Literature DB >> 17061025

A suite of Mathematica notebooks for the analysis of protein main chain 15N NMR relaxation data.

Leo Spyracopoulos1.   

Abstract

A suite of Mathematica notebooks has been designed to ease the analysis of protein main chain 15N NMR relaxation data collected at a single magnetic field strength. Individual notebooks were developed to perform the following tasks: nonlinear fitting of 15N-T1 and -T2 relaxation decays to a two parameter exponential decay, calculation of the principal components of the inertia tensor from protein structural coordinates, nonlinear optimization of the principal components and orientation of the axially symmetric rotational diffusion tensor, model-free analysis of 15N-T1, -T2, and {1H}-15N NOE data, and reduced spectral density analysis of the relaxation data. The principle features of the notebooks include use of a minimal number of input files, integrated notebook data management, ease of use, cross-platform compatibility, automatic visualization of results and generation of high-quality graphics, and output of analyses in text format.

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Year:  2006        PMID: 17061025     DOI: 10.1007/s10858-006-9083-0

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


  18 in total

1.  A relation between the principal axes of inertia and ligand binding.

Authors:  J Foote; A Raman
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-01       Impact factor: 11.205

2.  An effective method for the discrimination of motional anisotropy and chemical exchange.

Authors:  Julie M Kneller; Min Lu; Clay Bracken
Journal:  J Am Chem Soc       Date:  2002-03-06       Impact factor: 15.419

3.  Determination of the rotational diffusion tensor of macromolecules in solution from nmr relaxation data with a combination of exact and approximate methods--application to the determination of interdomain orientation in multidomain proteins.

Authors:  R Ghose; D Fushman; D Cowburn
Journal:  J Magn Reson       Date:  2001-04       Impact factor: 2.229

4.  The use of model selection in the model-free analysis of protein dynamics.

Authors:  Edward J d'Auvergne; Paul R Gooley
Journal:  J Biomol NMR       Date:  2003-01       Impact factor: 2.835

5.  Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding.

Authors:  D Yang; L E Kay
Journal:  J Mol Biol       Date:  1996-10-25       Impact factor: 5.469

6.  Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments.

Authors:  Francesca Massi; Michael J Grey; Arthur G Palmer
Journal:  Protein Sci       Date:  2005-03       Impact factor: 6.725

7.  Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected two-dimensional NMR spectroscopy: the central helix is flexible.

Authors:  G Barbato; M Ikura; L E Kay; R W Pastor; A Bax
Journal:  Biochemistry       Date:  1992-06-16       Impact factor: 3.162

8.  Spectral density function mapping using 15N relaxation data exclusively.

Authors:  N A Farrow; O Zhang; A Szabo; D A Torchia; L E Kay
Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

9.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease.

Authors:  L E Kay; D A Torchia; A Bax
Journal:  Biochemistry       Date:  1989-11-14       Impact factor: 3.162

10.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

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  28 in total

1.  Structure, interactions, and dynamics of the RING domain from human TRAF6.

Authors:  Pascal Mercier; Michael J Lewis; D Duong Hau; Linda F Saltibus; Wei Xiao; Leo Spyracopoulos
Journal:  Protein Sci       Date:  2007-02-27       Impact factor: 6.725

2.  Model-free analysis for large proteins at high magnetic field strengths.

Authors:  Shou-Lin Chang; Andrew P Hinck; Rieko Ishima
Journal:  J Biomol NMR       Date:  2007-06-26       Impact factor: 2.835

3.  Preserved Transmembrane Segment Topology, Structure, and Dynamics in Disparate Micellar Environments.

Authors:  David N Langelaan; Aditya Pandey; Muzaddid Sarker; Jan K Rainey
Journal:  J Phys Chem Lett       Date:  2017-05-12       Impact factor: 6.475

4.  Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics.

Authors:  Heidi S Alvey; Federico L Gottardo; Evgenia N Nikolova; Hashim M Al-Hashimi
Journal:  Nat Commun       Date:  2014-09-04       Impact factor: 14.919

5.  Guanine nucleotides differentially modulate backbone dynamics of the STAS domain of the SulP/SLC26 transport protein Rv1739c of Mycobacterium tuberculosis.

Authors:  Alok K Sharma; Liwen Ye; Seth L Alper; Alan C Rigby
Journal:  FEBS J       Date:  2011-12-22       Impact factor: 5.542

6.  Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav.

Authors:  Chih-Hong Chen; Victoria A Martin; Nina M Gorenstein; Robert L Geahlen; Carol Beth Post
Journal:  Mol Cell Biol       Date:  2011-05-23       Impact factor: 4.272

7.  A probe to monitor performance of ¹⁵N longitudinal relaxation experiments for proteins in solution.

Authors:  Rieko Ishima
Journal:  J Biomol NMR       Date:  2014-01-05       Impact factor: 2.835

8.  Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

Authors:  Xiancheng Zeng; Jeetender Chugh; Anette Casiano-Negroni; Hashim M Al-Hashimi; Charles L Brooks
Journal:  J Mol Biol       Date:  2014-05-09       Impact factor: 5.469

9.  Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

Authors:  Isaac J Kimsey; Katja Petzold; Bharathwaj Sathyamoorthy; Zachary W Stein; Hashim M Al-Hashimi
Journal:  Nature       Date:  2015-03-11       Impact factor: 49.962

10.  Solution structure and dynamics of the I214V mutant of the rabbit prion protein.

Authors:  Yi Wen; Jun Li; Minqian Xiong; Yu Peng; Wenming Yao; Jing Hong; Donghai Lin
Journal:  PLoS One       Date:  2010-10-07       Impact factor: 3.240

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