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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.

Structural highlights

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Applications in Biotechnology

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References

1. ↑ 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
2. ↑ 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