Computational protocol: Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective cell migration

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Protocol publication

[…] Structures of an ideal α-helical conformation of putative helices 1–5 and of random conformations for loops 1–4 were constructed by SYBYL-X, and the electrostatic potentials and hydrophobic properties on the molecular surfaces of the structures were calculated using eF-surf ().Helices 1 and 2 and the first half of helix 3 are involved in the interaction between JRAB-N and JRAB-C, indicating that these three helices should be located near each other. Coiled-coil prediction () revealed that helix 1 has the potential to form a coiled-coil within itself or with other helices, such as helix 3 or 5. Therefore we positioned helices 1–3 so that helices 1 and 2 and the first half of helix 3 were located close together and the hydrophobic regions of helices 1 and 3 contacted each other to form a coiled-coil–like conformation. On the other hand, helices 2–5 and loop 4 are involved in the interaction between Rab13 and JRAB-C. In addition, the features of the three effector proteins that we used in the structural alignment revealed that in general, two antiparallel helices are involved in Rab-binding via hydrophobic and electrostatically negative regions. On the basis of these observations, we positioned helices 4 and 5 so that helices 2 and 3 and helices 4 and 5 were antiparallel and located close together; consequently the surface properties of the putative Rab-binding site on JRAB-C resemble those in the three aligned effector proteins (). To construct a model of the interaction between JRAB-C and JRAB-N (LIM) or Rab13, we modeled the structures of JRAB-N (LIM) and Rab13 by comparative modeling (Fugue [ ] and Modeller [ ]) and calculated their surface properties (eF-surf [ ]). The structural model of LIM was placed on the JRAB-C model such that the protein-binding residues in LIM predicted by PSIVER () were in contact with the putative LIM-binding regions in the JRAB-C model. The Rab13 model was placed on JRAB-C based on the known structures of the three Rab–effector complexes. […]

Pipeline specifications

Software tools Sybyl-X, FUGUE, MODELLER, PSIVER
Application Protein structure analysis