Literature DB >> 18762868

Graphical interpretation of Boolean operators for protein NMR assignments.

Dries Verdegem1, Klaas Dijkstra, Xavier Hanoulle, Guy Lippens.   

Abstract

We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies "AND"-, "OR"- and "NOT"-like operations on planes pulled out of the classical three-dimensional spectra to obtain its functionality. The method's strength lies in the continuous graphical presentation of the spectra, allowing both a semi-automatic peaklist construction and sequential assignment. We demonstrate here its general use for the case of a folded protein with a well-dispersed spectrum, but equally for a natively unfolded protein where spectral resolution is minimal.

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Year:  2008        PMID: 18762868     DOI: 10.1007/s10858-008-9262-2

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


  79 in total

1.  Ansig for Windows: an interactive computer program for semiautomatic assignment of protein NMR spectra.

Authors:  M Helgstrand; P Kraulis; P Allard; T Härd
Journal:  J Biomol NMR       Date:  2000-12       Impact factor: 2.835

2.  Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

Authors:  Torsten Herrmann; Peter Güntert; Kurt Wüthrich
Journal:  J Mol Biol       Date:  2002-05-24       Impact factor: 5.469

3.  Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).

Authors:  Wolfram Gronwald; Sherif Moussa; Ralph Elsner; Astrid Jung; Bernhard Ganslmeier; Jochen Trenner; Werner Kremer; Klaus-Peter Neidig; Hans Robert Kalbitzer
Journal:  J Biomol NMR       Date:  2002-08       Impact factor: 2.835

4.  Reconsidering complete search algorithms for protein backbone NMR assignment.

Authors:  Olga Vitek; Chris Bailey-Kellogg; Bruce Craig; Paul Kuliniewicz; Jan Vitek
Journal:  Bioinformatics       Date:  2005-09-01       Impact factor: 6.937

5.  A computer-based protocol for semiautomated assignments and 3D structure determination of proteins.

Authors:  R P Meadows; E T Olejniczak; S W Fesik
Journal:  J Biomol NMR       Date:  1994-01       Impact factor: 2.835

6.  Automated combined assignment of NOESY spectra and three-dimensional protein structure determination.

Authors:  C Mumenthaler; P Güntert; W Braun; K Wüthrich
Journal:  J Biomol NMR       Date:  1997-12       Impact factor: 2.835

7.  Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence.

Authors:  D Zimmerman; C Kulikowski; L Wang; B Lyons; G T Montelione
Journal:  J Biomol NMR       Date:  1994-03       Impact factor: 2.835

8.  An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments.

Authors:  Christopher James Langmead; Bruce Randall Donald
Journal:  J Biomol NMR       Date:  2004-06       Impact factor: 2.835

9.  Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

Authors:  P J Kraulis
Journal:  J Mol Biol       Date:  1994-11-04       Impact factor: 5.469

10.  GANA--a genetic algorithm for NMR backbone resonance assignment.

Authors:  Hsin-Nan Lin; Kun-Pin Wu; Jia-Ming Chang; Ting-Yi Sung; Wen-Lian Hsu
Journal:  Nucleic Acids Res       Date:  2005-08-10       Impact factor: 16.971

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  11 in total

1.  Systematic identification of tubulin-interacting fragments of the microtubule-associated protein Tau leads to a highly efficient promoter of microtubule assembly.

Authors:  Caroline Fauquant; Virginie Redeker; Isabelle Landrieu; Jean-Michel Wieruszeski; Dries Verdegem; Olivier Laprévote; Guy Lippens; Benoît Gigant; Marcel Knossow
Journal:  J Biol Chem       Date:  2011-07-12       Impact factor: 5.157

2.  Spectroscopic studies of GSK3{beta} phosphorylation of the neuronal tau protein and its interaction with the N-terminal domain of apolipoprotein E.

Authors:  Arnaud Leroy; Isabelle Landrieu; Isabelle Huvent; Dominique Legrand; Bernadette Codeville; Jean-Michel Wieruszeski; Guy Lippens
Journal:  J Biol Chem       Date:  2010-08-02       Impact factor: 5.157

3.  POTENCI: prediction of temperature, neighbor and pH-corrected chemical shifts for intrinsically disordered proteins.

Authors:  Jakob Toudahl Nielsen; Frans A A Mulder
Journal:  J Biomol NMR       Date:  2018-02-05       Impact factor: 2.835

4.  Selective backbone labelling of ILV methyl labelled proteins.

Authors:  Nathalie Sibille; Xavier Hanoulle; Fanny Bonachera; Dries Verdegem; Isabelle Landrieu; Jean-Michel Wieruszeski; Guy Lippens
Journal:  J Biomol NMR       Date:  2009-03-14       Impact factor: 2.835

5.  Cyclophilin A allows the allosteric regulation of a structural motif in the disordered domain 2 of NS5A and thereby fine-tunes HCV RNA replication.

Authors:  Marie Dujardin; Vanesa Madan; Neha S Gandhi; François-Xavier Cantrelle; Hélène Launay; Isabelle Huvent; Ralf Bartenschlager; Guy Lippens; Xavier Hanoulle
Journal:  J Biol Chem       Date:  2019-07-17       Impact factor: 5.157

6.  Domain 3 of NS5A protein from the hepatitis C virus has intrinsic alpha-helical propensity and is a substrate of cyclophilin A.

Authors:  Dries Verdegem; Aurélie Badillo; Jean-Michel Wieruszeski; Isabelle Landrieu; Arnaud Leroy; Ralf Bartenschlager; François Penin; Guy Lippens; Xavier Hanoulle
Journal:  J Biol Chem       Date:  2011-04-13       Impact factor: 5.157

7.  Structure and antagonism of the receptor complex mediated by human TSLP in allergy and asthma.

Authors:  Kenneth Verstraete; Frank Peelman; Harald Braun; Juan Lopez; Dries Van Rompaey; Ann Dansercoer; Isabel Vandenberghe; Kris Pauwels; Jan Tavernier; Bart N Lambrecht; Hamida Hammad; Hans De Winter; Rudi Beyaert; Guy Lippens; Savvas N Savvides
Journal:  Nat Commun       Date:  2017-04-03       Impact factor: 14.919

8.  Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B.

Authors:  Xavier Hanoulle; Aurélie Badillo; Jean-Michel Wieruszeski; Dries Verdegem; Isabelle Landrieu; Ralf Bartenschlager; François Penin; Guy Lippens
Journal:  J Biol Chem       Date:  2009-03-18       Impact factor: 5.157

9.  A Proline-Tryptophan Turn in the Intrinsically Disordered Domain 2 of NS5A Protein Is Essential for Hepatitis C Virus RNA Replication.

Authors:  Marie Dujardin; Vanesa Madan; Roland Montserret; Puneet Ahuja; Isabelle Huvent; Helene Launay; Arnaud Leroy; Ralf Bartenschlager; François Penin; Guy Lippens; Xavier Hanoulle
Journal:  J Biol Chem       Date:  2015-06-17       Impact factor: 5.157

Review 10.  NMR Meets Tau: Insights into Its Function and Pathology.

Authors:  Guy Lippens; Isabelle Landrieu; Caroline Smet; Isabelle Huvent; Neha S Gandhi; Benoît Gigant; Clément Despres; Haoling Qi; Juan Lopez
Journal:  Biomolecules       Date:  2016-06-07
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