Sandbox Reserved 1101: Difference between revisions

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====Conformational change of the five-helix bundle====

The dimerization of the spidroin by the NTD domain begins by a rearrangement of the five-helix bundle during the monomer to dimer transition. An acidification along the spinning duct results in a conformational change of the NTD. So, for the NTD dimerization, a lowering of pH from 7 to 6 is important. Then, a subunit selects a partner with a complementary binding interface. When the NTD forms a dimer, its positive and negative poles are opposed, creating an environment conducive to salt bridges formation. Moreover, dimerization is really triggered and stabilized by protonation of some residues. Studies have also shown that a lowering more important of the pH ~~stabilize~~ even more the dimer. The plasticity of the dimer interface could also be a factor of the conformational selection during transition from monomer to dimer or during the transition from loosely to stably dimer.

The dimerization of the spidroin by the NTD domain begins by a rearrangement of the five-helix bundle during the monomer to dimer transition. An acidification along the spinning duct results in a conformational change of the NTD. So, for the NTD dimerization, a lowering of pH from 7 to 6 is important. Then, a subunit selects a partner with a complementary binding interface. When the NTD forms a dimer, its positive and negative poles are opposed, creating an environment conducive to salt bridges formation. Moreover, dimerization is really triggered and stabilized by protonation of some residues. Studies have also shown that a lowering more important of the pH stabilizes even more the dimer. The plasticity of the dimer interface could also be a factor of the conformational selection during transition from monomer to dimer or during the transition from loosely to stably dimer.

====Interactions====

Line 53:

Different types of interactions occur between specific residues during the NTD dimerization. Asp40, Lys65, Asp39 and Glu84 residues have been identified as being particularly important.

In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the intramolecular handshake interaction. The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that Asp39 is essential for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the variability in the interactions that take place to Lys65. This variability provides a mechanism for plasticity in the dimer interface allowing the transition from loosely to stably associated dimer.

In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the intramolecular handshake interaction. The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6 Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1 Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that Asp39 is essential for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the variability in the interactions that take place to Lys65. This variability provides a mechanism for plasticity in the dimer interface allowing the transition from loosely to stably associated dimer.

Another intramolecular handshake interaction occurs also between <scene name='82/829354/Asp17a-asp53a_interaction/1'>Asp17 and Asp53 in subunit A</scene>. This interaction doesn’t exist in subunit B because of the orientation of subunit A with respect to subunit B, Asp17 and Asp53 are too far away in order to engage this interaction.

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These asymmetric contacts play a well-defined role in dimer formation in many species of spiders but in ''N. clavipes'' several other novel interactions occur. For example, in comparison with the ''Euprosthenops australis'' NTD, ''N. clavipes'' NTD engage more than 38,5% of novel interactions. These ones result from the distinct topology of the three helices (H2, H3 and H5) compared to other species. Indeed, the specific angles at which the H2, H3 and H5 helices cross their counterparts in the asymmetric interface allow the correct positioning of residues and the establishment of these interactions.

~~Residues T47B, M55B and K54B are more buried at the dimer interface creating specific contacts.~~

::*''Van der Waals''

Residues T47B, M55B and K54B are more buried at the dimer interface creating specific contacts.

<scene name='82/829354/T47b-i48a-a51a-l69a/1'>T47B engage in Van Der Waals contacts with I48A, A51A and L69A residues</scene>. Also, <scene name='82/829354/M55b-d40a-t43a/2'>M55B is commited in Van Der Waals interactions with D40A and T43A</scene>. In subunits H2A and H2B, T47A and A51B engage in a Van Der Waals interaction of 4,1 Å, and that contribute to the plasticity of the dimer interface.

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@@ Line 44: / Line 44: @@
 ====Conformational change of the five-helix bundle====
-The dimerization of the spidroin by the NTD domain begins by a rearrangement of the five-helix bundle during the monomer to dimer transition. An acidification along the spinning duct results in a conformational change of the NTD. So, for the NTD dimerization, a lowering of pH from 7 to 6 is important.  Then, a subunit selects a partner with a complementary binding interface. When the NTD forms a dimer, its positive and negative poles are opposed, creating an environment conducive to salt bridges formation. Moreover, dimerization is really triggered and stabilized by protonation of some residues. Studies have also shown that a lowering more important of the pH stabilize even more the dimer. The plasticity of the dimer interface could also be a factor of the conformational selection during transition from monomer to dimer or during the transition from loosely to stably dimer.
+The dimerization of the spidroin by the NTD domain begins by a rearrangement of the five-helix bundle during the monomer to dimer transition. An acidification along the spinning duct results in a conformational change of the NTD. So, for the NTD dimerization, a lowering of pH from 7 to 6 is important.  Then, a subunit selects a partner with a complementary binding interface. When the NTD forms a dimer, its positive and negative poles are opposed, creating an environment conducive to salt bridges formation. Moreover, dimerization is really triggered and stabilized by protonation of some residues. Studies have also shown that a lowering more important of the pH stabilizes even more the dimer. The plasticity of the dimer interface could also be a factor of the conformational selection during transition from monomer to dimer or during the transition from loosely to stably dimer.
 ====Interactions====
@@ Line 53: / Line 53: @@
 Different types of interactions occur between specific residues during the NTD dimerization. Asp40, Lys65, Asp39 and Glu84 residues have been identified as being particularly important.
-In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the intramolecular handshake interaction. The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that Asp39 is essential for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the variability in the interactions that take place to Lys65. This variability provides a mechanism for plasticity in the dimer interface allowing the transition from loosely to stably associated dimer.
+In one side, <scene name='82/829354/Asp40b_glu84b/1'>Asp40 and Glu84 of subunit B</scene> engage in the intramolecular handshake interaction. The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges. <scene name='82/829354/Lys_65-asp39_interaction/2'>Lys65 of subunit A and Asp39 of subunit B</scene> engage in a short-range intermolecular salt bridge of 2,6 Å. In the other side, <scene name='82/829354/Lys_65b-asp40a_interaction/1'>Asp40 of subunit A and Lys65 of subunit B</scene> engage in a short-range intermolecular salt bridge of 3,1 Å. Asp39 is not involved in this part of the dimer. The structure of ''N. clavipes'' dimer interface differs from those of other species due to the asymmetric nature of the interface and the involvement of Asp39. It has been reported that Asp39 is essential for the NTD dimerization in other species of spiders and seems to be also important in ''N.clavipes''. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp39 and Asp40 and this allows the variability in the interactions that take place to Lys65. This variability provides a mechanism for plasticity in the dimer interface allowing the transition from loosely to stably associated dimer.
 Another intramolecular handshake interaction occurs also between <scene name='82/829354/Asp17a-asp53a_interaction/1'>Asp17 and Asp53 in subunit A</scene>. This interaction doesn’t exist in subunit B because of the orientation of subunit A with respect to subunit B, Asp17 and Asp53 are too far away in order to engage this interaction.
@@ Line 60: / Line 60: @@
 These asymmetric contacts play a well-defined role in dimer formation in many species of spiders but in ''N. clavipes'' several other novel interactions occur. For example, in comparison with the ''Euprosthenops australis'' NTD, ''N. clavipes'' NTD engage more than 38,5% of novel interactions.  These ones result from the distinct topology of the three helices (H2, H3 and H5) compared to other species. Indeed, the specific angles at which the H2, H3 and H5 helices cross their counterparts in the asymmetric interface allow the correct positioning of residues and the establishment of these interactions.
-Residues T47B, M55B and K54B are more buried at the dimer interface creating specific contacts.
 ::*''Van der Waals''
+Residues T47B, M55B and K54B are more buried at the dimer interface creating specific contacts.
 <scene name='82/829354/T47b-i48a-a51a-l69a/1'>T47B engage in Van Der Waals contacts with I48A, A51A and L69A residues</scene>. Also, <scene name='82/829354/M55b-d40a-t43a/2'>M55B is commited in Van Der Waals interactions with D40A and T43A</scene>. In subunits H2A and H2B, T47A and A51B engage in a Van Der Waals interaction of 4,1 Å, and that contribute to the plasticity of the dimer interface.