Literature DB >> 29151215

Protein Structure Elucidation from NMR Data with the Program Xplor-NIH.

Guillermo A Bermejo1, Charles D Schwieters2.   

Abstract

Xplor-NIH is a popular software package for biomolecular structure determination from NMR (and other) experimental data. This chapter illustrates its use with the de novo structure determination of the B1 domain of streptococcal protein G (GB1), based on distances from nuclear Overhauser effects, torsion angles from scalar couplings, and bond-vector orientations from residual dipolar couplings. Including Xplor-NIH's latest developments, a complete structure calculation script is discussed in detail, and is intended to serve as a basis for other applications.

Entities:  

Keywords:  NMR; Protein structure calculation; Xplor-NIH script

Mesh：

Substances：

Year:  2018        PMID： 29151215      PMCID： PMC6771931          DOI： 10.1007/978-1-4939-7386-6_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  15 in total

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Authors:  C D Schwieters; G M Clore
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2.  A maximum likelihood method for determining D(a)(PQ) and R for sets of dipolar coupling data.

Authors:  J J Warren; P B Moore
Journal:  J Magn Reson       Date:  2001-04       Impact factor: 2.229

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Authors:  Alexander Grishaev; Ad Bax
Journal:  J Am Chem Soc       Date:  2004-06-16       Impact factor: 15.419

4.  How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?

Authors:  G Marius Clore; Charles D Schwieters
Journal:  J Am Chem Soc       Date:  2004-03-10       Impact factor: 15.419

5.  Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.

Authors:  Guillermo A Bermejo; G Marius Clore; Charles D Schwieters
Journal:  Protein Sci       Date:  2012-10-18       Impact factor: 6.725

6.  Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin.

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Journal:  J Am Chem Soc       Date:  2010-01-20       Impact factor: 15.419

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Authors:  M Nilges; G M Clore; A M Gronenborn
Journal:  FEBS Lett       Date:  1988-03-14       Impact factor: 4.124

Review 8.  Using small angle solution scattering data in Xplor-NIH structure calculations.

Authors:  Charles D Schwieters; G Marius Clore
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-04-03       Impact factor: 9.795

9.  Improving NMR Structures of RNA.

Authors:  Guillermo A Bermejo; G Marius Clore; Charles D Schwieters
Journal:  Structure       Date:  2016-04-07       Impact factor: 5.006

10.  A practical implicit solvent potential for NMR structure calculation.

Authors:  Ye Tian; Charles D Schwieters; Stanley J Opella; Francesca M Marassi
Journal:  J Magn Reson       Date:  2014-04-02       Impact factor: 2.229
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  9 in total

1.  A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination.

Authors:  Charles D Schwieters; Guillermo A Bermejo; G Marius Clore
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3.  A Cholesterol Dimer Stabilizes the Inactivated State of an Inward-Rectifier Potassium Channel.

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Journal:  Angew Chem Int Ed Engl       Date:  2022-02-09       Impact factor: 15.336

Review 4.  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

5.  NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity.

Authors:  Sébastien Alphonse; Ankan Banerjee; Swathi Dantuluri; Stewart Shuman; Ranajeet Ghose
Journal:  Nucleic Acids Res       Date:  2021-09-27       Impact factor: 16.971

6.  Dynamic Na+/H+ exchanger 1 (NHE1) - calmodulin complexes of varying stoichiometry and structure regulate Ca2+-dependent NHE1 activation.

Authors:  Lise M Sjøgaard-Frich; Andreas Prestel; Emilie S Pedersen; Marc Severin; Kristian Kølby Kristensen; Johan G Olsen; Birthe B Kragelund; Stine Falsig Pedersen
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7.  Water Accessibility Refinement of the Extended Structure of KirBac1.1 in the Closed State.

Authors:  Reza Amani; Charles D Schwieters; Collin G Borcik; Isaac R Eason; Ruixian Han; Benjamin D Harding; Benjamin J Wylie
Journal:  Front Mol Biosci       Date:  2021-11-30

8.  Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.

Authors:  Georg Kuenze; Richard Bonneau; Julia Koehler Leman; Jens Meiler
Journal:  Structure       Date:  2019-09-12       Impact factor: 5.006

9.  The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin.

Authors:  Yang Li; Sarah R Sheftic; Simina Grigoriu; Charles D Schwieters; Rebecca Page; Wolfgang Peti
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  9 in total

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