The Interaction of FABP with Kapα

Abstract

Gene-activating lipophilic compounds are carried into the nucleus when loaded on fatty-acid-binding proteins (FABP). Some of these proteins are recognized by the α-Karyopherin (Kapα) through its nuclear localization signal (NLS) consisting of three positive residues that are not in a continuous sequence. The Importin system can distinguish between FABP loaded with activating and non-activating compounds. In the present study, we introduced molecular dynamics as a tool for clarifying the mechanism by which FABP4, loaded with activating ligand (linoleate) is recognized by Kapα. In the first phase, we simulated the complex between KapαΔIBB (termed “Armadillo”) that was crystallized with two NLS hepta-peptides. The trajectory revealed that the crystal-structure orientation of the peptides is rapidly lost and new interactions dominate. Though, the NLS sequence of FABP4 is cryptic, since the functional residues are not in direct sequence, implicating more than one possible conformation. Therefore, four possible docked conformations were generated, in which the NLS of FABP4 is interacting with either the major or the minor sites of Kapα, and the N → C vectors are parallel or anti-parallel. Out of these four basic starting positions, only the FABP4-minor site complex exhibited a large number of contact points. In this complex, the FABP interacts with the minor and the major sites, suppressing the self-inhibitory interaction of the Kapα, rendering it free to react with Kapβ. Finally, we propose that the transportable conformation generated an extended hydrophobic domain which expanded out of the boundary of the FABP4, allowing the loaded linoleate to partially migrate out of the FABP into a joint complex in which the Kapα contributes part of a combined binding pocket.

Extracellular mutation induces an allosteric effect across the membrane and hampers the activity of MRP1 (ABCC1)

“…A geometric clustering algorithm was performed to identify similar structures, based on the respective RMSD between all conformations sampled during the MD simulation 41 . A 3 Å predefined RMSD cut-off was chosen to determine the cluster group, to generate a sufficient number of clusters while maintaining statistical significance, e.g., 42 , 43 . The cluster number for each frame was calculated, summarized to a table consisting of the number of frames for each cluster.…”

Intracellular lipid binding protein family diversity from Oyster Crassostrea gigas: genomic and structural features of invertebrate lipid transporters

“…The nuclear localization signal (NLS), which is related to lipid delivery to nuclear receptors, was identified in the CgiLBP family. The typical vertebrate NLS involves residues K21, R29, and K30 in CRABP-II, and K21, R30, and R31 in FABP4, all located within the protein helix-loop-helix 26 31 . Based on sequence analysis and 3D models, CgiLBP5, CgiLBP6, CgiLBP10, CgiLBP11 and CgiLBP14 have exposed basic residues at these positions and may be involved in nuclear translocation.…”

Identification of a non-classical three-dimensional nuclear localization signal in the intestinal fatty acid binding protein

“…For the conventional NLS, basic residues are recognized by the α/β-importin heterodimer that also mediates the docking to the nuclear pore complex, followed by the protein complex translocation to the nucleus [ 62 ]. In a in silico study, Amber-Vitos et al [ 63 ] indicates that FABP4 interacts with α-importin, proposing the classical nuclear import mechanism as responsible for FABP transport. In spite of the scenario proposed by Amber-Vitos et al , our β-importin inhibition experiment indicates that the classical nuclear transport mechanism would not be involved in the Fabp2 nuclear translocation, and therefore another not diffusional mechanism should be responsible for its transfer [ 64 ].…”