Biochemical and Structural Characterization of Non-specific RNA-binding Zinc Finger Proteins

Download or read book Biochemical and Structural Characterization of Non-specific RNA-binding Zinc Finger Proteins written by Russell Gerald Burge and published by . This book was released on 2011 with total page 472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Using modeling and NMR methods, JAZ ZF1, ZF2, ZF3, and ZF4 were characterized structurally. Homology models were generated of JAZ ZF1 and JAZ ZF2 based on the NMR structures of the highly homologous finger domains of ZFa ZF1 and ZFa ZF2. Chemical-Shift-Rosetta (CS-Rosetta) models were generated of JAZ ZF1 and JAZ ZF2. The solution structure of JAZ ZF3, which was solved using standard NMR methods, is reported. Structural comparisons indicate that JAZ ZF3 is most similar to ZFa ZF2 and the zinc finger domain of IPTase. Models of protein-RNA complexes were generated employing NMR data to constrain docking using the h igh a mbiguity d riven biomolecular dock ing (HADDOCK) program. The HADDOCK protein-RNA docking protocol was validated by modeling a known protein-dsRNA complex. The docking procedure using NMR titration data was also validated. Protein chemical shift perturbation data ( 1 H- 15 N) were employed as ambiguous interaction restraints to drive docking of the zinc finger-dsRNA complexes. The NMR structures of ZFa ZF1 and JAZ ZF3 were used for the modeling of the protein RNA-complexes. In the case of JAZ ZF2, an experimentally validated homology model was used as the starting structure for the modeling of the complexes. JAZ ZF2, JAZ ZF3, and ZFa ZF1 were docked to an idealized A-form dsRNA model of a minimal RNA construct.