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User:Rebeca B. Candia/Sandbox 1

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However, to cover some important aspects of the structure and function of the molecule, it is particularly useful to represent its <scene name='78/788815/Secondary_structure/1'>secondary structure patterns</scene>.
However, to cover some important aspects of the structure and function of the molecule, it is particularly useful to represent its <scene name='78/788815/Secondary_structure/1'>secondary structure patterns</scene>.
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The trimeric structure of frataxin is stabilized by the <scene name='78/788815/Stabilization_of_trimer/1'>N-terminal extensions</scene> of each subunit, shown in <span style="color:yellow;background-color:darkgrey;font-weight:bold;">yellow</span>. Viewing <scene name='78/788815/Stabilization_of_trimer_back/2'>the other side</scene> of the molecule, we can notice how the N-terminal extensions, still in <span style="color:yellow;background-color:darkgrey;font-weight:bold;">yellow</span>, interact with the <font color='rosybrown'><b>adjacent monomer</b></font>. Taking a <scene name='78/788815/Stabilization_of_trimer_zoom_1/3'>closer look</scene>, it is possible figure out how the N-terminal loop of the first monomer, here described as chain A, is placed with respect to chain B.
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The trimeric structure of frataxin is mainly stabilized by the <scene name='78/788815/Stabilization_of_trimer/1'>N-terminal extensions</scene> of each subunit, shown in <span style="color:yellow;background-color:darkgrey;font-weight:bold;">yellow</span>. These consist of loops higly flexible in the monomer, but interestly, when in the trimeric arragement, they play a crucial role in mantaining it. Viewing <scene name='78/788815/Stabilization_of_trimer_back/2'>the other side</scene> of the molecule, we can notice how the N-terminal extensions, still in <span style="color:yellow;background-color:darkgrey;font-weight:bold;">yellow</span>, interact with the <font color='rosybrown'><b>adjacent monomer</b></font>. Taking a <scene name='78/788815/Stabilization_of_trimer_zoom_1/3'>closer look</scene>, it is possible figure out how the N-terminal loop of the first monomer, here described as chain A, is placed with respect to chain B.
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But how exactly is this process possible? <scene name='78/788815/Stabilization_of_trimer_resid1/4'>Exploring even further</scene> the details, it is possible to see some residues close enough to interact. The names associated with their positions can be seen by <scene name='78/788815/All_residues_at_end/1'>clicking here</scene>.
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<scene name='78/788815/Stabilization_of_trimer_resid1/4'>Exploring even further</scene> the details, it is possible to see some residues close enough to interact. The names associated with their positions can be seen by <scene name='78/788815/All_residues_at_end/1'>clicking here</scene>.
<scene name='78/788815/All_residues_at_end_transparen/3'>Click here</scene> to rotate this regio. We can <scene name='78/788815/All_residues_at_end_transp_hyd/1'>color</scene> the residues differently according to their hydrophilicity. In this new color scheme, <font color='fuchsia'><b>polar residues are represented in pink</b></font> while the <font color='darkgrey'><b>hydrophobic ones appear gray</b></font>. Now we are about to <scene name='78/788815/All_residues_at_end_transp_tur/1'>color</scene> all those relevant residues to specify their interactions. The <scene name='78/788815/All_residues_at_end_transp_pac/1'>package of hydrophobic residues</scene> can be seen. Here,<font color='navy'><b> Pro 62, Val 65 and Leu 68, shown in dark-blue</b></font>, are packed against the <font color='red'><b>polar uncharged aminoacids Thr 110 and Thr 118, in red</b></font> (other aminoacids ar shown in <font color='mediumturquoise'><b>turquoise</b></font>). This interaction among the hydrophobic residues contributes to the maneintance of the loop configuration of the N-terminal region at its extremity. Another important interaction is the <scene name='78/788815/All_residues_at_end_transp_bon/1'>hydrogen bond</scene> formed between <font color='orangered'><b>Glu 64</b></font> and <font color='blueviolet'><b>Thr 118</b></font>. Those are the only residues able to form hydrogen bond, since the <scene name='78/788815/Hydrogen_bond_n-term-correct/3'>distance separating them</scene> is within a range of approximately 3 Å (or 0.3 nm). <scene name='78/788815/Hydrogen_bond_n-term-correct/4'>In this image</scene>, pay special attention it the role of the <font color='red'><b>carbonyl oxygen</b></font> of Glu 64 involved in the hydrogen bonding. In this color scheme, <font color='grey'><b> carbons are grey</b></font>, <font color='red'><b>oxygens are red</b></font> and <font color='blue'><b>nitrogens are blue</b></font>.
<scene name='78/788815/All_residues_at_end_transparen/3'>Click here</scene> to rotate this regio. We can <scene name='78/788815/All_residues_at_end_transp_hyd/1'>color</scene> the residues differently according to their hydrophilicity. In this new color scheme, <font color='fuchsia'><b>polar residues are represented in pink</b></font> while the <font color='darkgrey'><b>hydrophobic ones appear gray</b></font>. Now we are about to <scene name='78/788815/All_residues_at_end_transp_tur/1'>color</scene> all those relevant residues to specify their interactions. The <scene name='78/788815/All_residues_at_end_transp_pac/1'>package of hydrophobic residues</scene> can be seen. Here,<font color='navy'><b> Pro 62, Val 65 and Leu 68, shown in dark-blue</b></font>, are packed against the <font color='red'><b>polar uncharged aminoacids Thr 110 and Thr 118, in red</b></font> (other aminoacids ar shown in <font color='mediumturquoise'><b>turquoise</b></font>). This interaction among the hydrophobic residues contributes to the maneintance of the loop configuration of the N-terminal region at its extremity. Another important interaction is the <scene name='78/788815/All_residues_at_end_transp_bon/1'>hydrogen bond</scene> formed between <font color='orangered'><b>Glu 64</b></font> and <font color='blueviolet'><b>Thr 118</b></font>. Those are the only residues able to form hydrogen bond, since the <scene name='78/788815/Hydrogen_bond_n-term-correct/3'>distance separating them</scene> is within a range of approximately 3 Å (or 0.3 nm). <scene name='78/788815/Hydrogen_bond_n-term-correct/4'>In this image</scene>, pay special attention it the role of the <font color='red'><b>carbonyl oxygen</b></font> of Glu 64 involved in the hydrogen bonding. In this color scheme, <font color='grey'><b> carbons are grey</b></font>, <font color='red'><b>oxygens are red</b></font> and <font color='blue'><b>nitrogens are blue</b></font>.

Revision as of 03:05, 17 June 2018

Frataxin

Caption for this structure

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References


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Proteopedia Page Contributors and Editors (what is this?)

Rebeca B. Candia

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