Literature DB >> 21389020

Nuclear magnetic resonance analysis of protein-DNA interactions.

S Campagne1, V Gervais, A Milon.   

Abstract

Recent methodological and instrumental advances in solution-state nuclear magnetic resonance have opened up the way to investigating challenging problems in structural biology such as large macromolecular complexes. This review focuses on the experimental strategies currently employed to solve structures of protein-DNA complexes and to analyse their dynamics. It highlights how these approaches can help in understanding detailed molecular mechanisms of target recognition.

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Year:  2011        PMID： 21389020      PMCID： PMC3119875          DOI： 10.1098/rsif.2010.0543

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN： 1742-5662            Impact factor:   4.118


  111 in total

1.  Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions.

Authors:  J Kuszewski; C Schwieters; G M Clore
Journal:  J Am Chem Soc       Date:  2001-05-02       Impact factor: 15.419

Review 2.  Recognition of specific DNA sequences.

Authors:  C W Garvie; C Wolberger
Journal:  Mol Cell       Date:  2001-11       Impact factor: 17.970

3.  Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain.

Authors:  Charalampos G Kalodimos; Alexandre M J J Bonvin; Roberto K Salinas; Rainer Wechselberger; Rolf Boelens; Robert Kaptein
Journal:  EMBO J       Date:  2002-06-17       Impact factor: 11.598

4.  The Xplor-NIH NMR molecular structure determination package.

Authors:  Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal:  J Magn Reson       Date:  2003-01       Impact factor: 2.229

Review 5.  Combinatorial gene regulation by eukaryotic transcription factors.

Authors:  L Chen
Journal:  Curr Opin Struct Biol       Date:  1999-02       Impact factor: 6.809

Review 6.  Structural characterization of proteins and complexes using small-angle X-ray solution scattering.

Authors:  Haydyn D T Mertens; Dmitri I Svergun
Journal:  J Struct Biol       Date:  2010-06-15       Impact factor: 2.867

7.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

8.  Crystal structure of ATF-2/c-Jun and IRF-3 bound to the interferon-beta enhancer.

Authors:  Daniel Panne; Tom Maniatis; Stephen C Harrison
Journal:  EMBO J       Date:  2004-10-28       Impact factor: 11.598

9.  Structural determinants of specific DNA-recognition by the THAP zinc finger.

Authors:  Sébastien Campagne; Olivier Saurel; Virginie Gervais; Alain Milon
Journal:  Nucleic Acids Res       Date:  2010-02-09       Impact factor: 16.971

10.  Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.

Authors:  Guohui Zheng; Xiang-Jun Lu; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2009-05-27       Impact factor: 16.971
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  15 in total

Review 1.  DNA-protein interactions: methods for detection and analysis.

Authors:  Bipasha Dey; Sameer Thukral; Shruti Krishnan; Mainak Chakrobarty; Sahil Gupta; Chanchal Manghani; Vibha Rani
Journal:  Mol Cell Biochem       Date:  2012-03-08       Impact factor: 3.396

2.  NMR studies on protein-nucleic acid interaction.

Authors:  Robert Kaptein
Journal:  J Biomol NMR       Date:  2013-05       Impact factor: 2.835

3.  A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes.

Authors:  Garima Khandelwal; Rebecca A Lee; B Jayaram; David L Beveridge
Journal:  Biophys J       Date:  2014-06-03       Impact factor: 4.033

4.  Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver.

Authors:  Yunhui Peng; Lexuan Sun; Zhe Jia; Lin Li; Emil Alexov
Journal:  Bioinformatics       Date:  2018-03-01       Impact factor: 6.937

5.  Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes.

Authors:  Ridvan Nepravishta; Channing C Pletka; Junji Iwahara
Journal:  J Biomol NMR       Date:  2020-07-18       Impact factor: 2.835

6.  Development of Vibrational Frequency Maps for Nucleobases.

Authors:  Yaoyukun Jiang; Lu Wang
Journal:  J Phys Chem B       Date:  2019-07-01       Impact factor: 2.991

7.  Autoinhibition of ETV6 (TEL) DNA binding: appended helices sterically block the ETS domain.

Authors:  H Jerome Coyne; Soumya De; Mark Okon; Sean M Green; Niraja Bhachech; Barbara J Graves; Lawrence P McIntosh
Journal:  J Mol Biol       Date:  2012-05-12       Impact factor: 5.469

8.  Identification of DNA-binding proteins using support vector machine with sequence information.

Authors:  Xin Ma; Jiansheng Wu; Xiaoyun Xue
Journal:  Comput Math Methods Med       Date:  2013-09-16       Impact factor: 2.238

9.  TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy.

Authors:  Dnyaneshwar B Gophane; Snorri Th Sigurdsson
Journal:  Beilstein J Org Chem       Date:  2015-02-09       Impact factor: 2.883

10.  Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein-DNA Complex.

Authors:  Kaustubh Sinha; Sahil S Sangani; Andrew D Kehr; Gordon S Rule; Linda Jen-Jacobson
Journal:  Biochemistry       Date:  2016-10-27       Impact factor: 3.162
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