Ferguson ZNF Sandbox: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
|||
| (2 intermediate revisions by the same user not shown) | |||
| Line 27: | Line 27: | ||
[[Image:2adr.jpg|right|300px]]Two mutants in the N-terminal domain of ADR1, a yeast transcription factor that contains two Cys2-His2 zinc finger sequences spanning residues 102-159 were studied at the Department of Biochemistry at the University of Washington<ref name="three">Hoffman, R.C.; Horvath, S.J.; Klevit, R.E. Structures of DNA-binding mutant zinc finger domains: implications for DNA binding. Protein Sci. 1993 June; 2(6): 951–965.</ref>. The structure to the left shows the region responsible for DNA binding and contains two zinc fingers. Within this region, there are two point mutants at position 118 in the N-terminal zinc finger (ADR1b: 102-130) that adversely affect the DNA-binding activity of ADR1 that been identified: H118A and H118Y. Comparisons of wild-type ADR1b and the two mutants revealed that neither mutation causes a significant structural perturbation. The structures indicate that the DNA binding properties of the His 118 mutants are dependent on the identity of the side chain at position 118, which makes a direct DNA contact in the wild-type ADR1 protein. The results suggest that the identity of the side chain at the middle DNA contact position in Cys2-His2 zinc fingers may be changed regarding the domain structure and this change can and will affect the affinity of the protein-DNA interaction<ref name="three" />. | [[Image:2adr.jpg|right|300px]]Two mutants in the N-terminal domain of ADR1, a yeast transcription factor that contains two Cys2-His2 zinc finger sequences spanning residues 102-159 were studied at the Department of Biochemistry at the University of Washington<ref name="three">Hoffman, R.C.; Horvath, S.J.; Klevit, R.E. Structures of DNA-binding mutant zinc finger domains: implications for DNA binding. Protein Sci. 1993 June; 2(6): 951–965.</ref>. The structure to the left shows the region responsible for DNA binding and contains two zinc fingers. Within this region, there are two point mutants at position 118 in the N-terminal zinc finger (ADR1b: 102-130) that adversely affect the DNA-binding activity of ADR1 that been identified: H118A and H118Y. Comparisons of wild-type ADR1b and the two mutants revealed that neither mutation causes a significant structural perturbation. The structures indicate that the DNA binding properties of the His 118 mutants are dependent on the identity of the side chain at position 118, which makes a direct DNA contact in the wild-type ADR1 protein. The results suggest that the identity of the side chain at the middle DNA contact position in Cys2-His2 zinc fingers may be changed regarding the domain structure and this change can and will affect the affinity of the protein-DNA interaction<ref name="three" />. | ||
====Other Folds in Zinc Fingers==== | ====Other Folds in Zinc Fingers==== | ||
| Line 38: | Line 39: | ||
=====Treble Clef Finger===== | =====Treble Clef Finger===== | ||
The <scene name='Ferguson_ZNF_Sandbox/Treble_clef_finger/1'>treble clef cinger</scene> consists of a beta hairpin at the N terminus as well as an alpha helix at the C terminus. Treble clef fingers, which are found to be incorporated in multi-domain proteins, are present in a diverse group of proteins that frequently do not share sequence and functional similarity with each other<ref name="four" />. | The <scene name='Ferguson_ZNF_Sandbox/Treble_clef_finger/1'>treble clef cinger</scene> consists of a beta hairpin at the N terminus as well as an alpha helix at the C terminus. Treble clef fingers, which are found to be incorporated in multi-domain proteins, are present in a diverse group of proteins that frequently do not share sequence and functional similarity with each other<ref name="four" />. | ||
=====Zinc Ribbon===== | |||
In the <scene name='Ferguson_ZNF_Sandbox/Zinc_ribbon/1'>zinc ribbon group</scene>, the ligands for binding are contributed by two zinc knuckles<ref name="four" />. The structure contains two beta hairpins, forming two similar sites. One of these hairpins is called the primary beta hairpin and contains the N-terminal zinc sub-site, such as the transcription factor TFIIB and transcriptional elongation factor SII<ref name="four" />. | |||
===Designer Zinc Fingers to Create DNA Scissors=== | ===Designer Zinc Fingers to Create DNA Scissors=== | ||
A breakthrough in the studies of zinc finger proteins has been the ability to cleave sites in a large genome through endonuclease activities<ref name="five">Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>. FokI endonuclease has two domans; one that binds to DNA and another that cleaves the DNA. By fusing a FokI mononmer with two zinc finger proteins, which bind adjacent sequences, will generate at least an 18 base pair sequence specific DNA nuclease that allows for selective targeting in mammalian genomes <ref name="five" /> | A breakthrough in the studies of zinc finger proteins has been the ability to cleave sites in a large genome through endonuclease activities<ref name="five">Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>. FokI endonuclease has two domans; one that binds to DNA and another that cleaves the DNA. By fusing a FokI mononmer with two zinc finger proteins, which bind adjacent sequences, the complex will generate at least an 18 base pair sequence specific DNA nuclease that allows for selective targeting in mammalian genomes <ref name="five" /> | ||
[[Image:ZFN DNA Scissors.jpg|center|400px]] | [[Image:ZFN DNA Scissors.jpg|center|400px]] | ||
