Putative linear motifs mediate the trafficking to apical and basolateral membranes

Abstract

Cell polarity refers to the asymmetric organisation of cellular components in various cells. Epithelial cells are the best known examples of polarized cells, featuring apical and basolateral membrane domains. Despite huge efforts, the exact rules governing the protein distribution in such domains are still elusive. In this study we examined linear motifs accumulating in these parts and based on the results we prepared Classical and Convolutional Neural Networks to classify human transmembrane proteins localizing into apical/basolateral membranes. Asymmetric expression of drug transporters results in vectorial drug transport, governing the pharmacokinetics of numerous substances, yet the data on how proteins are sorted in epithelial cells is very scattered. The provided dataset may offer help to experimentalists to characterize novel molecular targets to regulate transport processes more precisely.

Molecular dynamics of the human RhD and RhAG blood group proteins

“…As underlined by a multiple studies, the AlphaFold2 model does not work very well for membrane proteins, and people are working on new AI-based approaches that could improve it in the future with already interesting results (Wang et al, 2022;Huang and Ecker, 2023). A high fraction of membrane proteins form oligomeric structures, however, by often predicting them as monomeric, AlphaFold2 offers models that are not very useable (Dobson et al, 2023). Several approaches are being developed to overcome these limitations and also discover possible multiple conformations, particularly for globular proteins (Silva et al, 2023).…”