Editorial: Novel Insights into the Modulation of Protein Function by Lipids and Membrane Organization

Florina Zakany^1*Zsolt Török^2*Tamas Kovacs^1*

• ¹Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
• ²Laboratory of Molecular Stress Biology, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary, Szeged, Hungary

Although the plasma membrane was initially thought to solely represent a passive diffusion barrier separating the intra- and extracellular spaces, a continuously growing amount of evidence supports the active contribution of lipids and membrane organization to the regulation of the structure and function of transmembrane proteins. Membrane lipids can exert such actions through direct effects, that is ligand-like binding of lipids at specific binding sites on proteins, and indirect mechanisms mediated via alterations in membrane biophysical properties (fluidity, hydration, lipid order, thickness, elasticity, lateral pressure and dipole potential). Furthermore, lateral segregation tendency of biological membranes into dynamic nano- and micro-domains such as cholesterol-enriched lipid rafts and ceramide platforms, and its changes in response to altered lipid composition add a further level of complexity to the active modulatory roles of lipids in the functional regulation of proteins. By exerting permissive and cooperative actions on conformational changes associated with the activation of transmembrane proteins, such direct and indirect protein-lipid interactions modify a large variety of cellular functions such as signaling pathways, apoptosis, cell adhesion and migration, synaptic transmission, cytoskeletal organization, protein sorting, pathogen entry, formation of amyloid plaques or extracellular vesicles, stress and immunological responses (Zakany et al., 2020; Levental and Lyman, 2023). This Research Topic includes four studies that provide novel approaches and ideas about the intrinsic connection between functional modulation of proteins and lipids and organization of cellular membranes.Membrane bilayers have recently been proposed to act as extraordinarily precise, “finely-tuned molecular machines” due to the compositional complexity of the lipid species found in membranes and their multitudinous specific interactions with membrane proteins (Dingjan and Futerman, 2021). Recent advances in high-resolution X-ray crystallography and cryo-EM, and molecular dynamics simulation led to the description of a large multitude of such modulatory direct lipid-protein interactions (Corradi et al., 2019; Zakany et al., 2020). The Perspective of Dingjan and Futerman proposes that the ceramide-sensing negative feedback mechanism to avoid toxic ceramide accumulation in the endoplasmic reticulum is a manifestation of such a “finely-tuned” system through direct interactions between serine palmitoyl transferase with the inhibitory ORMDL subunit (SPT-ORMDL) and ceramide. After summarizing related literature cryo-EM data, the authors introduce a simplified computational model of the endoplasmic reticulum-localized sphingolipid flux, and analyze the energetic contribution of single residues on ceramide binding by calculating the docking score and the predicted binding free energy for mutant SPT-ORMDL complexes, which, while not being validated experimentally in the study, are in agreement with recently published experimental data. Furthermore, the authors also place their findings in context of intriguing mechanistic questions about the evolution of the (glyco)sphingolipid biosynthetic pathway (Biran et al., 2024). Nicotinic acetylcholine receptor (nAchR), the paradigm member of the pentameric ligand-gated ion channel superfamily of neurotransmitter receptors, is also modulated by membrane lipids and, in turn, exerts influence on its membrane surroundings. The neuromuscular synapse including a large quantity of nAChR molecules at an exceptionally high density represents a unique case that is distinct from the conventional raft-versus-non-raft organization but rather constitutes a large two-dimensional nAChR ‘picket’ with gap-filling lipids under the influence of the receptors, which develops during neurodevelopment and synaptogenesis. The review of Barrantes overviews current knowledge about the mechanisms of nAChR modulation by membrane lipids both through direct and indirect mechanisms and points at distinctive singular modes of crosstalk with the membrane milieu resulting from its large abundance and density at the neuromuscular synapse, and characterized by an organization of numerous directly bound ‘non-annular’ and more dynamic ‘annular’ lipids complementing recent reviews in the field (Borroni and Barrantes, 2021; Barrantes, 2023) from a biophysical perspective. Although many lipid interaction sites were suggested by biochemical-biophysical and atomistic structural studies on the nAChR, their pathophysiological relevance has not yet been demonstrated.Mechanosensitive ion channels, playing substantial roles in endothelial mechanotransduction and thus regulation of the blood pressure, are activated by mechanical forces, such as shear stress, a frictional force generated by the blood flow and membrane tension generated by stretch (Beverley et al., 2025) and their endothelial stiffening-induced functional alterations can contribute to cardiovascular disease and aging (Aguilar et al., 2022). The comprehensive review of Beverley and Levitan summarizes how cholesterol, intrinsically related to the pathogenesis of cardiovascular diseases, modifies functions of mechanosensitive ion channels including i) Piezo channels through altering their microenvironment and regulating their interaction with auxiliary proteins such as stomatin-like protein 3 (STOML3); ii) various Kir channels via direct binding at different sites; iii) TRPV4 by direct binding and partitioning into caveolar microdomains; and iv) voltage-regulated anion channels (VRAC) through membrane biophysics-related mechanisms. While the authors convincingly demonstrate the relevance of cholesterol-mediated modulation of mechanosensitive ion channels based on computational and simple cellular studies, this needs to be supported in the future by in vivo studies that are only sporadic in animal models and practically completely missing in humans.Cyclodextrins are cyclic oligosaccharides capable of forming soluble complexes with hydrophobic compounds such as lipids or drugs and thus frequently used as carriers in pharmaceutical formulations (Kali et al., 2024). However, these compounds are recently getting acknowledged as potential active therapeutic compounds (Kovacs et al., 2022a). Consistently, methyl-β-cyclodextrin, the most effective cyclodextrin to complex cholesterol, was recently shown both in vitro and in vivo to exert analgesic effects via inhibiting TRPV1 and TRPA1 channels through membrane cholesterol depletion and lipid raft disruption (Horvath et al., 2020). As a continuation of the study, Nehr-Majoros et al. show that other cyclodextrins, devoid of hemolytic and toxic effects of methyl-β-cyclodextrin and thus more suitable for human application, are also able to reduce TRPV1 and TRPA1 activation via altering membrane microenvironment by cholesterol depletion in simple cellular models. This study is in accordance with i) recent reports describing alternative means of raft disruption and consequent antinociceptive effects (Payrits et al., 2024); and findings that cyclodextrin derivatives with relatively low in vitro cholesterol-complexing ability can affect activity of ion channels (Kovacs et al., 2021) and exert beneficial actions in diseases such as suggested previously in SARS-CoV-2 infection (Kovacs et al., 2023). While the study introduces non-cytotoxic cyclodextrins as promising plausible candidates for human analgesia, their efficiency should be verified in future in vivo and, subsequently, in human studies. Furthermore, potential off-target and side effects should be examined as well.Taken together, manuscripts in the Research Topic underline the extensive and versatile nature of biologically substantial lipid-protein interactions. However, this field of research still faces numerous major challenges and open questions that include those listed below. 1) Although computational and atomistic structural tools identified innumerable potential direct lipid-protein interactions, these should be verified in more realistic membranes in MD simulations, with optimized sample preparation protocols for cryo-EM, and, particularly, experimentally (Muller et al., 2019; Biou, 2023). 2) The examination of membrane biophysical properties and their biological relevance currently represents a rather neglected area of research, which can be related to the generally unmet need for measurement techniques suitable for high-throughput and subcellular studies in living cells such as those described recently (Danylchuk et al., 2021; Zakany et al., 2021; Andronico et al., 2024; Wong and Budin, 2024; Szabo et al., 2025). 3) The lateral organization of membranes still represent an unresolved mystery, particularly in intracellular membranes (Levental et al., 2020; Wang et al., 2020). 4) Most importantly, the contribution of membrane lipid-related alterations, albeit being extensively recognized, are very far from being understood in the pathogenesis of diseases intrinsically related to alterations in membrane lipid composition such as tumors, metabolic, neurodegenerative or lysosomal storage disorders. This is further aggravated by the scarcity of animal and human studies in the field due to the limited translatability of biophysical insights gained with in vitro or simple cellular models. Nevertheless, a continuously growing number of studies, including the four published in the Research Topic, support the hypothesis of the therapeutic applicability of membrane lipid therapy, i.e. approaches targeting the abnormal lipid homeostasis and modifying membrane lipid composition, structure, and lateral nanodomain organization of the cell membrane in human pathological conditions (Casares et al., 2019; Kovacs et al., 2022b).