Fitting SPMT Models to Plasmodium Sporozoite

Initially, T. gondii SPMT model (PDB 7MIZ) was fitted to the P. falciparum sporozoite SPMT EM map as a rigid body in Chimera^{72 (link)}, the fit was then visualised in ChimeraX^{73 (link)}. The resulting fit was unambiguous with TgTrxL2 (which is not expressed in Plasmodium but is part of the Toxoplasma ILH) outside and the remaining protein chains inside the map. Due to the difference in ellipticity between the P. falciparum and T. gondii maps, protofilaments and TrxL1/SPM1 half arcs were fitted as separate units. Structural prediction of PfTrxL1 (https://alphafold.ebi.ac.uk/entry/Q8I2W0)^{79 (link)} was aligned with TgTrxL1 (PDB 7MIZ) using matchmaker^{80 (link)} in ChimeraX.

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Ferreira J.L., Pražák V., Vasishtan D., Siggel M., Hentzschel F., Binder A.M., Pietsch E., Kosinski J., Frischknecht F., Gilberger T.W, & Grünewald K. (2023). Variable microtubule architecture in the malaria parasite. Nature Communications, 14, 1216.

Publication 2023

Arcs Body Maps Plasmodium Protein Rigid Sporozoite Toxoplasma

Corresponding Organization :

Other organizations : Centre for Structural Systems Biology, Heidelberg University, Bernhard Nocht Institute for Tropical Medicine, Leibniz Institute of Virology (LIV)

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Variable analysis

independent variables

Fitting of T. gondii SPMT model (PDB 7MIZ) to the P. falciparum sporozoite SPMT EM map as a rigid body
Alignment of structural prediction of PfTrxL1 (https://alphafold.ebi.ac.uk/entry/Q8I2W0) with TgTrxL1 (PDB 7MIZ) using matchmaker in ChimeraX

dependent variables

Visualization of the resulting fit in ChimeraX
Observation of TgTrxL2 (which is not expressed in Plasmodium but is part of the Toxoplasma ILH) being outside and the remaining protein chains being inside the map
Fitting of protofilaments and TrxL1/SPM1 half arcs as separate units due to the difference in ellipticity between the P. falciparum and T. gondii maps

control variables

Not explicitly mentioned

positive controls

Not specified

negative controls

Not specified

Annotations

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