Sandbox Reserved 1101: Difference between revisions

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5IZ2 is the '''NTD domain''' of a protein called [https://en.wikipedia.org/wiki/Spidroin_ spidroin]. This protein is a component of the '''dragline silk'''. There are several types of spidroin, and those that form the core of the silk are called '''MaSp1''' (Major ampullate Spidroin-1), which are produced by in the major ampullate gland of spiders.

5IZ2 is the '''NTD domain''' of a protein called [https://en.wikipedia.org/wiki/Spidroin_ spidroin]. This protein is a component of the '''dragline silk'''. There are several types of spidroin, and those that form the core of the silk are called '''MaSp1''' (Major ampullate Spidroin-1), which are produced by in the major ampullate gland of spiders<ref name="Atkison"/>.

The NTD domain of these proteins is very important since it plays a major role in the '''dimerization of spidroins'''. Indeed, thanks to the NTD organization, two spidroins can be combined, leading to the production of fibres with exceptional physical qualities.

The NTD domain of these proteins is very important since it plays a major role in the '''dimerization of spidroins'''<ref name="Atkison"/>. Indeed, thanks to the NTD organization, two spidroins can be combined, leading to the production of fibres with exceptional physical qualities<ref name="José">José Roberto Aparecido dos Santos-Pinto, Helen Andrade Arcuri, Helga Priewalder, Heliana Clara Salles, Mario Sergio Palma and Gert Lubec, 2015. Structural Model for the Spider Silk Protein Spidroin‑1, Journal of Proteome research, 14, p.3859-3870.</ref>.

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One monomer of NTD (N-Terminal Domain) is composed of 5 parallel [https://en.wikipedia.org/wiki/Alpha_helix_ α-helix] (<scene name='82/829354/A/1'>H1 to H5</scene>).

One monomer of NTD (N-Terminal Domain) is composed of 5 parallel [https://en.wikipedia.org/wiki/Alpha_helix_ α-helix] (<scene name='82/829354/A/1'>H1 to H5</scene>)<ref name="Cadle"/>.

In each subunit, the orientation of helices 2, 3 and 5 is different from the orientation of helices 1 and 4. Indeed, helices 1 and 4 form the rigid body of the NTD domain, while helices 2, 3 and 5 are involved in intermolecular contacts, so they play an important role in the dimerization process.

In each subunit, the orientation of helices 2, 3 and 5 is different from the orientation of helices 1 and 4. Indeed, helices 1 and 4 form the rigid body of the NTD domain, while helices 2, 3 and 5 are involved in intermolecular contacts, so they play an important role in the dimerization process<ref name="Atkison"/>.

Moreover, at the opposite extremities of each subunits of the monomer there are '''clusters of acidic residus''' (Asp36, Asp39, Asp40, Glu79, Asp91) in one part, and '''clusters of basic residus''' (Lys54, Arg57, Lys60, Lys64, Lys65) in the other part. In addition to this, the subunits A and B are organized antiparallel, which allows an access to charges poles.

The charged residues (the acidic and basic ones) are responsible for creating a '''dipole moment''', which therefore implies a non-uniform charge arrangement within the subunits. This is important for the dimerization process, that is why they are highly conserved residues.

The charged residues (the acidic and basic ones) are responsible for creating a '''dipole moment''', which therefore implies a non-uniform charge arrangement within the subunits. This is important for the dimerization process, that is why they are highly conserved residues<ref name="Atkison"/>.

Compared with spidroin of other species of spider, the 2 subunits (A and B) of the dimerized NTD of the spidroin produced by ''N. Clavipes'' are slightly different, due to a '''different helices arrangement'''. So they do not completely overlap. This allows the creation of '''new intermolecular contact networks'''. There is also a <scene name='82/829354/Chain_z/1'>chain Z</scene> composed of 3 amino acids (Ser, Tyr, Gly), but it role is not well established yet.

Compared with spidroin of other species of spider, the 2 subunits (A and B) of the dimerized NTD of the spidroin produced by ''N. Clavipes'' are slightly different, due to a '''different helices arrangement'''. So they do not completely overlap. This allows the creation of '''new intermolecular contact networks'''. There is also a <scene name='82/829354/Chain_z/1'>chain Z</scene> composed of 3 amino acids (Ser, Tyr, Gly), but it role is not well established yet<ref name="Atkison"/>.

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@@ Line 5: / Line 5: @@
 ----
-IZ2 is the '''NTD domain''' of a protein called [https://en.wikipedia.org/wiki/Spidroin_ spidroin]. This protein is a component of the '''dragline silk'''. There are several types of spidroin, and those that form the core of the silk are called '''MaSp1''' (Major ampullate Spidroin-1), which are produced by in the major ampullate gland of spiders.
+IZ2 is the '''NTD domain''' of a protein called [https://en.wikipedia.org/wiki/Spidroin_ spidroin]. This protein is a component of the '''dragline silk'''. There are several types of spidroin, and those that form the core of the silk are called '''MaSp1''' (Major ampullate Spidroin-1), which are produced by in the major ampullate gland of spiders<ref name="Atkison"/>.
-The NTD domain of these proteins is very important since it plays a major role in the '''dimerization of spidroins'''. Indeed, thanks to the NTD organization, two spidroins can be combined, leading to the production of fibres with exceptional physical qualities.
+The NTD domain of these proteins is very important since it plays a major role in the '''dimerization of spidroins'''<ref name="Atkison"/>. Indeed, thanks to the NTD organization, two spidroins can be combined, leading to the production of fibres with exceptional physical qualities<ref name="José">José Roberto Aparecido dos Santos-Pinto, Helen Andrade Arcuri, Helga Priewalder, Heliana Clara Salles, Mario Sergio Palma and Gert Lubec, 2015. Structural Model for the Spider Silk Protein Spidroin‑1, Journal of Proteome research, 14, p.3859-3870.</ref>.
@@ Line 20: / Line 19: @@
 <Structure load='5iz2' size='350' frame='true' align='right' caption='NTD monomer' scene='Insert optional scene name here' />
-One monomer of NTD (N-Terminal Domain) is composed of 5 parallel [https://en.wikipedia.org/wiki/Alpha_helix_ α-helix] (<scene name='82/829354/A/1'>H1 to H5</scene>).
+One monomer of NTD (N-Terminal Domain) is composed of 5 parallel [https://en.wikipedia.org/wiki/Alpha_helix_ α-helix] (<scene name='82/829354/A/1'>H1 to H5</scene>)<ref name="Cadle"/>.
-In each subunit, the orientation of helices 2, 3 and 5 is different from the orientation of helices 1 and 4. Indeed, helices 1 and 4 form the rigid body of the NTD domain, while helices 2, 3 and 5 are involved in intermolecular contacts, so they play an important role in the dimerization process.
+In each subunit, the orientation of helices 2, 3 and 5 is different from the orientation of helices 1 and 4. Indeed, helices 1 and 4 form the rigid body of the NTD domain, while helices 2, 3 and 5 are involved in intermolecular contacts, so they play an important role in the dimerization process<ref name="Atkison"/>.
 Moreover, at the opposite extremities of each subunits of the monomer there are '''clusters of acidic residus''' (Asp36, Asp39, Asp40, Glu79, Asp91) in one part, and '''clusters of basic residus''' (Lys54, Arg57, Lys60, Lys64, Lys65) in the other part. In addition to this, the subunits A and B are organized antiparallel, which allows an access to charges poles.
-The charged residues (the acidic and basic ones) are responsible for creating a '''dipole moment''', which therefore implies a non-uniform charge arrangement within the subunits. This is important for the dimerization process, that is why they are highly conserved residues.
+The charged residues (the acidic and basic ones) are responsible for creating a '''dipole moment''', which therefore implies a non-uniform charge arrangement within the subunits. This is important for the dimerization process, that is why they are highly conserved residues<ref name="Atkison"/>.
-Compared with spidroin of other species of spider, the 2 subunits (A and B) of the dimerized NTD of the spidroin produced by ''N. Clavipes'' are slightly different, due to a '''different helices arrangement'''. So they do not completely overlap. This allows the creation of '''new intermolecular contact networks'''. There is also a <scene name='82/829354/Chain_z/1'>chain Z</scene> composed of 3 amino acids (Ser, Tyr, Gly), but it role is not well established yet.
+Compared with spidroin of other species of spider, the 2 subunits (A and B) of the dimerized NTD of the spidroin produced by ''N. Clavipes'' are slightly different, due to a '''different helices arrangement'''. So they do not completely overlap. This allows the creation of '''new intermolecular contact networks'''. There is also a <scene name='82/829354/Chain_z/1'>chain Z</scene> composed of 3 amino acids (Ser, Tyr, Gly), but it role is not well established yet<ref name="Atkison"/>.