Proteopedia - User contributions [en]

Ferguson ZNF Sandbox

2011-11-18T17:01:31Z

Jordan Ferguson: /* Designer Zinc Fingers to Create DNA Scissors */

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref name="one">Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref name="one" />. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref name="two">PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref name="one" />.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref name="two" />.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====Gag Knuckle=====

<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>This fold</scene> is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues<ref name="four">Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

=====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" />.

=====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===

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]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref name="five" />.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T17:00:12Z

Jordan Ferguson: /* Zinc Ribbon */

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref name="one">Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref name="one" />. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref name="two">PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref name="one" />.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref name="two" />.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====Gag Knuckle=====

<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>This fold</scene> is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues<ref name="four">Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

=====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" />.

=====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===

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" />

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref name="five" />.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:59:11Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref name="one">Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref name="one" />. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref name="two">PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref name="one" />.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref name="two" />.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====Gag Knuckle=====

<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>This fold</scene> is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues<ref name="four">Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

=====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" />.

=====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===

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" />

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref name="five" />.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:51:38Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref name="one">Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref name="one" />. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref name="two">PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref name="one" />.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref name="two" />.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====Gag Knuckle=====

<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>This fold</scene> is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues<ref name="four">Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

=====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" />.

===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" />

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref name="five" />.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:35:44Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

====Other Folds in Zinc Fingers====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>Gag Knuckle</scene>=====

This fold is classified by two beta strands connected by a turn, known as the zinc knuckle, with a loop. Gag knuckles are shorter than the classical domains, with only about 20 residues instead of the usual 30 residues<ref>Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

=====<scene name='Ferguson_ZNF_Sandbox/Treble_clef_finger/1'>Treble Clef Finger</scene>=====

The treble clef zinc finger fold 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>Krishna, S. Sri. "SURVEY AND SUMMARY: Structural Classification of Zinc Fingers." Nucleic Acids Res 31.2 (2003): 532-50.</ref>.

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:14:54Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

====Other Folds in Zinc Fingers====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====<scene name='Ferguson_ZNF_Sandbox/Gag_knuckle/1'>Gag Knuckle</scene>=====

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:09:28Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

====Other Folds in Zinc Fingers====

There is a large variety of folding patterns of the zinc finger protein. These patterns have been classified into eight different folding groups based on chain conformation and secondary structure. Several of these fold groups are presented below

=====Gag Knuckle=====

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:02:57Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

[[Image:ZFN DNA Scissors.jpg|center|400px]]
'''This figure is from Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42'''

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T16:00:54Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

[[Image:ZFN DNA Scissors.jpg|center|300px]]

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

File:ZFN DNA Scissors.jpg

2011-11-18T15:58:09Z

Jordan Ferguson: From Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42. Site specific cutting requires heterodimerization of two independently designed ZFNs. Each ZFN binds to at least ni

From Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.

Site specific cutting requires heterodimerization of two independently designed ZFNs. Each ZFN binds to at least nine nucleotides and flanks a 5 to 6 bp spacer.

Ferguson ZNF Sandbox

2011-11-18T15:56:09Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

==The Zinc Finger==

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain <scene name='Zinc_Fingers/Zinc_fingers_cys/3'>two invariant cysteines</scene> and <scene name='Zinc_Fingers/Zinc_fingers_his/4'>two invariant histidines</scene><ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but usually not in prokaryotic organisms.

===Zinc Finger Structure===

The zinc fingers of a protein are normally 20 to 30 amino acids in length and help to create a solid, stable structure <ref>Goodsell, David. Zinc Fingers. RCSB. PDB. March, 2007. Web</ref>. Each finger contains two invariant Cys residues and two His residues and each binds a Zn2+ ion which is liganded tetrahedrally by the Cys and His residues<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>. The zinc finger contains a two-stranded antiparallel beta sheet and an alpha helix.

The three-dimensional structure of a zinc finger binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding. <ref>PMID:2503871</ref>.

In some zinc finger structures, the His binding residues are replaced by two Cys residues. In other structures, there are six Cys residues that bind two zinc ions. In any case, the Zn2+ ions group together into small globular domains, which eliminates the need for larger, hydrophobic protein cores<ref>Voet, Donald; Voet, Judith G.; Pratt, Charlotte W. Fundamentals of Biochemistry: Life at the Molecular Level. 3rd Ed. Hoboken, NJ: Wiley, 2008</ref>.
{{STRUCTURE_1tf6| PDB=1tf6 | SCENE= }}
====DNA Binding====

In TFIIIA, there are nine consecutive zinc fingers. Individual zinc fingers can be positioned in both the major groove and across the minor groove of DNA. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove. <scene name='Ferguson_ZNF_Sandbox/1tf6/3'>1tf6</scene> shows a dimer with 6 zinc fingers on each bound to a stretch of DNA. With this interaction, TFIIIA helps control the transcription of the gene for ribosomal RNA. The string of zinc fingers curls along the DNA or RNA strands, binding in the grooves and <scene name='Zinc_Fingers/Zinc_fingers_1zaa_dna/4'>extending amino acids inwards</scene> to read the bases. A single zinc finger does not bind very tightly and can only recognize 2 or 3 base pairs, but several can be strung together, causing the group to bind more tightly and allows it to read longer DNA sequences. This modular approach is so appealing that researchers are currently trying to design artificial zinc fingers with different specificities<ref>PMID:2503871</ref>.

=====Specificity=====

The DNA binding specificity is determined by sidechain-base interactions involving residues located at the end or on the surface of the helix <ref>Laity, John. "Zinc Finger Proteins: New Insights into Structural and Functional Diversity." Current Opinion in Structural Biology 11.1 (2001): 39-46.</ref>. Interactions between the phosphate backbone of DNA and linked zinc fingers may also play a role in the specificity.

====DNA Binding in mutant zinc finger domains====

[[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>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>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>.

===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>MMMMMM</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>Davis, David, and David Stokoe. "Zinc Finger Nucleases as Tools to Understand and Treat Human Diseases." BMC Medicine 8.1 (2010): 42.</ref>.

As seen in the figure above, two zinc finger trimers are bound to the DNA sequence creating a dimer of FokI. Each zinc finger binds to nine or more nucleotides. After the cleavage by this complex, overhanging ends are left, which sometimes results in deletions or insertions. If this occurs in a coding region, the outcome could be a shift in the reading frame, which can lead to a null allele of the gene that is targeted<ref></ref>.

==References==
<references/>

Ferguson ZNF Sandbox

2011-11-18T15:14:01Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-18T15:13:30Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-18T15:10:15Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-18T15:07:10Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-17T05:05:08Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-16T05:16:24Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-16T05:14:55Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-16T05:07:59Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-16T04:51:54Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T07:39:41Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T07:37:07Z

Jordan Ferguson:

File:2adr.jpg

2011-11-10T07:35:35Z

Jordan Ferguson: uploaded a new version of "Image:2adr.jpg": The region responsible for sequence-specific DNA binding by the transcription factor ADR1 contains two Cys2-His2 zinc fingers and an additional N-terminal proximal accessory region (PAR).

Source PDB http://www.rscb.org/pdb

Ferguson ZNF Sandbox

2011-11-10T07:30:48Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T07:04:02Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T06:49:56Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T06:46:36Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T06:37:27Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T06:10:53Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:32:31Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:29:23Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:27:02Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:26:31Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:21:36Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:14:22Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T05:13:00Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T04:59:30Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T03:24:44Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T03:17:39Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T03:14:48Z

Jordan Ferguson:

Ferguson ZNF Sandbox

2011-11-10T00:49:51Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

===The Zinc Finger===

The DNA-binding motif known as the zinc finger was first discovered by Klug in Transcription Factor IIIA in ''Xenopus laevis'', the African clawed toad. TFIIIA is a 344 residue protein that contains 9 repeated modules, which are about 30 residues each, that contain two invariant Cys residues and two invariant His residues. These are able to bind a zinc ion, allowing the protein to fold tightly around it. This protein stabilizer is found in thousands of different proteins in both plants and animals, but not in prokaryotic organisms.

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.

==Zinc Finger Structure==
1ZNF is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. The March 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Zinc Fingers'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_3 10.2210/rcsb_pdb/mom_2007_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNF OCA].

==Reference==
<ref group="xtra">PMID:2503871</ref><references group="xtra"/>
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Xenopus laevis]]
[[Category: Zinc Fingers]]
[[Category: Case, D A.]]
[[Category: Gippert, G P.]]
[[Category: Lee, M S.]]
[[Category: Soman, K V.]]
[[Category: Wright, P E.]]
[[Category: Zinc finger dna binding domain]]

Ferguson ZNF Sandbox

2011-11-10T00:36:55Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]

{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

===Transcription Factor IIIA (TFIIIA) Zinc Finger===

TFIIIA in ''Xenopus laevis''

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.

==About this Structure==
1ZNF is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. The March 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Zinc Fingers'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_3 10.2210/rcsb_pdb/mom_2007_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNF OCA].

==Reference==
<ref group="xtra">PMID:2503871</ref><references group="xtra"/>
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Xenopus laevis]]
[[Category: Zinc Fingers]]
[[Category: Case, D A.]]
[[Category: Gippert, G P.]]
[[Category: Lee, M S.]]
[[Category: Soman, K V.]]
[[Category: Wright, P E.]]
[[Category: Zinc finger dna binding domain]]

Ferguson ZNF Sandbox

2011-11-10T00:21:47Z

Jordan Ferguson:

[[Image:1znf.png|left|200px]]


{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

===THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER DNA-BINDING DOMAIN===

The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.

==About this Structure==
1ZNF is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. The March 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Zinc Fingers'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_3 10.2210/rcsb_pdb/mom_2007_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNF OCA].

==Reference==
<ref group="xtra">PMID:2503871</ref><references group="xtra"/>
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Xenopus laevis]]
[[Category: Zinc Fingers]]
[[Category: Case, D A.]]
[[Category: Gippert, G P.]]
[[Category: Lee, M S.]]
[[Category: Soman, K V.]]
[[Category: Wright, P E.]]
[[Category: Zinc finger dna binding domain]]

Ferguson ZNF Sandbox

2011-11-09T05:32:49Z

Jordan Ferguson: New page: {{Seed}} 200px <!-- The line below this paragraph, containing "STRUCTURE_1znf", creates the "Structure Box" on the page. You may change the PDB parameter (which se...

{{Seed}}
[[Image:1znf.png|left|200px]]


{{STRUCTURE_1znf| PDB=1znf | SCENE= }}

===THREE-DIMENSIONAL SOLUTION STRUCTURE OF A SINGLE ZINC FINGER DNA-BINDING DOMAIN===


{{ABSTRACT_PUBMED_2503871}}

==About this Structure==
1ZNF is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. The March 2007 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Zinc Fingers'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2007_3 10.2210/rcsb_pdb/mom_2007_3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZNF OCA].

==Reference==
<ref group="xtra">PMID:2503871</ref><references group="xtra"/>
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Xenopus laevis]]
[[Category: Zinc Fingers]]
[[Category: Case, D A.]]
[[Category: Gippert, G P.]]
[[Category: Lee, M S.]]
[[Category: Soman, K V.]]
[[Category: Wright, P E.]]
[[Category: Zinc finger dna binding domain]]

Ferguson Gal4 sandbox

2011-10-25T15:12:44Z

Jordan Ferguson:

[[Image:1d66.png|left|200px]]


{{STRUCTURE_1d66| PDB=1d66 | SCENE= }}

===DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX===

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

<scene name='Ferguson_Gal4_sandbox/Zinc_binding/1'>Zn(2+)-containing domain</scene>

==About this Structure==
[[1d66]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA].

==See Also==
*[[Hydrogen in macromolecular models]]

==Reference==
<ref group="xtra">PMID:1557122</ref><references group="xtra"/>
[[Category: Saccharomyces cerevisiae]]
[[Category: Carey, M.]]
[[Category: Harrison, S C.]]
[[Category: Marmorstein, R.]]
[[Category: Ptashne, M.]]
[[Category: Double helix]]
[[Category: Protein-dna complex]]
[[Category: Transcription/dna complex]]

Ferguson Gal4 sandbox

2011-10-25T15:11:39Z

Jordan Ferguson:

[[Image:1d66.png|left|200px]]


{{STRUCTURE_1d66| PDB=1d66 | SCENE= }}

===DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX===

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

<scene name='Ferguson_Gal4_sandbox/Zinc_binding/1'>TextToBeDisplayed</scene>

==About this Structure==
[[1d66]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA].

==See Also==
*[[Hydrogen in macromolecular models]]

==Reference==
<ref group="xtra">PMID:1557122</ref><references group="xtra"/>
[[Category: Saccharomyces cerevisiae]]
[[Category: Carey, M.]]
[[Category: Harrison, S C.]]
[[Category: Marmorstein, R.]]
[[Category: Ptashne, M.]]
[[Category: Double helix]]
[[Category: Protein-dna complex]]
[[Category: Transcription/dna complex]]

Ferguson Gal4 sandbox

2011-10-25T15:01:50Z

Jordan Ferguson:

[[Image:1d66.png|left|200px]]


{{STRUCTURE_1d66| PDB=1d66 | SCENE= }}

===DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX===

A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.

==About this Structure==
[[1d66]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA].

==See Also==
*[[Hydrogen in macromolecular models]]

==Reference==
<ref group="xtra">PMID:1557122</ref><references group="xtra"/>
[[Category: Saccharomyces cerevisiae]]
[[Category: Carey, M.]]
[[Category: Harrison, S C.]]
[[Category: Marmorstein, R.]]
[[Category: Ptashne, M.]]
[[Category: Double helix]]
[[Category: Protein-dna complex]]
[[Category: Transcription/dna complex]]

Ferguson Gal4 sandbox

2011-10-25T15:00:33Z

Jordan Ferguson: New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_1d66", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...

[[Image:1d66.png|left|200px]]


{{STRUCTURE_1d66| PDB=1d66 | SCENE= }}

===DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX===


{{ABSTRACT_PUBMED_1557122}}

==About this Structure==
[[1d66]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA].

==See Also==
*[[Hydrogen in macromolecular models]]

==Reference==
<ref group="xtra">PMID:1557122</ref><references group="xtra"/>
[[Category: Saccharomyces cerevisiae]]
[[Category: Carey, M.]]
[[Category: Harrison, S C.]]
[[Category: Marmorstein, R.]]
[[Category: Ptashne, M.]]
[[Category: Double helix]]
[[Category: Protein-dna complex]]
[[Category: Transcription/dna complex]]

JF Sandbox

2011-03-02T23:55:11Z

Jordan Ferguson:

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JF Sandbox

2011-03-02T23:52:16Z

Jordan Ferguson: