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Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data
No full textIn many cases of protein structure determination by NMR a high-quality structure is required. An important
contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and
methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists.
Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure
and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral
group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking
into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local
environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and
used on NMR data of -helical and -sheet proteins using homology models and/or X-ray structures. The program
produced no erroneus stereospecific assignments provided the NOEs were carefully picked and the 3D model was
sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was
superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with
low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach
that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the
NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar
coupling information is available
Semi-automatic Stereospecific Resonance and NOESY Assignment of Proteins Based on the Tertiary Structure – the Program nmr2st
No full textThe Third Intracellular Loop of the alpha1B-Adrenergic Receptor: Structural Features as derived by NMR and MD Calculations
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Solution Structure of Cytoplasmic Domains of the a1B-Adrenergic Receptor; Implications with Respect to Biological Functions
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Structural Features of the Third Intracellular Loop of the a1B-Adrenergic Receptor as Derived by NMR and MD Calculations
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