetzky O
For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed (1)H(alpha), (13)C(alpha), (13)C(beta), or (13)C' chemical shifts with the random coil values. Here, we...
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[NMR paper] Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) che
Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate.
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J Am Chem Soc. 2002 Jan 23;124(3):372-3
Authors: Pintacuda G, Otting G
Gd-diethylenetriamine pentaacetic acid-bismethylamide, Gd(DTPA-BMA), is shown to be a reagent suitable for the identification of protein surfaces. Compared to the conventionally used spin-label TEMPOL, Gd(DTPA-BMA) is a stronger relaxation agent, requiring lesser concentrations...
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[NMR paper] Protein dynamics measurements by TROSY-based NMR experiments.
Protein dynamics measurements by TROSY-based NMR experiments.
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J Magn Reson. 2000 Apr;143(2):423-6
Authors: Zhu G, Xia Y, Nicholson LK, Sze KH
The described TROSY-based experiments for investigating backbone dynamics of proteins make it possible to elucidate internal motions in large proteins via measurements of T(1), T(2), and NOE of backbone (15)N nuclei. In our proposed sequences, the INEPT sequence is eliminated and the PEP sequence is replaced by the ST2-PT...