Cell membranes are complex multicomponent systems, which are highly heterogeneous in the lipid distribution and composition. To date, most molecular simulations have focussed on relatively simple lipid compositions, helping to inform our understanding of in vitro experimental studies. Here we describe on simulations of complex asymmetric plasma membrane model, which contains seven different lipids species including the glycolipid GM3 in the outer leaflet and the anionic lipid, phosphatidylinositol 4,5-bisphophate (PIP2), in the inner leaflet. Plasma membrane models consisting of 1500 lipids and resembling the in vivo composition were constructed and simulations were run for 5 µs. In these simulations the most striking feature was the formation of nano-clusters of GM3 within the outer leaflet. In simulations of protein interactions within a plasma membrane model, GM3, PIP2, and cholesterol all formed favorable interactions with the model α-helical protein. A larger scale simulation of a model plasma membrane containing 6000 lipid molecules revealed correlations between curvature of the bilayer surface and clustering of lipid molecules. In particular, the concave (when viewed from the extracellular side) regions of the bilayer surface were locally enriched in GM3. In summary, these simulations explore the nanoscale dynamics of model bilayers which mimic the in vivo lipid composition of mammalian plasma membranes, revealing emergent nanoscale membrane organization which may be coupled both to fluctuations in local membrane geometry and to interactions with proteins.

The interactions of membrane proteins are influenced by their lipid environment, with key lipid species able to regulate membrane protein function. Advances in high resolution microscopy can reveal the organisation and dynamics of proteins and lipids within living cells at resolutions < 200 nm. Parallel advances in molecular simulations provide near-atomic resolution models of the dynamics of the organisation of membranes of in vivo like complexity. We explore the dynamics of proteins and lipids in crowded and complex plasma membrane models, thereby closing the length and complexity gap between computations and experiments. Our simulations provide insights into the mutual interplay between lipids and proteins in determining mesoscale (20 to 100 nm) fluctuations of the bilayer, and in enabling oligomerization and clustering of membrane proteins.

The serotonergic system plays an important role in many psychiatric disorders. Its role in depression is well established (1). The majority of antidepressants, including TCAs, 6 cause increased synaptic serotonin (5-HT) levels via blockade of 5-HT reuptake into the presynaptic neuron (2-4) by competitive inhibition of hSERT. TCAs have been in clinical use since the 1950s, with imipramine being the first and most prominent compound (5). In severely depressed hospitalized patients, TCAs appear to be more efficacious than selective serotonin reuptake inhibitors (6). TCAs remain in widespread clinical use, especially for treatment-resistant depression (7).hSERT belongs to the neurotransmitter sodium symporter family (2, 8). These transporters utilize the electrochemical gradient of sodium and chloride ions to accumulate 5-HT against its own gradient (9 -11). No experimentally solved structures of the monoamine transporters exist, including hSERT and the dopamine and norepinephrine transporters. However, the structure of LeuT, a bacterial homolog of the neurotransmitter sodium symporters, in a substrate-occluded conformation, was reported in 2005 (12). Two sodium ions (12) and a chloride ion bind near the central substrate site (13-14) structurally and functionally coupling sodium and chloride binding to substrate binding. Recently, different transport mechanisms have been suggested (15,16).Subsequently, a low affinity noncompetitive binding site for TCAs in the extracellular vestibule of the LeuT 11 Å above the central binding site was identified (17,18). The relevance of the LeuT vestibular site for TCA binding to the physiologically relevant target, hSERT, is a matter of debate. This study identifies the central binding site, not the putative vestibular site, as relevant for TCA binding to hSERT and furthermore describes and validates the orientation of TCAs within this site.In this paper, we present induced fit docking studies of imipramine and selected analogs in the previously described homology models of hSERT (19). We present binding affinity studies of 10 imipramine analogs (Fig. 1 Copenhagen Ø, Denmark. 4 To whom correspondence may be addressed. E-mail: birgit@chem.au.dk. 5 To whom correspondence may be addressed. E-mail: owiborg@post.tele.dk. 6 The abbreviations used are: TCA, tricyclic antidepressant; 5-HT, serotonin; hSERT, human SERT; WT, wild type; PaMLAC, paired mutation ligand analog complementation; MD, molecular dynamics; r.m.s., root mean square.

Large coarse-grained simulations show that integral membrane proteins alter the bending rigidity of lipid bilayers.

Receptor tyrosine kinases (RTKs) play a critical role in diverse cellular processes and their activity is regulated by lipids in the surrounding membrane, including PIP2 (phosphatidylinositol-4,5-bisphosphate) in the inner leaflet, and GM3 (monosialodihexosylganglioside) in the outer leaflet. However, the precise details of the interactions at the molecular level remain to be fully characterised. Using a multiscale molecular dynamics simulation approach, we comprehensively characterise anionic lipid interactions with all 58 known human RTKs. Our results demonstrate that the juxtamembrane (JM) regions of RTKs are critical for inducing clustering of anionic lipids, including PIP2, both in simple asymmetric bilayers, and in more complex mixed membranes. Clustering is predominantly driven by interactions between a conserved cluster of basic residues within the first five positions of the JM region, and negatively charged lipid headgroups. This highlights a conserved interaction pattern shared across the human RTK family. In particular predominantly the N-terminal residues of the JM region are involved in the interactions with PIP2, whilst residues within the distal JM region exhibit comparatively less lipid specificity. Our results suggest that JM–lipid interactions play a key role in RTK structure and function, and more generally in the nanoscale organisation of receptor-containing cell membranes.