Abstract
The large-conductance Ca2+-activated K+ (BK) channel is broadly expressed in various mammalian cells and tissues such as neurons, skeletal and smooth muscles, exocrine cells, and sensory cells of the inner ear. Previous studies suggest that BK channels are promiscuous binders involved in a multitude of protein-protein interactions. To gain a better understanding of the potential mechanisms underlying BK interactions, we analyzed the abundance, distribution, and potential mechanisms of intrinsic disorder in 27 BK channel variants from mouse cochlea, 104 previously reported BK-associated proteins (BKAPS) from cytoplasmic and membrane/cytoskeletal regions, plus BK β- and γ-subunits. Disorder was evaluated using the MFDp algorithm, which is a consensus-based predictor that provides a strong and competitive predictive quality and PONDR, which can determine long intrinsically disordered regions (IDRs). Disorder-based binding sites or molecular recognition features (MoRFs) were found using MoRFpred and ANCHOR. BKAP functions were categorized based on Gene Ontology (GO) terms. The analyses revealed that the BK variants contain a number of IDRs. Intrinsic disorder is also common in BKAPs, of which ∼5% are completely disordered. However, intrinsic disorder is very differently distributed within BK and its partners. Approximately 65% of the disordered segments in BK channels are long (IDRs) (>50 residues), whereas >60% of the disordered segments in BKAPs are short IDRs that range in length from 4 to 30 residues. Both α and γ subunits showed various amounts of disorder as did hub proteins of the BK interactome. Our analyses suggest that intrinsic disorder is important for the function of BK and its BKAPs. Long IDRs in BK are engaged in protein-protein and protein-ligand interactions, contain multiple post-translational modification sites, and are subjected to alternative splicing. The disordered structure of BK and its BKAPs suggests one of the underlying mechanisms of their interaction.
Highlights
The large-conductance Ca2+-activated K+ (BK) channels, known as Slo1, MaxiK, BKCa, and KCa1.1 channels, are large conductance channels (100–300 pS), that act as sensors for membrane voltage and intracellular Ca2+, linking cell excitability, metabolism, and signaling
Datasets No animals were used in this study, only previously published sequences of 27 BK channel variants for mouse cochlea [24], together with 104 and 71 published proteins [22,23] that interact with the BK channel in the membrane/cytoskeletal and cytoplasmic regions, respectively
Characterization of BK Channels Since the considered 22 BK channels variants are very similar in their sequences and differ primarily through alternative splicing events in the kcnma1 gene, we aligned them based on multiple sequence alignment (MSA) with ClustalW [45] using default parameters. For these 22 BK channel variants, we provide majority vote-based profiles, which are based on the consideration of a given annotation if it occurs in at least 50% of variants at a given position in the chain
Summary
The large-conductance Ca2+-activated K+ (BK) channels, known as Slo, MaxiK, BKCa, and KCa1.1 channels, are large conductance channels (100–300 pS), that act as sensors for membrane voltage and intracellular Ca2+, linking cell excitability, metabolism, and signaling. BK has seven transmembrane-spanning regions (S0–S6) with an extracellular N-terminus (S0) that provides a binding site for a b-subunit. Transmembrane regions S1–S4 are responsible for sensing voltage changes, while S5–S6 form a pore that conducts ions. BK has a long C-terminal region with target sequences for channel modulation, such as a Ca2+-bowl, composed of many positively charged amino acids, RCK1 and RCK2 domains that regulate K+ conductance, a tetramerization domain, LZ motifs, a hemebinding motif, phosphorylation sites, and a caveolin-targeting domain. The LZ motifs are essential for protein-protein interactions and they modulate channel activity and expression (see [1] for recent review)
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