Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.

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TitleImproved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.
Publication TypeJournal Article
Year of Publication2014
AuthorsMaltsev, AS, Grishaev, A, Roche, J, Zasloff, M, Bax, A
JournalJ Am Chem Soc
Volume136
Issue10
Pagination3752-5
Date Published2014 Mar 12
ISSN1520-5126
KeywordsAnti-Bacterial Agents, Cholestanols, Humans, Liquid Crystals, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Ubiquitin
Abstract

The antibiotic squalamine forms a lyotropic liquid crystal at very low concentrations in water (0.3-3.5% w/v), which remains stable over a wide range of temperature (1-40 °C) and pH (4-8). Squalamine is positively charged, and comparison of the alignment of ubiquitin relative to 36 previously reported alignment conditions shows that it differs substantially from most of these, but is closest to liquid crystalline cetyl pyridinium bromide. High precision residual dipolar couplings (RDCs) measured for the backbone (1)H-(15)N, (15)N-(13)C', (1)H(α)-(13)C(α), and (13)C'-(13)C(α) one-bond interactions in the squalamine medium fit well to the static structural model previously derived from NMR data. Inclusion into the structure refinement procedure of these RDCs, together with (1)H-(15)N and (1)H(α)-(13)C(α) RDCs newly measured in Pf1, results in improved agreement between alignment-induced changes in (13)C' chemical shift, (3)JHNHα values, and (13)C(α)-(13)C(β) RDCs and corresponding values predicted by the structure, thereby validating the high quality of the single-conformer structural model. This result indicates that fitting of a single model to experimental data provides a better description of the average conformation than does averaging over previously reported NMR-derived ensemble representations. The latter can capture dynamic aspects of a protein, thus making the two representations valuable complements to one another.

DOI10.1021/ja4132642
Alternate JournalJ. Am. Chem. Soc.
PubMed ID24568736
PubMed Central IDPMC3954408
Grant List / / Intramural NIH HHS / United States