User:João Victor Paccini Coutinho/Sandbox 1

Frataxin is a protein capable of storing, releasing and detoxifying intracellular iron. A mutation in this protein can trigger the Friedreich's ataxia, a neurodegenerative disease caused due to incapacity to form iron-sulfur groups necessary to activating the mitochondrial enzyme involved in the electron transportation chain, aconitase.

It is presented as a polymeric molecule that is composed of several subunits of a trimer of organized units, which exhibit several interactions between one another to maintain the structure of the trimer, (?) for example the interactions of the N-terminal chains with the interacions of the N-terminals between each other bases, forming not only the core of the trimer, but the canal as well.

In the box at the right, it is possible to see its <scene name='78/788815/Spacefill_model/1'>general structure</scene> in a space-fill model, in which each color represents a different monomer.

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>.

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 '''yellow'''. 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 yellow, interact with the adjacent monomer. Taking a <scene name='78/788815/Stabilization_of_trimer_zoom_1/3'>closer look</scene>, we figure out how the N-terminal loop of the first monomer, here described as chain A, is placed with respect to chain B.

But how exactly is this process possible? If we <scene name='78/788815/Stabilization_of_trimer_resid1/4'>explore even further</scene> the details, we see some residues close enough to interact. Those are their <scene name='78/788815/All_residues_at_end/1'>names</scene> specified by their positions.

Let's now <scene name='78/788815/All_residues_at_end_transparen/1'>view</scene> (...) We can <scene name='78/788815/All_residues_at_end_transp_hyd/1'>color</scene> the residues differently according to their hydrophilicity. Polar residues are represented in pink, while the hydrophobic ones appear gray. 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, Pro 62, Val 65 and Leu 68, shown in dark-blue, are packed against the polar uncharged aminoacids Thr 110 and Thr 118, in red. 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 Glu 64 and Thr 118. 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 . Pay special attention it the role of the carbonyl oxygen of Glu 64 involved in the hydrogen bonding.

Now, we can devote our attention to examine what occurs at the <scene name='78/788815/Stabilization_of_trimer_base/1'>base of the N-terminal region</scene>.Those are the <scene name='78/788815/Residues_at_base_-_2/1'>residues involved</scene> in it. If we color the residues according to their <scene name='78/788815/Residues_at_base_-_2_polarity/1'>polarity</scene>,

<scene name='78/788815/Residues_at_right/1'>At the right</scene>, we see

If we take a closer look to the <scene name='78/786054/125-128/1'><scene name='78/788815/Central_pore_residue_216/1'>central channel</scene></scene> <scene name='78/788815/Residues_at_right/3'>thing</scene>