Sandbox Reserved 1101: Difference between revisions
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'''5IZ2 : Crystal structure of the ''N. Clavipes'' spidroin NTD''' | '''5IZ2 : Crystal structure of the ''N. Clavipes'' spidroin NTD''' | ||
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5IZ2 is the NTD domain of a protein called spidroin[https://en.wikipedia.org/wiki/Spidroin]. This protein is a component of the dragline silk. | 5IZ2 is the '''NTD domain''' of a protein called '''spidroin'''[https://en.wikipedia.org/wiki/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. | ||
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. | |||
The NTD domain of these proteins is very important because it plays a major role in the dimerisation of spidroins. Indeed, thanks to the NTD organization, 2 spidroins can be combined, leading to the production of fibres with exceptional physical qualities. | The NTD domain of these proteins is very important because it plays a major role in the dimerisation of spidroins. Indeed, thanks to the NTD organization, 2 spidroins can be combined, leading to the production of fibres with exceptional physical qualities. | ||
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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. | ||
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. So, this create a dipole moment. | 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. So, this create a dipole moment. 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. | |||
Compared with spidroin of other species of spider, the 2 subunits (A and B) of the NTD domain 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. | |||
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In one side, Asp40 and Glu84 of subunit A engage in the intramolecular handshake interaction. Lys65 of subunit A and Asp39 of subunit B engage in a short-range intermolecular salt bridge of 2,6Å. In the other side, Asp40 of subunit A and Lys65 of subunit B engage in a short-range intermolecular salt bridge of 3,1Å. Asp39 is not involved in this part of the dimer. | In one side, Asp40 and Glu84 of subunit A engage in the intramolecular handshake interaction. Lys65 of subunit A and Asp39 of subunit B engage in a short-range intermolecular salt bridge of 2,6Å. In the other side, Asp40 of subunit A and Lys65 of subunit B 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 (16). The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges between Asp39 and Lys65 and between Asp40 and Lys65. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp96 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. | 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 (16). The asymmetric nature and the difference of topology of the subunits allow the formation of salt bridges between Asp39 and Lys65 and between Asp40 and Lys65. These interactions make subunits alignment better. Acidic residues are conserved around residues Asp96 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. | ||
