Literature DB >> 14752254

Improving the accuracy of NMR structures of large proteins using pseudocontact shifts as long-range restraints.

Vadim Gaponenko1, Siddhartha P Sarma, Amanda S Altieri, David A Horita, Jess Li, R Andrew Byrd.   

Abstract

We demonstrate improved accuracy in protein structure determination for large (>/=30 kDa), deuterated proteins (e.g. STAT4(NT)) via the combination of pseudocontact shifts for amide and methyl protons with the available NOEs in methyl-protonated proteins. The improved accuracy is cross validated by Q-factors determined from residual dipolar couplings measured as a result of magnetic susceptibility alignment. The paramagnet is introduced via binding to thiol-reactive EDTA, and multiple sites can be serially engineered to obtain data from alternative orientations of the paramagnetic anisotropic susceptibility tensor. The technique is advantageous for systems where the target protein has strong interactions with known alignment media.

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Year:  2004        PMID: 14752254     DOI: 10.1023/B:JNMR.0000013706.09264.36

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  32 in total

1.  De novo determination of protein structure by NMR using orientational and long-range order restraints.

Authors:  J C Hus; D Marion; M Blackledge
Journal:  J Mol Biol       Date:  2000-05-19       Impact factor: 5.469

2.  Direct structure refinement of high molecular weight proteins against residual dipolar couplings and carbonyl chemical shift changes upon alignment: an application to maltose binding protein.

Authors:  W Y Choy; M Tollinger; G A Mueller; L E Kay
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

3.  Proton nuclear magnetic resonance hyperfine shifts as indicators of tertiary structural changes accompanying the Bohr effect in monomeric insect hemoglobins.

Authors:  G N La Mar; M Overkamp; H Sick; K Gersonde
Journal:  Biochemistry       Date:  1978-01-24       Impact factor: 3.162

4.  Structure of the amino-terminal protein interaction domain of STAT-4.

Authors:  U Vinkemeier; I Moarefi; J E Darnell; J Kuriyan
Journal:  Science       Date:  1998-02-13       Impact factor: 47.728

5.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Authors:  G Cornilescu; F Delaglio; A Bax
Journal:  J Biomol NMR       Date:  1999-03       Impact factor: 2.835

6.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

7.  Calmodulin tagging provides a general method of using lanthanide induced magnetic field orientation to observe residual dipolar couplings in proteins in solution.

Authors:  J Feeny; B Birdsall; A F Bradbury; R R Biekofsky; P M Bayley
Journal:  J Biomol NMR       Date:  2001-09       Impact factor: 2.835

8.  Bicelle-based liquid crystals for NMR-measurement of dipolar couplings at acidic and basic pH values.

Authors:  M Ottiger; A Bax
Journal:  J Biomol NMR       Date:  1999-02       Impact factor: 2.835

9.  Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.

Authors:  J Kraulis; G M Clore; M Nilges; T A Jones; G Pettersson; J Knowles; A M Gronenborn
Journal:  Biochemistry       Date:  1989-09-05       Impact factor: 3.162

10.  Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.

Authors:  J R Tolman; J M Flanagan; M A Kennedy; J H Prestegard
Journal:  Proc Natl Acad Sci U S A       Date:  1995-09-26       Impact factor: 11.205

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  23 in total

1.  Engineering encodable lanthanide-binding tags into loop regions of proteins.

Authors:  Katja Barthelmes; Anne M Reynolds; Ezra Peisach; Hendrik R A Jonker; Nicholas J DeNunzio; Karen N Allen; Barbara Imperiali; Harald Schwalbe
Journal:  J Am Chem Soc       Date:  2011-02-02       Impact factor: 15.419

2.  Advances in Nuclear Magnetic Resonance for Drug Discovery.

Authors:  Robert Powers
Journal:  Expert Opin Drug Discov       Date:  2009-10-01       Impact factor: 6.098

3.  Efficient chi-tensor determination and NH assignment of paramagnetic proteins.

Authors:  Christophe Schmitz; Michael John; Ah Young Park; Nicholas E Dixon; Gottfried Otting; Guido Pintacuda; Thomas Huber
Journal:  J Biomol NMR       Date:  2006-06-10       Impact factor: 2.835

4.  Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect.

Authors:  Tomohide Saio; Kenji Ogura; Masashi Yokochi; Yoshihiro Kobashigawa; Fuyuhiko Inagaki
Journal:  J Biomol NMR       Date:  2009-05-26       Impact factor: 2.835

5.  Investigation of the utility of selective methyl protonation for determination of membrane protein structures.

Authors:  Steve C C Shih; Ileana Stoica; Natalie K Goto
Journal:  J Biomol NMR       Date:  2008-09-02       Impact factor: 2.835

6.  Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts.

Authors:  Christophe Schmitz; Mitchell J Stanton-Cook; Xun-Cheng Su; Gottfried Otting; Thomas Huber
Journal:  J Biomol NMR       Date:  2008-06-24       Impact factor: 2.835

Review 7.  Site-specific labeling of proteins with NMR-active unnatural amino acids.

Authors:  David H Jones; Susan E Cellitti; Xueshi Hao; Qiong Zhang; Michael Jahnz; Daniel Summerer; Peter G Schultz; Tetsuo Uno; Bernhard H Geierstanger
Journal:  J Biomol NMR       Date:  2009-08-09       Impact factor: 2.835

8.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

Authors:  Witold Andrałojć; Konstantin Berlin; David Fushman; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Luca Sgheri
Journal:  J Biomol NMR       Date:  2015-06-05       Impact factor: 2.835

9.  FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data.

Authors:  Mauro Rinaldelli; Azzurra Carlon; Enrico Ravera; Giacomo Parigi; Claudio Luchinat
Journal:  J Biomol NMR       Date:  2014-11-22       Impact factor: 2.835

10.  Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR.

Authors:  Hanna E Lindfors; Peter E de Koning; Jan Wouter Drijfhout; Brigida Venezia; Marcellus Ubbink
Journal:  J Biomol NMR       Date:  2008-06-17       Impact factor: 2.835

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