Literature DB >> 35340613

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

Xue-Ni Hou1, Hidehito Tochio1.   

Abstract

It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches. © International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2021.

Entities:  

Keywords:  Ensemble reconstruction; Multi-domain proteins; Nuclear magnetic resonance; Pseudocontact shifts; Residual dipolar couplings

Year:  2022        PMID: 35340613      PMCID: PMC8921464          DOI: 10.1007/s12551-021-00916-4

Source DB:  PubMed          Journal:  Biophys Rev        ISSN: 1867-2450


  98 in total

1.  Automated NMR structure calculation with CYANA.

Authors:  Peter Güntert
Journal:  Methods Mol Biol       Date:  2004

2.  REDCAT: a residual dipolar coupling analysis tool.

Authors:  Homayoun Valafar; James H Prestegard
Journal:  J Magn Reson       Date:  2004-04       Impact factor: 2.229

3.  NMR studies on domain diffusion and alignment in modular GB1 repeats.

Authors:  Joseph D Walsh; Katlyn Meier; Rieko Ishima; Angela M Gronenborn
Journal:  Biophys J       Date:  2010-10-20       Impact factor: 4.033

4.  Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy.

Authors:  Jia-Liang Chen; Yin Yang; Lin-Lin Zhang; Haobo Liang; Thomas Huber; Xun-Cheng Su; Gottfried Otting
Journal:  Phys Chem Chem Phys       Date:  2016-02-17       Impact factor: 3.676

5.  Prediction of structures of multidomain proteins from structures of the individual domains.

Authors:  Andrew M Wollacott; Alexandre Zanghellini; Paul Murphy; David Baker
Journal:  Protein Sci       Date:  2006-12-22       Impact factor: 6.725

Review 6.  Paramagnetic NMR in solution and the solid state.

Authors:  Andrew J Pell; Guido Pintacuda; Clare P Grey
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2018-05-24       Impact factor: 9.795

7.  Assessing Structural Preferences of Unstructured Protein Regions by NMR.

Authors:  Azzurra Carlon; Lucia Gigli; Enrico Ravera; Giacomo Parigi; Angela M Gronenborn; Claudio Luchinat
Journal:  Biophys J       Date:  2019-10-14       Impact factor: 4.033

8.  Recovering a representative conformational ensemble from underdetermined macromolecular structural data.

Authors:  Konstantin Berlin; Carlos A Castañeda; Dina Schneidman-Duhovny; Andrej Sali; Alfredo Nava-Tudela; David Fushman
Journal:  J Am Chem Soc       Date:  2013-11-06       Impact factor: 15.419

9.  AIDA: ab initio domain assembly server.

Authors:  Dong Xu; Lukasz Jaroszewski; Zhanwen Li; Adam Godzik
Journal:  Nucleic Acids Res       Date:  2014-05-15       Impact factor: 16.971

10.  Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences.

Authors:  Mauro Rinaldelli; Enrico Ravera; Vito Calderone; Giacomo Parigi; Garib N Murshudov; Claudio Luchinat
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-03-19
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