TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer

TMVisDB: Annotation and 3D-visualization of Transmembrane Proteins

Since the rise of cellular life, transmembrane proteins (TMPs) have been crucial to various cellular processes through their central role as gates and gatekeepers. Despite their importance, experimental high-resolution structures for TMPs remain underrepresented due to experimental challenges. Given its performance leap, structure predictions have begun to close the gap. However, identifying the membrane regions and topology in three-dimensional structure files on a large scale still requires additional in silico predictions. Here, we introduce TMVisDB to sieve through millions of predicted structures for TMPs. This resource enables both browsing through 46 million predicted TMPs and visualizing them along with their topological annotations without having to tap into costly predictions of the AlphaFold3-style. TMVisDB joins AlphaFoldDB structure predictions and transmembrane topology predictions from the protein language model (pLM) based method TMbed. We showcase the utility of TMVisDB for the analysis of proteins through two use cases, namely the B-lymphocyte antigen CD20 (Homo sapiens) and the cellulose synthase (Novosphingobium sp. P6W). We demonstrate the value of TMVisDB for large-scale analyses through findings pertaining to all TMPs predicted for the human proteome. TMVisDB is freely available at https://tmvisdb.rostlab.org.

MolMeDB: Molecules on Membranes Database

Biological membranes act as barriers or reservoirs for many compounds within the human body. As such, they play an important role in pharmacokinetics and pharmacodynamics of drugs and other molecular species. Until now, most membrane/drug interactions have been inferred from simple partitioning between octanol and water phases. However, the observed variability in membrane composition and among compounds themselves stretches beyond such simplification as there are multiple drug–membrane interactions. Numerous experimental and theoretical approaches are used to determine the molecule–membrane interactions with variable accuracy, but there is no open resource for their critical comparison. For this reason, we have built Molecules on Membranes Database (MolMeDB), which gathers data about over 3600 compound–membrane interactions including partitioning, penetration and positioning. The data have been collected from scientific articles published in peer-reviewed journals and complemented by in-house calculations from high-throughput COSMOmic approach to set up a baseline for further comparison. The data in MolMeDB are fully searchable and browsable by means of name, SMILES, membrane, method or dataset and we offer the collected data openly for further reuse and we are open to further additions. MolMeDB can be a powerful tool that could help researchers better understand the role of membranes and to compare individual approaches used for the study of molecule/membrane interactions.

Pro-metastatic signaling of the trans fatty acid elaidic acid is associated with lipid rafts

Trans fatty acids (TFAs) are risk factors for cardiovascular disorders, and the cancer-promoting effects of TFAs have been previously reported. The present study examined the effects and signaling of elaidic acid (EA), a TFA, in colorectal cancer (CRC) cells. Oral intake of EA was found to increase metastasis of HT29 human CRC cells. Results indicated that, in the plasma membrane, EA was integrated into cholesterol rafts, which contain epidermal growth factor receptors (EGFR). EA increased nanog and c-myc, and decreased PGC-1A through lipid raft-associated EGFR signaling in HT29 cells. Depletion of cholesterol by methyl-β-cyclodextrin treatment abrogated the EA-induced stemness and oxidative phosphorylation. Simvastatin treatment also abrogated EA-enhanced tumor growth. These results indicate that EA enhances the stemness by activating EGFR in lipid rafts.