Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Abstract

Multiscale modeling provides a very powerful means of studying complex biological systems. An important component of this strategy involves coarse-grained (CG) simplifications of regions of the system, which allow effective exploration of complex systems. Here we studied aspects of CG modeling of the human zinc transporter ZnT2. Zinc is an essential trace element with 10% of the proteins in the human proteome capable of zinc binding. Thus, zinc deficiency or impairment of zinc homeostasis disrupt key cellular functions. Mammalian zinc transport proceeds via two transporter families: ZnT and ZIP; however, little is known about the zinc permeation pathway through these transporters. As a step towards this end, we herein undertook comprehensive computational analyses employing multiscale techniques, focusing on the human zinc transporter ZnT2 and its bacterial homologue, YiiP. Energy calculations revealed a favorable pathway for zinc translocation via alternating access. We then identified key residues presumably involved in the passage of zinc ions through ZnT2 and YiiP, and functionally validated their role in zinc transport using site-directed mutagenesis of ZnT2 residues. Finally, we use a CG Monte Carlo simulation approach to sample the transition between the inward-facing and the outward-facing states. We present our structural models of the inward- and outward-facing conformations of ZnT2 as a blueprint prototype of the transporter conformations, including the putative permeation pathway and participating residues. The insights gained from this study may facilitate the delineation of the pathways of other zinc transporters, laying the foundations for the molecular basis underlying ion permeation. This may possibly facilitate the development of therapeutic interventions in pathological states associated with zinc deficiency and other disorders based on loss-of-function mutations in solute carriers.

Alterations in ZnT1 expression and function lead to impaired intracellular zinc homeostasis in cancer

“…ZnT1 contains the canonical HD-DH zinc-binding motif, conserved among zinc transporters 28 . Notably, when comparing the 3D positions of the zincbinding motif (Site A) 29 , in the ZnT1 and ZnT2 models, as well as with the YiiP equivalent Fe/Zn binding site (PDB 3H90), we found similar 3D organization (Fig. 3b).…”

“…3b). Given that we have previously shown that the ZnT2 model, which is also based on YiiP, is able to predict the zinc permeation pathway along the transporter 29 , and given the very low homology between ZnT1 and ZnT2 (less than 20% amino acid identity), we believe the similarity in Site A is a good indication of the new ZnT1 model validity, and, in consequence, can be used to rationalize the impact of each of the eight mutants found by this study on ZnT1. Thus, we present here the resulting high-accuracy partial 3D model of ZnT1, focusing on the TM helices, and, using the model, we attempt to rationalize the structural and functional impact of the eight mutations tested in this study, as follows ( Fig.…”

ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion

“…The structural model for the simulation systems of ZnT2 in the inward-facing (IF) and outward-facing (OF) conformations were based on our recent study [21], in which PDB IDs 3H90 (x-ray at 2.9Å resolution [22]) and 5VRF (cryo-EM at 4.1Å resolution [23]) were used as templates for the OF and IF conformations, respectively (see S1 Text for a brief summary of the modeling process). For each system, the transporter homodimer was inserted into a 30 Å-thick particle grid emulating a hydrophobic membrane using the MOLARIS software package [24,25].…”

“…In a recent study, we have delineated the putative zinc permeation pathway through the human ZnT2 [21]. Using computational and evolutionary considerations, we determined the residues contributing to the zinc binding site, and modeled the inward- and outward-facing (cytoplasmic- and vesicular lumen-facing, respectively) conformations of ZnT2.…”

Boric Acid (H3(BO3): Recognize The Molecular Interactions in Solutions

“…Senyawa asam borat memiliki kelarutan yang sedikit jika dilrutkan di dalam alkohol, (139)(140)(141)(142) cukup larut dalam piridina (143) dan akan sangat sedikit larut (144) ketika pelarutnya aseton. (142; 145-148) Kelarutan suatu senyawa dapat dipengaruhi oleh beberapa faktor diantaranya sifat dari zat terlarut (solute) (149)(150)(151)(152)(153) dan pelarut (154) (solvent) (105; 139; 142; 155; 156) dimana zat terlarut yang bersifat polar (214)(215)(216) akan mudah larut dalam solvent (243)(244)(245)(246) yang bersifat polar begitupun sebaliknya. Suhu, konsentrasi, (106; 149; 157-159) pengaruh penambahan ion senama (236)(237) juga sangat berpengaruh terhadap kelarutan (247)(248)(249) suatu senyawa.…”