Literature DB >> 12060747

Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment.

Thomas Szyperski1, Deok C Yeh, Dinesh K Sukumaran, Hunter N B Moseley, Gaetano T Montelione.   

Abstract

A suite of reduced-dimensionality (13)C,(15)N,(1)H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain the high spectral resolution required for efficient automated analysis. "Sampling limited" and "sensitivity limited" data collection regimes are defined, respectively, depending on whether the sampling of the indirect dimensions or the sensitivity of a multidimensional NMR experiments per se determines the minimally required measurement time. We show that reduced-dimensionality NMR spectroscopy is a powerful approach to avoid the "sampling limited regime"--i.e., a standard set of ten experiments proposed here allows one to effectively adapt minimal measurement times to sensitivity requirements. This is of particular interest in view of the greatly increased sensitivity of NMR spectrometers equipped with cryogenic probes. As a step toward fully automated analysis, the program AUTOASSIGN has been extended to provide sequential backbone and (13)C(beta) resonance assignments from these reduced-dimensionality NMR data.

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Year:  2002        PMID: 12060747      PMCID: PMC123011          DOI: 10.1073/pnas.122224599

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  14 in total

Review 1.  Automated analysis of NMR assignments and structures for proteins.

Authors:  H N Moseley; G T Montelione
Journal:  Curr Opin Struct Biol       Date:  1999-10       Impact factor: 6.809

Review 2.  Protein NMR spectroscopy in structural genomics.

Authors:  G T Montelione; D Zheng; Y J Huang; K C Gunsalus; T Szyperski
Journal:  Nat Struct Biol       Date:  2000-11

3.  High-resolution solution NMR structure of the Z domain of staphylococcal protein A.

Authors:  M Tashiro; R Tejero; D E Zimmerman; B Celda; B Nilsson; G T Montelione
Journal:  J Mol Biol       Date:  1997-10-03       Impact factor: 5.469

4.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.

Authors:  D S Wishart; B D Sykes; F M Richards
Journal:  Biochemistry       Date:  1992-02-18       Impact factor: 3.162

5.  Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments.

Authors:  A R Ortiz; A Kolinski; J Skolnick
Journal:  J Mol Biol       Date:  1998-03-27       Impact factor: 5.469

6.  Automated analysis of protein NMR assignments using methods from artificial intelligence.

Authors:  D E Zimmerman; C A Kulikowski; Y Huang; W Feng; M Tashiro; S Shimotakahara; C Chien; R Powers; G T Montelione
Journal:  J Mol Biol       Date:  1997-06-20       Impact factor: 5.469

7.  Direct measurement of angles between bond vectors in high-resolution NMR.

Authors:  B Reif; M Hennig; C Griesinger
Journal:  Science       Date:  1997-05-23       Impact factor: 47.728

8.  Three-dimensional (1)H-TOCSY-relayed ct-[(13)C, (1)H]-HMQC for aromatic spin system identification in uniformly (13)C-labeled proteins.

Authors:  O Zerbe; T Szyperski; M Ottiger; K Wüthrich
Journal:  J Biomol NMR       Date:  1996-03       Impact factor: 2.835

9.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution.

Authors:  K Pervushin; R Riek; G Wider; K Wüthrich
Journal:  Proc Natl Acad Sci U S A       Date:  1997-11-11       Impact factor: 11.205

10.  Protein dynamics studied by rotating frame 15N spin relaxation times.

Authors:  T Szyperski; P Luginbühl; G Otting; P Güntert; K Wüthrich
Journal:  J Biomol NMR       Date:  1993-03       Impact factor: 2.835

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  74 in total

Review 1.  Radial sampling for fast NMR: Concepts and practices over three decades.

Authors:  Brian E Coggins; Ronald A Venters; Pei Zhou
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-07-30       Impact factor: 9.795

2.  Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme.

Authors:  Wei Qiang
Journal:  J Magn Reson       Date:  2011-08-30       Impact factor: 2.229

3.  Reconstruction of the three-dimensional NMR spectrum of a protein from a set of plane projections.

Authors:  Eriks Kupce; Ray Freeman
Journal:  J Biomol NMR       Date:  2003-12       Impact factor: 2.835

4.  Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.

Authors:  Carolyn M Slupsky; Robert F Boyko; Valerie K Booth; Brian D Sykes
Journal:  J Biomol NMR       Date:  2003-12       Impact factor: 2.835

5.  GFT NMR experiments for polypeptide backbone and 13Cbeta chemical shift assignment.

Authors:  Seho Kim; Thomas Szyperski
Journal:  J Biomol NMR       Date:  2004-02       Impact factor: 2.835

6.  Resonance assignments for the 21 kDa engineered fluorescein-binding lipocalin FluA.

Authors:  Gaohua Liu; Jeffrey L Mills; Tracy A Hess; Seho Kim; Jack J Skalicky; Dinesh K Sukumaran; Eriks Kupce; Arne Skerra; Thomas Szyperski
Journal:  J Biomol NMR       Date:  2003-10       Impact factor: 2.835

7.  G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment.

Authors:  Hanudatta S Atreya; Thomas Szyperski
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-21       Impact factor: 11.205

8.  (3,2)D GFT-NMR experiments for fast data collection from proteins.

Authors:  Youlin Xia; Guang Zhu; Sudha Veeraraghavan; Xiaolian Gao
Journal:  J Biomol NMR       Date:  2004-08       Impact factor: 2.835

9.  Resonance assignments for the 18 kDa protein CC1736 from Caulobacter crescentus.

Authors:  Yang Shen; Hanudatta S Atreya; Rong Xiao; Thomas B Acton; Ritu Shastry; LiChung Ma; Gaetano T Montelione; Thomas Szyperski
Journal:  J Biomol NMR       Date:  2004-08       Impact factor: 2.835

10.  A time-saving strategy for MAS NMR spectroscopy by combining nonuniform sampling and paramagnetic relaxation assisted condensed data collection.

Authors:  Shangjin Sun; Si Yan; Changmiao Guo; Mingyue Li; Jeffrey C Hoch; John C Williams; Tatyana Polenova
Journal:  J Phys Chem B       Date:  2012-11-12       Impact factor: 2.991

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