DOI: 10.1002/pro.5560020607. Representing an ensemble of NMR‐derived protein structures by a single structure

Representing an ensemble of NMR‐derived protein structures by a single structure

10.1002/pro.5560020607

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractThe usefulness of representing an ensemble of NMR‐derived protein structures by a single structure has been investigated. Two stereochemical properties have been used to assess how a single structure relates to the ensemble from which it was derived, namely the distribution of ϕΨ torsion angles and the distribution of χ1 torsion angles. The results show that the minimized average structure derived from the ensemble (a total of 11 ensembles from the Brookhaven Protein Data Bank were analyzed) does not always correspond well with this ensemble, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue. An alternative method that selects the member of the ensemble which is closest to the “average” of the ensemble has been investigated (a total of 23 ensembles from the Brookhaven Protein Data Bank were analyzed). Although this method selected a structure that on the whole corresponded more closely to the ensemble than did the minimized average structure, this is still not a totally reliable means of selecting a single structure to represent the ensemble. This suggests that it is advisable to study the ensemble as a whole. A study has also been made of the practice of selecting the “best” rather than the most representative member of the ensemble. This too suggests that the ensemble should be studied as a whole. A study of the conformational space occupied by the ensemble also suggests the need to consider the ensemble as a whole, particularly for those ensembles generated with a smaller number of experimentally derived restraints per residue.

Bibliography

Sutcliffe, M. J. (1993). Representing an ensemble of NMRâderived protein structures by a single structure. Protein Science, 2(6), 936â944. Portico.

Authors 1

Michael J. Sutcliffe (first)

References 31 Referenced 28

{'key': 'e_1_2_1_2_2', 'first-page': '107', 'volume-title': 'Crystallographic Databases—Information Content, Software Systems, Scientific Applications', 'author': 'Abola E.E.', 'year': '1987'} / Crystallographic Databases—Information Content, Software Systems, Scientific Applications by Abola E.E. (1987)
10.1016/S0022-2836(77)80200-3
10.1016/0022-2836(85)90134-2
10.1021/bi00459a004
10.1021/bi00431a033
10.1021/bi00469a016
10.1016/S0021-9258(19)38261-4 / J. Biol. Chem. / Solution structure of neurotoxin I from sea anemone Stichodactyla helianthus by Fogh R.H. (1990)
10.1021/bi00432a038
10.1021/bi00224a017
10.1126/science.1871600
10.1016/0022-2836(91)90755-U
10.1016/0079-6107(91)90007-F
{'key': 'e_1_2_1_14_2', 'first-page': '673', 'article-title': 'A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intermolecular 1H‐1H proximities in solution', 'volume': '46', 'author': 'Havel T.F.', 'year': '1984', 'journal-title': 'Bull. Math. Biol.'} / Bull. Math. Biol. / A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intermolecular 1H‐1H proximities in solution by Havel T.F. (1984)
10.1016/0022-2836(89)90137-X
10.1016/0022-2836(88)90364-6
10.1021/bi00444a016
{'key': 'e_1_2_1_18_2', 'volume-title': 'PROCHECK, version 2.0.', 'author': 'Laskowski R.A.', 'year': '1992'} / PROCHECK, version 2.0. by Laskowski R.A. (1992)
10.1126/science.2503871
10.1016/S0022-2836(83)80306-4
10.1016/0022-2836(92)90328-H
10.1107/S0567739482001806
10.1002/prot.340120407
10.1016/0022-2836(91)90189-D
10.1021/bi00492a004
{'key': 'e_1_2_1_26_2', 'volume-title': 'Numerical Recipes.', 'author': 'Press W.H.', 'year': '1987'} / Numerical Recipes. by Press W.H. (1987)
10.1006/jmbi.1993.1097
10.1021/bi00454a005
10.1021/bi00126a017
10.1002/prot.340060403
10.1016/0022-2836(85)90347-X
10.1021/bi00464a002

Dates

Type	When
Created	16 years, 6 months ago (Feb. 9, 2009, 7:27 p.m.)
Deposited	1 year, 10 months ago (Oct. 25, 2023, 9:59 p.m.)
Indexed	2 months, 1 week ago (June 26, 2025, 9:29 a.m.)
Issued	32 years, 3 months ago (June 1, 1993)
Published	32 years, 3 months ago (June 1, 1993)
Published Online	16 years, 8 months ago (Dec. 31, 2008)
Published Print	32 years, 3 months ago (June 1, 1993)

Funders 0

None

BibTeX

@article{Sutcliffe_1993, title={Representing an ensemble of NMR‐derived protein structures by a single structure}, volume={2}, ISSN={1469-896X}, url={http://dx.doi.org/10.1002/pro.5560020607}, DOI={10.1002/pro.5560020607}, number={6}, journal={Protein Science}, publisher={Wiley}, author={Sutcliffe, Michael J.}, year={1993}, month=jun, pages={936–944} }

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