About

Solute Carrier (SLC) transporter is the largest membrane transporter superfamily localized in the cell membrane.

The SLC transporters play a key role in carrying small molecules without the energy of ATP, while the ABC transporters actively transport their substrates with the energy from ATP hydrolysis. So far, about 400 types of SLC transporter genes have been identified, and classified into 52 families (SLC1-SLC52) based on their function, substrate similarity, sequence similarity and the number of transmembrane regions (mostly 10-14). The ligands of each SLC transporter family covers a broad range of small molecules such as ions, amino acids, peptides, lipids, hormones, neurotransmitters, drugs and so on. This multi-selectivity greatly contributes to delivering nutrition into the cells and releasing unnecessary substances outside the cells, maintaining homeostasis of cells and tissues.

Despite their functional importance, many of their three-dimensional structures, evolutionary history and relationship to diseases are still unknown. We, therefore, built a new database to assist the search for the relationship amongst structural properties and pathogenic mutations on human SLC transporters especially focusing on topological properties.

iMusta4SLC is a relational database connecting annotations, sequence characteristics, conformational features, mutations, and disease information of human SLC transporters. The interface of the website was developed on Flask (http://flask.pocoo.org) which is a web development framework for Python.

SLC family classification was from SLC Tables (http://slc.bioparadigms.org) - BioParadigms (http://www.bioparadigms.org). DNA sequences and amino acid sequences were obtained from NCBI (https://www.ncbi.nlm.nih.gov). The mutations and related disease data were obtained from ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) which stores information of the relationship between variants and clinical phenotypes in general. Domain classification was conducted by HMMer (http://hmmer.org). We searched Protein Data Bank (PDB) for three-dimensional structures and templates of each SLC transporter. Topology prediction was performed using TopCons2 (http://topcons.cbr.su.se), which is a consensus prediction method and its server implementation, including topology prediction methods such as Philius, PolyPhobius, SPOCTOPUS, OCTOPUS and SCAMPI.

How to Use

reference: A. Higuchi, N. Nonaka, K. Yura (2018) iMusta4SLC: Database for the structural property and variations of solute carrier transporters, Biophysics and Physicobiology, Vol. 15 (doi:10.2142/biophysico.15.0_00).