Amino-acid selective isotope labeling enables simultaneous overlapping signal decomposition and information extraction from NMR spectra

[1]  M. Kirpichnikov,et al.  CombLabel: rational design of optimized sequence-specific combinatorial labeling schemes. Application to backbone assignment of membrane proteins with low stability , 2019, Journal of Biomolecular NMR.

[2]  V. Dötsch,et al.  Protein labeling strategies for liquid-state NMR spectroscopy using cell-free synthesis. , 2018, Progress in nuclear magnetic resonance spectroscopy.

[3]  S. Ono,et al.  Efficient Constrained Tensor Factorization by Alternating Optimization with Primal-Dual Splitting , 2017, 2018 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[4]  John E. Schiel,et al.  Multivariate Analysis of Two-Dimensional 1H, 13C Methyl NMR Spectra of Monoclonal Antibody Therapeutics To Facilitate Assessment of Higher Order Structure. , 2017, Analytical chemistry.

[5]  Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution , 2017, Journal of biomolecular NMR.

[6]  A. Bax,et al.  Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data , 2016, Journal of Biomolecular NMR.

[7]  V. Dötsch,et al.  Acceleration of protein backbone NMR assignment by combinatorial labeling: Application to a small molecule binding study , 2017, Biopolymers.

[8]  V. Dötsch,et al.  From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins. , 2016, Structure.

[9]  T. Kigawa,et al.  NMR spectral analysis using prior knowledge , 2016 .

[10]  Rajashekar Varma Kadumuri,et al.  Rapid NMR Assignments of Proteins by Using Optimized Combinatorial Selective Unlabeling , 2016, Chembiochem : a European journal of chemical biology.

[11]  V. Orekhov,et al.  Non‐uniform sampling: post‐Fourier era of NMR data collection and processing , 2015, Magnetic resonance in chemistry : MRC.

[12]  T. Kigawa,et al.  Stable isotope labeling strategy based on coding theory , 2015, Journal of biomolecular NMR.

[13]  V. Dötsch,et al.  An extended combinatorial 15N, 13Cα, and $$ ^{13} {\text{C}}^{\prime } $$13C′ labeling approach to protein backbone resonance assignment , 2015, Journal of biomolecular NMR.

[14]  M. Gill,et al.  Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms , 2015, Journal of Biomolecular NMR.

[15]  G. Clore Practical Aspects of Paramagnetic Relaxation Enhancement in Biological Macromolecules. , 2015, Methods in enzymology.

[16]  V. Dötsch,et al.  Time-shared experiments for efficient assignment of triple-selectively labeled proteins. , 2014, Journal of magnetic resonance.

[17]  Mehdi Mobli,et al.  Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR. , 2014, Progress in nuclear magnetic resonance spectroscopy.

[18]  S. Hyberts,et al.  Perspectives in magnetic resonance: NMR in the post-FFT era. , 2014, Journal of magnetic resonance.

[19]  F. Fogolari,et al.  Reduction of conformational mobility and aggregation in W60G β2‐microglobulin: assessment by 15N NMR relaxation , 2013, Magnetic resonance in chemistry : MRC.

[20]  Yuya Kodama,et al.  Rapid identification of ligand-binding sites by using an assignment-free NMR approach. , 2013, Journal of medicinal chemistry.

[21]  S. Choe,et al.  Advances in NMR structures of integral membrane proteins. , 2013, Current opinion in structural biology.

[22]  John L Markley,et al.  Biophysical characterization of α-synuclein and its controversial structure , 2013, Intrinsically disordered proteins.

[23]  A. Sali,et al.  Facile backbone structure determination of human membrane proteins by NMR spectroscopy , 2012, Nature Methods.

[24]  Daniel Nietlispach,et al.  Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins , 2012, Journal of biomolecular NMR.

[25]  Gerhard Wagner,et al.  Application of iterative soft thresholding for fast reconstruction of NMR data non-uniformly sampled with multidimensional Poisson Gap scheduling , 2012, Journal of Biomolecular NMR.

[26]  V. Dötsch,et al.  Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment , 2012, Journal of biomolecular NMR.

[27]  H. Atreya,et al.  Amino acid selective labeling and unlabeling for protein resonance assignments. , 2012, Advances in experimental medicine and biology.

[28]  L. Gladden,et al.  Fast multidimensional NMR spectroscopy using compressed sensing. , 2011, Angewandte Chemie.

[29]  V. Orekhov,et al.  Accelerated NMR spectroscopy by using compressed sensing. , 2011, Angewandte Chemie.

[30]  T. Kigawa,et al.  A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution. , 2011, Analytical biochemistry.

[31]  P. Güntert,et al.  Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm , 2011, Journal of biomolecular NMR.

[32]  H. Atreya,et al.  Amino acid selective unlabeling for sequence specific resonance assignments in proteins , 2010, Journal of biomolecular NMR.

[33]  W. Kwiatkowski,et al.  Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis , 2010, Proceedings of the National Academy of Sciences.

[34]  G. Otting Protein NMR using paramagnetic ions. , 2010, Annual review of biophysics.

[35]  V. Dötsch,et al.  Cell-free expression and stable isotope labelling strategies for membrane proteins , 2010, Journal of biomolecular NMR.

[36]  T. Kigawa Cell-free protein production system with the E. coli crude extract for determination of protein folds. , 2010, Methods in molecular biology.

[37]  N. Dixon,et al.  Cell-free synthesis and combinatorial selective 15N-labeling of the cytotoxic protein amoebapore A from Entamoeba histolytica. , 2009, Protein expression and purification.

[38]  J. Herzfeld,et al.  Spectroscopy by integration of frequency and time domain information for fast acquisition of high-resolution dark spectra. , 2009, Journal of the American Chemical Society.

[39]  Hidekazu Hiroaki,et al.  High-resolution multi-dimensional NMR spectroscopy of proteins in human cells , 2009, Nature.

[40]  S. Becker,et al.  Assignment‐free solution NMR method reveals CesT as an unswapped homodimer , 2008, Protein science : a publication of the Protein Society.

[41]  Brian E Coggins,et al.  High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN , 2008, Journal of biomolecular NMR.

[42]  Wolfgang Jahnke,et al.  Solution Conformations and Dynamics of ABL Kinase-Inhibitor Complexes Determined by NMR Substantiate the Different Binding Modes of Imatinib/Nilotinib and Dasatinib*♦ , 2008, Journal of Biological Chemistry.

[43]  P. Güntert,et al.  Transmembrane segment enhanced labeling as a tool for the backbone assignment of α-helical membrane proteins , 2008, Proceedings of the National Academy of Sciences.

[44]  T. Kigawa,et al.  A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis , 2007, Journal of Structural and Functional Genomics.

[45]  David L Donoho,et al.  NMR data processing using iterative thresholding and minimum l(1)-norm reconstruction. , 2007, Journal of magnetic resonance.

[46]  Gerhard Wagner,et al.  Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. , 2007, Journal of the American Chemical Society.

[47]  T. Kigawa,et al.  Improving cell-free protein synthesis for stable-isotope labeling , 2007, Journal of biomolecular NMR.

[48]  Nicholas E. Dixon,et al.  15N‐Labelled proteins by cell‐free protein synthesis , 2006 .

[49]  I. Campbell,et al.  Cell‐free expression and selective isotope labelling in protein NMR , 2006, Magnetic resonance in chemistry : MRC.

[50]  Gottfried Otting,et al.  Amino-acid Type Identification in 15N-HSQC Spectra by Combinatorial Selective 15N-labelling , 2006, Journal of biomolecular NMR.

[51]  Volker Dötsch,et al.  Efficient strategy for the rapid backbone assignment of membrane proteins. , 2005, Journal of the American Chemical Society.

[52]  Vladislav Yu Orekhov,et al.  High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. , 2005, Journal of the American Chemical Society.

[53]  I. Shimada NMR techniques for identifying the interface of a larger protein-protein complex: cross-saturation and transferred cross-saturation experiments. , 2005, Methods in enzymology.

[54]  Andrea M Hounslow,et al.  A combinatorial selective labeling method for the assignment of backbone amide NMR resonances. , 2004, Journal of the American Chemical Society.

[55]  D. Wemmer,et al.  Protein Signal Assignments Using Specific Labeling and Cell-Free Synthesis , 2004, Journal of biomolecular NMR.

[56]  Takanori Kigawa,et al.  Preparation of Escherichia coli cell extract for highly productive cell-free protein expression , 2004, Journal of Structural and Functional Genomics.

[57]  Martin Billeter,et al.  MUNIN: Application of three-way decomposition to the analysis of heteronuclear NMR relaxation data** , 2001, Journal of biomolecular NMR.

[58]  M. Billeter,et al.  MUNIN: A new approach to multi-dimensional NMR spectra interpretation , 2001, Journal of biomolecular NMR.

[59]  Rasmus Bro,et al.  The N-way Toolbox for MATLAB , 2000 .

[60]  J. D. Engel,et al.  Keap1 represses nuclear activation of antioxidant responsive elements by Nrf2 through binding to the amino-terminal Neh2 domain. , 1999, Genes & development.

[61]  G. Clore,et al.  3D NMR experiments for measuring 15N relaxation data of large proteins: application to the 44 kDa ectodomain of SIV gp41. , 1998, Journal of magnetic resonance.

[62]  E D Laue,et al.  Dual amino acid-selective and site-directed stable-isotope labeling of the human c-Ha-Ras protein by cell-free synthesis , 1998, Journal of biomolecular NMR.

[63]  R. Bro PARAFAC. Tutorial and applications , 1997 .

[64]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[65]  T. Kigawa,et al.  Cell-free synthesis and amino acid-selective stable isotope labeling of proteins for NMR analysis , 1995, Journal of biomolecular NMR.

[66]  D. Shortle Assignment of amino acid type in 1H-15N correlation spectra by labeling with 14N-amino acids. , 1994, Journal of magnetic resonance. Series B.

[67]  Ad Bax,et al.  Methodological advances in protein NMR , 1993 .

[68]  G. Wagner,et al.  A constant-time three-dimensional triple-resonance pulse scheme to correlate intraresidue 1HN, 15N, and 13C′ chemical shifts in 15N13C-labelled proteins , 1992 .

[69]  L Mayne,et al.  Protein folding studied using hydrogen-exchange labeling and two-dimensional NMR. , 1992, Annual review of biophysics and biomolecular structure.

[70]  H. Nakamura,et al.  Assignments of backbone 1H, 13C, and 15N resonances and secondary structure of ribonuclease H from Escherichia coli by heteronuclear three-dimensional NMR spectroscopy. , 1991, Biochemistry.

[71]  A. Gronenborn,et al.  Analysis of the backbone dynamics of interleukin-1.beta. using two-dimensional inverse detected heteronuclear nitrogen-15-proton NMR spectroscopy , 1990 .

[72]  L. Kay,et al.  A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. , 1990, Biochemistry.

[73]  L. Kay,et al.  A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin , 1990 .

[74]  I. Johnstone,et al.  Maximum entropy reconstruction of complex (phase-sensitive) spectra , 1990 .

[75]  L. Kay,et al.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. , 1989, Biochemistry.

[76]  G. Daniell,et al.  Maximum entropy and NMR—A new approach , 1989 .

[77]  E. Laue,et al.  Conventional and exponential sampling for 2D NMR experiments with application to a 2D NMR spectrum of a protein , 1987 .

[78]  J. Skilling,et al.  Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments , 1987 .

[79]  M. Kainosho,et al.  Assignment of the three methionyl carbonyl carbon resonances in Streptomyces subtilisin inhibitor by a carbon-13 and nitrogen-15 double-labeling technique. A new strategy for structural studies of proteins in solution. , 1982, Biochemistry.