DNA-protein interactions

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Revision as of 03:22, 3 September 2015

DNA-Protein interactions

While DNA contains all the genetic material in a cell, proteins play an important role in regulating the transcription of DNA to RNA, not to mention replication, repair and packaging.. The interactions between DNA and proteins are important in this process. Most sequence specific interactions occur in the , as the in this groove. In contrast, the contains more of the of DNA.

Helix-Turn-Helix Interactions with DNA

The first DNA binding domain characterized was the helix-turn-helix. In a such as the Cro repressor, two α helices are joined by a turn; there may be additional supporting structures, such as additional helices or beta strands, but this is the basic motif. In most cases, the contributes most to DNA recognition, and hence it is often called the "recognition helix". It binds to the major groove of DNA through a series of hydrogen bonds and various Van der Waals interactions with exposed bases. For example, forms hydrogen bonds with both A219 and A220 of the DNA strand. There are also ionic interactions between basic protein residues, such as , with the backbone phosphate groups. The N-terminal alpha helix stabilizes the interaction between the interaction between protein and DNA, but does not play a particularly strong role in its recognition.[2] The recognition helix and its preceding helix always have the same relative orientation.[

Leucine zippers

Zinc fingers

is a transcription factor that induces genes required for the metabolism of galactose, specifically enzymes involved in the conversion of galactose to glucose, and is an example of a zinc finger DNA binding protein. The protein binds as a to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, (residues 8-40), an extended (41-49), and an (50-64). The small, , which contains two metal ions tetrahedrally coordinated by six cysteines. This metal binding domain recognizes a conserved at each end of the site through direct contacts with the , including hydrogen bonding between a . 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.

References

This text shows how to insert references: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Proteopedia Page Contributors and Editors (what is this?)

Ann Taylor, Eric Martz, Michal Harel

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	== Zinc fingers ==		== Zinc fingers ==
-	<scene name='71/711660/Gal4/1'>GAL4</scene> is a transcription factor that induces genes required for the metabolism of galactose, specifically enzymes involved in the conversion of galactose to glucose, and is an example of a zinc finger DNA binding protein. The protein binds as a <scene name='Taylor_Gal4_Sandbox/Dimer/1'>dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='Taylor_Gal4_Sandbox/Metal_binding_domain/2'>metal binding domain</scene>(residues 8-40), an extended <scene name='Taylor_Gal4_Sandbox/Linker/1'>linker</scene>(41-49), and an <scene name='Taylor_Gal4_Sandbox/Dimerization/1'>alpha-helical dimerization element</scene> (50-64). The small, <scene name='Taylor_Gal4_Sandbox/Zn_binding/1'>Zn(2+)-containing domain</scene>, which contains two metal ions tetrahedrally coordinated by six cysteines. This metal binding domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the <scene name='Taylor_Gal4_Sandbox/Major_groove/1'>major groove</scene>. 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='71/711660/Gal4/1'>GAL4</scene> is a transcription factor that induces genes required for the metabolism of galactose, specifically enzymes involved in the conversion of galactose to glucose, and is an example of a zinc finger DNA binding protein. The protein binds as a <scene name='Taylor_Gal4_Sandbox/Dimer/1'>dimer</scene> to a symmetrical 17-base-pair sequence. Each subunit folds into three distinct modules: a compact, <scene name='Taylor_Gal4_Sandbox/Metal_binding_domain/2'>metal binding domain</scene>(residues 8-40), an extended <scene name='Taylor_Gal4_Sandbox/Linker/1'>linker</scene>(41-49), and an <scene name='Taylor_Gal4_Sandbox/Dimerization/1'>alpha-helical dimerization element</scene> (50-64). The small, <scene name='Taylor_Gal4_Sandbox/Zn_binding/1'>Zn(2+)-containing domain</scene>, which contains two metal ions tetrahedrally coordinated by six cysteines. This metal binding domain recognizes a conserved <scene name='71/711660/Ccg/1'>CCG triplet</scene> at each end of the site through direct contacts with the <scene name='Taylor_Gal4_Sandbox/Major_groove/1'>major groove</scene>, including hydrogen bonding between a <scene name='71/711660/Gal_4_lys_to_g/1'>lysine and the conserved G</scene>. 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.

DNA-protein interactions

From Proteopedia

Revision as of 03:22, 3 September 2015