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5IZ2 : Crystal structure of the N. Clavipes spidroin NTD
5IZ2 is the NTD domain of a protein called spidroin[1]. 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. 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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This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Global structure of the N. Clavipes Spidroin-1
Monomer structure of the spidroin NTD domain
One monomer of NTD is composed of 2 subunits, A and B, each of them composed of 5 α-helices. There is also a chain Z composed of 3 amino acids (Ser, Tyr, Gly), but it role is not well established yet.
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. And, as the subunits A and B are organized antiparallel, it allows an access to charges poles.
Dimerization of the spidroin by the NTD domain
The dimerization of the spidroin by the NTD domain begins by a rearrangement of the five-helix bundle occurs during the monomer to dimer transition. An acidification of the medium 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.
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, 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.
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Structural highlights
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
