NF-Y Transcription Factor Sandbox - Revision history

Michele White at 16:08, 7 November 2013

Michele White — Thu, 07 Nov 2013 16:08:34 GMT

←Older revision		Revision as of 16:08, 7 November 2013
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	===DNA Interaction===		===DNA Interaction===

-	NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>~~electrostatic~~ interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.	+	NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>ionic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

	== References ==		== References ==
	<references />		<references />

Alyssa Wall at 16:03, 7 November 2013

Alyssa Wall — Thu, 07 Nov 2013 16:03:38 GMT

←Older revision		Revision as of 16:03, 7 November 2013
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	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />~~({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}})~~. The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene>({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}) that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

Alyssa Wall at 15:56, 7 November 2013

Alyssa Wall — Thu, 07 Nov 2013 15:56:37 GMT

←Older revision		Revision as of 15:56, 7 November 2013
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	== Protein Function ==		== Protein Function ==

-	<p>~~These~~ PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.</p>	+	<p>The post-translational modifications (PTMs) that NF-Y transcription factor is associated with aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.</p>
	<p>NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.</p>		<p>NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.</p>

Alyssa Wall at 15:52, 7 November 2013

Alyssa Wall — Thu, 07 Nov 2013 15:52:46 GMT

←Older revision		Revision as of 15:52, 7 November 2013
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-	<StructureSection load='4awl' size='350' side='right' caption='Structure of ~~Variola Topoisomerase 1B~~ with DNA (PDB entry [[~~3igc~~]])' scene=''>	+	<StructureSection load='4awl' size='350' side='right' caption='Structure of NF-Y Transcription Factor with DNA (PDB entry [[4awl]])' scene=''>
	== Overview ==		== Overview ==

Michele White at 14:58, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:58:19 GMT

←Older revision		Revision as of 14:58, 7 November 2013
Line 9:		Line 9:
	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the ~~<scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene>~~	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
-	<scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+

Michele White at 14:57, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:57:35 GMT

←Older revision		Revision as of 14:57, 7 November 2013
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	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene>
		+	<scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

Michele White at 14:49, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:49:44 GMT

←Older revision		Revision as of 14:49, 7 November 2013
Line 9:		Line 9:
	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

Michele White at 14:45, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:45:04 GMT

←Older revision		Revision as of 14:45, 7 November 2013
Line 9:		Line 9:
	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the ~~<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene>~~	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
-	<scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+

Michele White at 14:44, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:44:02 GMT

←Older revision		Revision as of 14:44, 7 November 2013
Line 9:		Line 9:
	<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.		<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

-	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.	+	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene>
		+	<scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

Michele White at 14:37, 7 November 2013

Michele White — Thu, 07 Nov 2013 14:37:53 GMT

←Older revision		Revision as of 14:37, 7 November 2013
Line 11:		Line 11:
	<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.		<br>The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

-	<br>Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

	== Protein Function ==		== Protein Function ==
Line 17:		Line 16:
	<p>These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.</p>		<p>These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.</p>
	<p>NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.</p>		<p>NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.</p>
		+
		+	<br>The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

	===DNA Interaction===		===DNA Interaction===