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

doi:10.1007/978-1-4939-7386-6_14

. 2018:1688:311-340.

doi: 10.1007/978-1-4939-7386-6_14.

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

Guillermo A Bermejo¹, Charles D Schwieters²

Affiliations

¹ Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA. guillermo.bermejo@nih.gov.
² Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA. charles.schwieters@nih.gov.

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

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

Guillermo A Bermejo et al. Methods Mol Biol. 2018.

. 2018:1688:311-340.

doi: 10.1007/978-1-4939-7386-6_14.

Authors

Guillermo A Bermejo¹, Charles D Schwieters²

Affiliations

¹ Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA. guillermo.bermejo@nih.gov.
² Center for Information Technology, National Institutes of Health, 12 South Drive, MSC 5624, Bethesda, MD, 20892, USA. charles.schwieters@nih.gov.

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

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.

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

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References

1. Schwieters CD, Kuszewski JJ, Tjandra N and Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:66–74 - PubMed
1. Schwieters CD, Kuszewski JJ, and Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Progr Nucl Magn Reson Spectrosc 48:47–62 - PubMed
1. Brünger AT (1993) XPLOR Manual Version 3.1. Yale University Press, New Haven: http://xplor.csb.yale.edu/xplor-info/
1. Huang J-r and Grzesiek S (2010) Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin. J Am Chem Soc 132:694–705 - PubMed
1. Iwahara J, Schwieters CD and Clore GM (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126:5879–5896 - PubMed

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[1] Schwieters CD, Kuszewski JJ, Tjandra N and Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:66–74 - PubMed

[2] Schwieters CD, Kuszewski JJ, Tjandra N and Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160:66–74 - PubMed

[3] Schwieters CD, Kuszewski JJ, and Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Progr Nucl Magn Reson Spectrosc 48:47–62 - PubMed

[4] Schwieters CD, Kuszewski JJ, and Clore GM (2006) Using Xplor-NIH for NMR molecular structure determination. Progr Nucl Magn Reson Spectrosc 48:47–62 - PubMed

[5] Brünger AT (1993) XPLOR Manual Version 3.1. Yale University Press, New Haven: http://xplor.csb.yale.edu/xplor-info/

[6] Brünger AT (1993) XPLOR Manual Version 3.1. Yale University Press, New Haven: http://xplor.csb.yale.edu/xplor-info/

[7] Huang J-r and Grzesiek S (2010) Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin. J Am Chem Soc 132:694–705 - PubMed

[8] Huang J-r and Grzesiek S (2010) Ensemble calculations of unstructured proteins constrained by RDC and PRE data: a case study of urea-denatured ubiquitin. J Am Chem Soc 132:694–705 - PubMed

[9] Iwahara J, Schwieters CD and Clore GM (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126:5879–5896 - PubMed

[10] Iwahara J, Schwieters CD and Clore GM (2004) Ensemble approach for NMR structure refinement against 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule. J Am Chem Soc 126:5879–5896 - PubMed

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

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

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