Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F.

Autor: Karagöl A; Istanbul University Istanbul Medical Faculty, Istanbul, Turkey., Karagöl T; Istanbul University Istanbul Medical Faculty, Istanbul, Turkey., Smorodina E; Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway., Zhang S; Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2024 Apr 10; Vol. 19 (4), pp. e0289644. Date of Electronic Publication: 2024 Apr 10 (Print Publication: 2024).
DOI: 10.1371/journal.pone.0289644
Abstrakt: Glutamate transporters play key roles in nervous physiology by modulating excitatory neurotransmitter levels, when malfunctioning, involving in a wide range of neurological and physiological disorders. However, integral transmembrane proteins including the glutamate transporters remain notoriously difficult to study, due to their localization within the cell membrane. Here we present the structural bioinformatics studies of glutamate transporters and their water-soluble variants generated through QTY-code, a protein design strategy based on systematic amino acid substitutions. These include 2 structures determined by X-ray crystallography, cryo-EM, and 6 predicted by AlphaFold2, and their predicted water-soluble QTY variants. In the native structures of glutamate transporters, transmembrane helices contain hydrophobic amino acids such as leucine (L), isoleucine (I), and phenylalanine (F). To design water-soluble variants, these hydrophobic amino acids are systematically replaced by hydrophilic amino acids, namely glutamine (Q), threonine (T) and tyrosine (Y). The QTY variants exhibited water-solubility, with four having identical isoelectric focusing points (pI) and the other four having very similar pI. We present the superposed structures of the native glutamate transporters and their water-soluble QTY variants. The superposed structures displayed remarkable similarity with RMSD 0.528Å-2.456Å, despite significant protein transmembrane sequence differences (41.1%->53.8%). Additionally, we examined the differences of hydrophobicity patches between the native glutamate transporters and their QTY variants. Upon closer inspection, we discovered multiple natural variations of L->Q, I->T, F->Y and Q->L, T->I, Y->F in these transporters. Some of these natural variations were benign and the remaining were reported in specific neurological disorders. We further investigated the characteristics of hydrophobic to hydrophilic substitutions in glutamate transporters, utilizing variant analysis and evolutionary profiling. Our structural bioinformatics studies not only provided insight into the differences between the hydrophobic helices and hydrophilic helices in the glutamate transporters, but they are also expected to stimulate further study of other water-soluble transmembrane proteins.
Competing Interests: Massachusetts Institute of Technology (MIT) filed several patent applications for the QTY code for GPCRs and OH2Laboratories licensed the technology from MIT to work on water-soluble GPCR variants. However, this article does not study GPCRs. SZ is an inventor of the QTY code and has a minor equity of OH2Laboratories. S.Z. founded a startup 511 Therapeutics to generate therapeutic monoclonal antibodies against solute carrier transporters to treat pancreatic cancer. S.Z. has majority equity in 511 Therapeutics. 511 Therapeutics sponsored the study but had no influence and interference in the design of the study, in the data collection, analyses, or interpretation of data and in the writing of the manuscript, or in the decision to publish the results. All other authors have no competing interest. Additional statements Shuguang Zhang is also a co-founder and Scientific Advisor for 3DMatrix Co Ltd in Japan that produces self-assembling peptide hydrogels for accelerating wound healing for surgical and dental wound healing applications. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
(Copyright: © 2024 Karagöl et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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