研究目的
To determine the three-dimensional structure of the retinal degeneration 3 (RD3) protein using NMR spectroscopy and validate it through site-directed mutagenesis to understand its role in regulating retinal guanylyl cyclase and its implications in blindness.
研究成果
The NMR structure of RD3 reveals an elongated four-helix bundle with a localized RetGC binding interface. Mutagenesis validates the structure, showing that specific residues affect affinity. This provides a foundation for understanding RD3's role in vision and blindness, with implications for future studies on RD3/RetGC complexes and disease mechanisms.
研究不足
The RD3d variant has reduced affinity for RetGC compared to wild type, indicating that truncated regions may contribute to cyclase interaction. The structure is based on a soluble variant, not full-length RD3, and some parts (e.g., C-terminus) are unstructured. The study does not fully resolve the stoichiometry of RD3 binding to RetGC or its interactions with other cellular proteins.
1:Experimental Design and Method Selection:
Designed a soluble variant of RD3 (RD3d) to overcome aggregation issues. Used NMR spectroscopy for structural determination, supported by site-directed mutagenesis and functional assays.
2:Sample Selection and Data Sources:
Expressed recombinant human RD3 and its variants in E. coli and HEK293 cells. Purified proteins for NMR and activity assays.
3:List of Experimental Equipment and Materials:
NMR spectrometer (Bruker Avance III 600 MHz), SEC-MALS system (Wyatt Technologies), circular dichroism spectrometer (Chirascan), confocal microscope (Olympus FV1000), various biochemical reagents and kits.
4:Experimental Procedures and Operational Workflow:
Expressed and purified RD3 variants; performed NMR experiments for structure calculation; conducted functional assays for RetGC inhibition and co-localization studies in cells; used mutagenesis to validate structural insights.
5:Data Analysis Methods:
NMR data processed with NMRPipe and analyzed with SPARKY; structural calculations with Xplor-NIH; functional data analyzed with statistical tests (e.g., Student's t-test) and software like Synergy Kaleidagraph.
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NMR Spectrometer
Avance III 600 MHz
Bruker
Used for NMR spectroscopy to determine the structure of RD3 protein.
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Confocal Microscope
FV1000 Spectral
Olympus
Used for confocal imaging to study co-localization of proteins in cells.
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Centrifugal Filter
Amicon Ultra-15
Thermo Fisher Scientific
Used for concentration and purification of protein samples.
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PCR Polymerase
PhusionFlash
Thermo Scientific
Used for high-fidelity PCR in mutagenesis.
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SEC-MALS System
miniDawn
Wyatt Technologies
Used for multi-angle light scattering analysis to determine molar mass of proteins.
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Circular Dichroism Spectrometer
Chirascan
Applied Photophysics Limited
Used to measure circular dichroism spectra to analyze protein secondary structure.
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Size Exclusion Column
Superdex 200 HR10x30
GE Healthcare
Used for size exclusion chromatography to purify proteins.
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E. coli Strain
BL21(DE3) Codon Plus
Stratagene
Used for expression of recombinant proteins.
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HEK293 Cells
Used for expression of RetGC1 and co-localization studies.
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Pf1 Bacteriophage
Asla Biotech Ltd.
Used as an orienting medium for residual dipolar coupling measurements in NMR.
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