Literature DB >> 26477262

Practical Aspects of Paramagnetic Relaxation Enhancement in Biological Macromolecules.

G Marius Clore1.   

Abstract

In this brief review, we summarize various aspects of NMR paramagnetic relaxation enhancement (PRE). We discuss the types of spin labels used in NMR studies, describe the relevant theory used to accurately calculate PREs from coordinates, including how to take into account the fact that paramagnetic labels tend to be highly mobile and sample a wide range of conformational space, and outline methods to refine structures or ensembles of structures directly against PRE data using simulated annealing. Finally, we show how the PRE can be used to detect, characterize, and visualize sparsely populated states of proteins and their complexes that are invisible to all other biophysical techniques.
© 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Conformational transitions; Paramagnetic relaxation enhancement; Sparsely populated invisible states; Spin labels; Structure determination

Mesh:

Substances:

Year:  2015        PMID: 26477262      PMCID: PMC6361390          DOI: 10.1016/bs.mie.2015.06.032

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  35 in total

1.  Ensemble approach for NMR structure refinement against (1)H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule.

Authors:  Junji Iwahara; Charles D Schwieters; G Marius Clore
Journal:  J Am Chem Soc       Date:  2004-05-12       Impact factor: 15.419

2.  Target enzyme recognition by calmodulin: 2.4 A structure of a calmodulin-peptide complex.

Authors:  W E Meador; A R Means; F A Quiocho
Journal:  Science       Date:  1992-08-28       Impact factor: 47.728

Review 3.  Weak alignment NMR: a hawk-eyed view of biomolecular structure.

Authors:  Ad Bax; Alexander Grishaev
Journal:  Curr Opin Struct Biol       Date:  2005-10       Impact factor: 6.809

4.  Detecting transient intermediates in macromolecular binding by paramagnetic NMR.

Authors:  Junji Iwahara; G Marius Clore
Journal:  Nature       Date:  2006-04-27       Impact factor: 49.962

5.  Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data.

Authors:  J L Battiste; G Wagner
Journal:  Biochemistry       Date:  2000-05-09       Impact factor: 3.162

6.  Solution structure of a calmodulin-target peptide complex by multidimensional NMR.

Authors:  M Ikura; G M Clore; A M Gronenborn; G Zhu; C B Klee; A Bax
Journal:  Science       Date:  1992-05-01       Impact factor: 47.728

7.  The ATCUN domain as a probe of intermolecular interactions: application to calmodulin-peptide complexes.

Authors:  Tapas K Mal; Mitsuhiko Ikura; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2002-11-27       Impact factor: 15.419

8.  EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement.

Authors:  Junji Iwahara; D Eric Anderson; Elizabeth C Murphy; G Marius Clore
Journal:  J Am Chem Soc       Date:  2003-06-04       Impact factor: 15.419

9.  Protein global fold determination using site-directed spin and isotope labeling.

Authors:  V Gaponenko; J W Howarth; L Columbus; G Gasmi-Seabrook; J Yuan; W L Hubbell; P R Rosevear
Journal:  Protein Sci       Date:  2000-02       Impact factor: 6.725

10.  Binding ability of a HHP-tagged protein towards Ni2+ studied by paramagnetic NMR relaxation: the possibility of obtaining long-range structure information.

Authors:  Malene Ringkjøbing Jensen; Conni Lauritzen; Søren Weis Dahl; John Pedersen; Jens J Led
Journal:  J Biomol NMR       Date:  2004-06       Impact factor: 2.835

View more
  30 in total

1.  DNA binding induces a cis-to-trans switch in Cre recombinase to enable intasome assembly.

Authors:  Aparna Unnikrishnan; Carlos Amero; Deepak Kumar Yadav; Kye Stachowski; Devante Potter; Mark P Foster
Journal:  Proc Natl Acad Sci U S A       Date:  2020-09-23       Impact factor: 11.205

2.  Sequence-independent recognition of the amyloid structural motif by GFP protein family.

Authors:  Sherry C S Xu; Josephine G LoRicco; Anthony C Bishop; Nathan A James; Welby H Huynh; Scott A McCallum; Nadia R Roan; George I Makhatadze
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-24       Impact factor: 11.205

3.  Towards interpretation of intermolecular paramagnetic relaxation enhancement outside the fast exchange limit.

Authors:  Alberto Ceccon; G Marius Clore; Vitali Tugarinov
Journal:  J Biomol NMR       Date:  2016-08-24       Impact factor: 2.835

4.  Cu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR.

Authors:  Leah M Seebald; Christopher M DeMott; Srivathsan Ranganathan; Papa Nii Asare Okai; Anastasia Glazunova; Alan Chen; Alexander Shekhtman; Maksim Royzen
Journal:  Inorg Chem       Date:  2017-03-22       Impact factor: 5.165

5.  K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function.

Authors:  Shufen Cao; Stacey Chung; SoonJeung Kim; Zhenlu Li; Danny Manor; Matthias Buck
Journal:  J Biol Chem       Date:  2019-02-21       Impact factor: 5.157

6.  Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.

Authors:  Dustin C Woods; Jeff Wereszczynski
Journal:  Nucleic Acids Res       Date:  2020-04-17       Impact factor: 16.971

7.  High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.

Authors:  Ye Tian; Charles D Schwieters; Stanley J Opella; Francesca M Marassi
Journal:  J Biomol NMR       Date:  2016-12-29       Impact factor: 2.835

Review 8.  Applications of NMR to structure determination of RNAs large and small.

Authors:  Ravi P Barnwal; Fan Yang; Gabriele Varani
Journal:  Arch Biochem Biophys       Date:  2017-06-16       Impact factor: 4.013

Review 9.  NMR-based investigations into target DNA search processes of proteins.

Authors:  Junji Iwahara; Levani Zandarashvili; Catherine A Kemme; Alexandre Esadze
Journal:  Methods       Date:  2018-05-10       Impact factor: 3.608

10.  Path to Collagenolysis: COLLAGEN V TRIPLE-HELIX MODEL BOUND PRODUCTIVELY AND IN ENCOUNTERS BY MATRIX METALLOPROTEINASE-12.

Authors:  Stephen H Prior; Todd S Byrne; Dorota Tokmina-Roszyk; Gregg B Fields; Steven R Van Doren
Journal:  J Biol Chem       Date:  2016-02-17       Impact factor: 5.157

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.