Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants

Emily Pan; Fei Tao; Eva Smorodina; Shuguang Zhang

doi:10.1017/qrd.2024.2

Structural bioinformatics studies of six human ABC transporters and their AlphaFold2-predicted water-soluble QTY variants

QRB Discov. 2024 Jan 19:5:e1. doi: 10.1017/qrd.2024.2. eCollection 2024.

Authors

Emily Pan¹, Fei Tao², Eva Smorodina³, Shuguang Zhang⁴

Affiliations

¹ The Lawrenceville School, Lawrenceville, NJ, USA.
² Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
³ Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway.
⁴ Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

Abstract

Human ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins and perform diverse functions. Many of them are associated with multidrug resistance that often results in cancer treatment with poor outcomes. Here, we present the structural bioinformatics study of six human ABC membrane transporters with experimentally determined cryo-electron microscopy (CryoEM) structures including ABCB7, ABCC8, ABCD1, ABCD4, ABCG1, ABCG5, and their AlphaFold2-predicted water-soluble QTY variants. In the native structures, there are hydrophobic amino acids such as leucine (L), isoleucine (I), valine (V), and phenylalanine (F) in the transmembrane alpha helices. These hydrophobic amino acids are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T), and tyrosine (Y). Therefore, these QTY variants become water soluble. We also present the superposed structures of native ABC transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with root mean square deviations between 1.064 and 3.413 Å despite significant (41.90-54.33%) changes to the protein sequence of the transmembrane domains. We also show the differences in hydrophobicity patches between the native ABC transporters and their QTY variants. We explain the rationale behind why the QTY membrane protein variants become water soluble. Our structural bioinformatics studies provide insight into the differences between the hydrophobic helices and hydrophilic helices and will likely further stimulate designs of water-soluble multispan transmembrane proteins and other aggregated proteins. The water-soluble ABC transporters may be useful as soluble antigens to generate therapeutic monoclonal antibodies for combating multidrug resistance in clinics.

Keywords: QTY code; convert hydrophobic alpha helix to hydrophilic alpha helix; membrane protein design; protein structural predictions; water-soluble integral membrane proteins.