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I was reading a paper and came across a sentence (highlighted one) about NMR spectroscopy.

Several Leishmania Rabs, like Rab1, Rab5a, Rab5b, and Rab7, have been functionally characterized. LdRab5a is a GTPase that has been shown to bind to GTP and hydrolyze it to GDP. It specifically regulates fluid-phase endocytosis. Although the G1–G5 loop sequences are well conserved in LdRab5, it has unique interswitch region with substitutions and a 20-residue insertion with respect to the human Rab5. The unique insertion feature of LdRab5a prompted us to choose NMR spectroscopy as the most suitable technique for determining its structure.

It is pertinent to mention that NMR solution structure has not been determined for any Rab protein from any organism. This would also provide the opportunity for exploring the residue-specific dynamics for LdRab5a in particular and reveal the general implications for the Rab family of proteins. Hence, we have undertaken the determination of solution structure and characterization of backbone relaxation dynamics for LdRab5a by using NMR spectroscopy. However, stabilization of LdRab5a through systematic and specific mutations and deletions was necessary to arrive at a construct that was stable enough for recording long multidimensional NMR experiments.

Why do we need to have a unique interswitch region so as to use the NMR spectroscopy technique?

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    $\begingroup$ Well you can't analyse switching with crystallography, 'cause you get only one structure. NMR can provide insight into dynamic behaviour. $\endgroup$ – Mithoron Jan 15 at 20:48
  • $\begingroup$ You don't need to have this. The rest of the structure was already clear, it was just about this "interswitch" (I have no idea what that is exactly). They had the background and equipment to do the analysis, and it proved sucessful, I guess. Read the rest of the paper, and the references within, and you will likely find that the idea wasn't a very long shot. $\endgroup$ – Karl Jan 15 at 21:11
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    $\begingroup$ Here is a link to the paper (not yet available on PubMedCentral) $\endgroup$ – Karsten Theis Jan 15 at 22:59
  • $\begingroup$ I don't think describing switching behavior was (directly) the goal in this case. Also, in principle you can capture (crystallize) a protein in different conformations - not easy and not a dynamic description but this can provide structures. $\endgroup$ – Buck Thorn Jan 16 at 9:20
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The insert in the Ld ortholog occurs in a beta sheet and suggests the presence of additional strands in that sheet compared to the human variant. The structure of the human protein has been determined by crystallography. It would therefore appear that it should be possible to determine the structure of the Ld protein the same way (via crystallography), provided a crystallizable construct is identified.

Based on the available reference provided, the insertion feature from LdRab5a appears to make the protein unstable in vitro and difficult to crystallize, leaving NMR as the only good alternative for a structure determination. However, it seems the insertion feature also rendered the protein too unstable to be able to complete long NMR experiments, so the authors chose to remove the insert in order to stabilize the protein and perform NMR.

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