NF-Y Transcription Factor Sandbox
From Proteopedia
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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/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" />. | ||
Revision as of 14:44, 7 November 2013
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