Sandbox Reserved 654: Difference between revisions

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[[Image:F1.medium.gif |thumb|250 px|right| Acetylation of the lysine and its effects on chromatin remodeling.]]

The mechanism of protein-protein interaction for the bromodomain of PCAF with target proteins, such as histones<ref name =aaa>Zeng, L. et al (2008) Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 16: 643–652 [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339198/]</ref> and Tat<ref name=aa/>, begins with the acetylation of lysine residues. The acetylation causes a conformational changes in the histones, which allows for transcriptional machinery to access DNA. The bromodomains of PCAF have three major points of contact that allow for site-specific histone recognition. First, the <scene name='Sandbox_Reserved_654/Kac50/1'>acetylated lysine</scene> of the target protein enters a hydrophobic pocket embedded between the ZA and BC loops at the bottom of the protein. The Asn803 residue in the bromodomain forms a hydrogen bond with the amide nitrogen of the acetyl-lysine. Next, residues in the ZA and/or BC loops interact with residues adjacent to the acetyl-lysine, which reinforces the acetyl-lysine binding in the bromodomain. Finally, additional residues in the ZA and BC loops that face opposite to the bromodomain form hydrophobic and/ or electrostatic interaction with the target protein 3 residues away from the acetyl-lysine. This residue clamps on the BC loop together with the acetyl-lysine side chain that is bound inside the hydrophobic pocket of the bromodomain<ref name =aaa/>.

The mechanism of protein-protein interaction for the bromodomain of PCAF with target proteins, such as histones<ref name =aaa>Zeng, L. et al (2008) Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 16: 643–652 [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339198/]</ref> and Tat<ref name=aa/>, begins with the acetylation of lysine residues. The acetylation causes a conformational changes in the histones, which allows for transcriptional machinery to access DNA. The bromodomains of PCAF have three major points of contact that allow for site-specific histone recognition. First, the <scene name='Sandbox_Reserved_654/Kac50/1'>acetylated lysine</scene> of the target protein enters a <scene name='Sandbox_Reserved_654/Kac50_pocket/1'>hydrophobic pocket</scene> embedded between the ZA and BC loops at the bottom of the protein. The Asn803 residue in the bromodomain forms a hydrogen bond with the amide nitrogen of the acetyl-lysine. Next, residues in the ZA and/or BC loops interact with residues adjacent to the acetyl-lysine, which reinforces the acetyl-lysine binding in the bromodomain. Finally, additional residues in the ZA and BC loops that face opposite to the bromodomain form hydrophobic and/ or electrostatic interaction with the target protein 3 residues away from the acetyl-lysine. This residue clamps on the BC loop together with the acetyl-lysine side chain that is bound inside the hydrophobic pocket of the bromodomain<ref name =aaa/>.

Sandbox Reserved 654: Difference between revisions

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Revision as of 01:29, 20 November 2012 view source Robert Cutrell (talk \| contribs) 64 edits No edit summary ← Older edit		Revision as of 02:00, 20 November 2012 view source Robert Cutrell (talk \| contribs) 64 edits No edit summary Newer edit →
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	[[Image:F1.medium.gif \|thumb\|250 px\|right\| Acetylation of the lysine and its effects on chromatin remodeling.]]		[[Image:F1.medium.gif \|thumb\|250 px\|right\| Acetylation of the lysine and its effects on chromatin remodeling.]]
	The mechanism of protein-protein interaction for the bromodomain of PCAF with target proteins, such as histones<ref name =aaa>Zeng, L. et al (2008) Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 16: 643–652 [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339198/]</ref> and Tat<ref name=aa/>, begins with the acetylation of lysine residues. The acetylation causes a conformational changes in the histones, which allows for transcriptional machinery to access DNA. The bromodomains of PCAF have three major points of contact that allow for site-specific histone recognition. First, the <scene name='Sandbox_Reserved_654/Kac50/1'>acetylated lysine</scene> of the target protein enters a hydrophobic pocket embedded between the ZA and BC loops at the bottom of the protein. The Asn803 residue in the bromodomain forms a hydrogen bond with the amide nitrogen of the acetyl-lysine. Next, residues in the ZA and/or BC loops interact with residues adjacent to the acetyl-lysine, which reinforces the acetyl-lysine binding in the bromodomain. Finally, additional residues in the ZA and BC loops that face opposite to the bromodomain form hydrophobic and/ or electrostatic interaction with the target protein 3 residues away from the acetyl-lysine. This residue clamps on the BC loop together with the acetyl-lysine side chain that is bound inside the hydrophobic pocket of the bromodomain<ref name =aaa/>.		The mechanism of protein-protein interaction for the bromodomain of PCAF with target proteins, such as histones<ref name =aaa>Zeng, L. et al (2008) Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 16: 643–652 [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339198/]</ref> and Tat<ref name=aa/>, begins with the acetylation of lysine residues. The acetylation causes a conformational changes in the histones, which allows for transcriptional machinery to access DNA. The bromodomains of PCAF have three major points of contact that allow for site-specific histone recognition. First, the <scene name='Sandbox_Reserved_654/Kac50/1'>acetylated lysine</scene> of the target protein enters a <scene name='Sandbox_Reserved_654/Kac50_pocket/1'>hydrophobic pocket</scene> embedded between the ZA and BC loops at the bottom of the protein. The Asn803 residue in the bromodomain forms a hydrogen bond with the amide nitrogen of the acetyl-lysine. Next, residues in the ZA and/or BC loops interact with residues adjacent to the acetyl-lysine, which reinforces the acetyl-lysine binding in the bromodomain. Finally, additional residues in the ZA and BC loops that face opposite to the bromodomain form hydrophobic and/ or electrostatic interaction with the target protein 3 residues away from the acetyl-lysine. This residue clamps on the BC loop together with the acetyl-lysine side chain that is bound inside the hydrophobic pocket of the bromodomain<ref name =aaa/>.