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Improved Cross Validation of a Static Ubiquitin Structure Derived from High Precision Residual Dipolar Couplings Measured in a Drug-Based Liquid Crystalline Phase
Improved Cross Validation of a Static Ubiquitin Structure Derived from High Precision Residual Dipolar Couplings Measured in a Drug-Based Liquid Crystalline Phase
- Source :
- Journal of the American Chemical Society
- Publication Year :
- 2014
- Publisher :
- American Chemical Society (ACS), 2014.
-
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.
- Subjects :
- Models, Molecular
Protein Conformation
Ubiquitin
Chemistry
Communication
Analytical chemistry
General Chemistry
Residual
Biochemistry
Catalysis
Cross-validation
Anti-Bacterial Agents
Liquid Crystals
Crystallography
Dipole
chemistry.chemical_compound
Colloid and Surface Chemistry
Protein structure
Liquid crystal
Lyotropic liquid crystal
Squalamine
Phase (matter)
Humans
Nuclear Magnetic Resonance, Biomolecular
Cholestanols
Subjects
Details
- ISSN :
- 15205126 and 00027863
- Volume :
- 136
- Database :
- OpenAIRE
- Journal :
- Journal of the American Chemical Society
- Accession number :
- edsair.doi.dedup.....a3a65bf923b34299d13ba93150dee2a2
- Full Text :
- https://doi.org/10.1021/ja4132642