Literature DB >> 26044033

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

Witold Andrałojć1, Konstantin Berlin, David Fushman, Claudio Luchinat, Giacomo Parigi, Enrico Ravera, Luca Sgheri.   

Abstract

Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.

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Year:  2015        PMID: 26044033      PMCID: PMC4782772          DOI: 10.1007/s10858-015-9951-6

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


  112 in total

1.  Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins.

Authors:  Claudio Luchinat; Malini Nagulapalli; Giacomo Parigi; Luca Sgheri
Journal:  J Magn Reson       Date:  2011-12-30       Impact factor: 2.229

2.  Conformational space of flexible biological macromolecules from average data.

Authors:  Ivano Bertini; Andrea Giachetti; Claudio Luchinat; Giacomo Parigi; Maxim V Petoukhov; Roberta Pierattelli; Enrico Ravera; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

3.  Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy.

Authors:  Mathias A S Hass; Peter H J Keizers; Anneloes Blok; Yoshitaka Hiruma; Marcellus Ubbink
Journal:  J Am Chem Soc       Date:  2010-07-28       Impact factor: 15.419

4.  Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state.

Authors:  Linda Cerofolini; Gregg B Fields; Marco Fragai; Carlos F G C Geraldes; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Dmitri I Svergun; João M C Teixeira
Journal:  J Biol Chem       Date:  2013-09-11       Impact factor: 5.157

5.  "Four-dimensional" protein structures: examples from metalloproteins.

Authors:  Marco Fragai; Claudio Luchinat; Giacomo Parigi
Journal:  Acc Chem Res       Date:  2006-12       Impact factor: 22.384

Review 6.  Paramagnetic tagging of diamagnetic proteins for solution NMR.

Authors:  Fernando Rodriguez-Castañeda; Peter Haberz; Andrei Leonov; Christian Griesinger
Journal:  Magn Reson Chem       Date:  2006-07       Impact factor: 2.447

7.  Structural characterization of flexible proteins using small-angle X-ray scattering.

Authors:  Pau Bernadó; Efstratios Mylonas; Maxim V Petoukhov; Martin Blackledge; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2007-04-06       Impact factor: 15.419

Review 8.  Characterizing RNA dynamics at atomic resolution using solution-state NMR spectroscopy.

Authors:  Jameson R Bothe; Evgenia N Nikolova; Catherine D Eichhorn; Jeetender Chugh; Alexandar L Hansen; Hashim M Al-Hashimi
Journal:  Nat Methods       Date:  2011-10-28       Impact factor: 28.547

9.  Direct and selective tagging of cysteine residues in peptides and proteins with 4-nitropyridyl lanthanide complexes.

Authors:  Kathryn L Gempf; Stephen J Butler; Alexander M Funk; David Parker
Journal:  Chem Commun (Camb)       Date:  2013-08-29       Impact factor: 6.222

10.  Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.

Authors:  Alexander S Maltsev; Alexander Grishaev; Julien Roche; Michael Zasloff; Ad Bax
Journal:  J Am Chem Soc       Date:  2014-03-03       Impact factor: 15.419

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  5 in total

1.  Identification of productive and futile encounters in an electron transfer protein complex.

Authors:  Witold Andrałojć; Yoshitaka Hiruma; Wei-Min Liu; Enrico Ravera; Masaki Nojiri; Giacomo Parigi; Claudio Luchinat; Marcellus Ubbink
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

2.  Linkage-specific conformational ensembles of non-canonical polyubiquitin chains.

Authors:  Carlos A Castañeda; Apurva Chaturvedi; Christina M Camara; Joseph E Curtis; Susan Krueger; David Fushman
Journal:  Phys Chem Chem Phys       Date:  2016-02-17       Impact factor: 3.676

Review 3.  Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.

Authors:  Xue-Ni Hou; Hidehito Tochio
Journal:  Biophys Rev       Date:  2022-01-11

4.  Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.

Authors:  Witold Andrałojć; Enrico Ravera; Loïc Salmon; Giacomo Parigi; Hashim M Al-Hashimi; Claudio Luchinat
Journal:  Phys Chem Chem Phys       Date:  2016-02-17       Impact factor: 3.676

Review 5.  Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques.

Authors:  Linda Cerofolini; Marco Fragai; Enrico Ravera; Christoph A Diebolder; Ludovic Renault; Vito Calderone
Journal:  Biomolecules       Date:  2019-08-14
  5 in total

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