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Tang M Sperling LJ Berthold DA Schwieters CD Nesbitt AE Nieuwkoop AJ Gennis RB Rienstra CM 《Journal of biomolecular NMR》2011,51(3):227-233
X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals. 相似文献
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van de Loo FA 《Arthritis research & therapy》2011,13(2):111
It has long been recognized that laboratory tests are useful in the diagnosis of disease and to monitor treatment outcome.
Their performance has become even more demanding with the development of personalized medicine. In patients with rheumatoid
arthritis (RA) the standard biochemical tests measure serological markers of disease, such as C-reactive protein, and RA-associated
auto-antibodies, such as rheumatoid factor and anti-citrullinated protein antibodies. The information obtained from these
markers does not, however, provide a complete picture of the disease and treatment efficacy. New biomarkers based on cytokine
receptor complexes are promising for RA theragnostics. 相似文献
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Boettcher JM Davis-Harrison RL Clay MC Nieuwkoop AJ Ohkubo YZ Tajkhorshid E Morrissey JH Rienstra CM 《Biochemistry》2011,50(12):2264-2273
Membranes play key regulatory roles in biological processes, with bilayer composition exerting marked effects on binding affinities and catalytic activities of a number of membrane-associated proteins. In particular, proteins involved in diverse processes such as vesicle fusion, intracellular signaling cascades, and blood coagulation interact specifically with anionic lipids such as phosphatidylserine (PS) in the presence of Ca(2+) ions. While Ca(2+) is suspected to induce PS clustering in mixed phospholipid bilayers, the detailed structural effects of this ion on anionic lipids are not established. In this study, combining magic angle spinning (MAS) solid-state NMR (SSNMR) measurements of isotopically labeled serine headgroups in mixed lipid bilayers with molecular dynamics (MD) simulations of PS lipid bilayers in the presence of different counterions, we provide site-resolved insights into the effects of Ca(2+) on the structure and dynamics of lipid bilayers. Ca(2+)-induced conformational changes of PS in mixed bilayers are observed in both liposomes and Nanodiscs, a nanoscale membrane mimetic of bilayer patches. Site-resolved multidimensional correlation SSNMR spectra of bilayers containing (13)C,(15)N-labeled PS demonstrate that Ca(2+) ions promote two major PS headgroup conformations, which are well resolved in two-dimensional (13)C-(13)C, (15)N-(13)C, and (31)P-(13)C spectra. The results of MD simulations performed on PS lipid bilayers in the presence or absence of Ca(2+) provide an atomic view of the conformational effects underlying the observed spectra. 相似文献
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ABSTRACT: Co-evolving positions within protein sequences have been used as spatial constraints to develop a computational approach for modeling membrane protein structures. 相似文献