Spontaneous Membrane Nanodomain Formation in the Absence or Presence of the Neurotransmitter Serotonin

Cholesterol-Dependent Serotonin Insertion Controlled by Gangliosides in Model Lipid Membranes

Serotonin is distinct among synaptic neurotransmitters because it is amphipathic and released from synaptic vesicles at concentrations superior to its water solubility limit (270 mM in synaptic vesicles for a solubility limit of 110 mM). Hence, serotonin is mostly aggregated in the synaptic cleft, due to extensive aromatic stacking. This important characteristic has received scant attention, as most representations of the serotonergic synapse take as warranted that serotonin molecules are present as monomers after synaptic vesicle exocytosis. Using a combination of in silico and physicochemical approaches and a new experimental device mimicking synaptic conditions, we show that serotonin aggregates are efficiently dissolved by gangliosides (especially GM1) present in postsynaptic membranes. This initial interaction, driven by electrostatic forces, attracts serotonin from insoluble aggregates and resolves micelles into monomers. Serotonin also interacts with cholesterol via a set of CH-π and van der Waals interactions. Thus, gangliosides and cholesterol act together as a functional serotonin-collecting funnel on brain cell membranes. Based on this unique mode of interaction with postsynaptic membranes, we propose a new model of serotonergic transmission that takes into account the post-exocytosis solubilizing effect of gangliosides and cholesterol on serotonin aggregates.

Phospholipid Membranes as Chemically and Functionally Tunable Materials

The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.

Characterization of domain formation in complex membranes

A widely known property of lipid membranes is their tendency to undergo a separation into disordered (Ld) and ordered (Lo) domains. This impacts the local structure of the membrane relevant for the physical (e.g., enhanced electroporation) and biological (e.g., protein sorting) significance of these regions. The increase in computing power, advancements in simulation software, and more detailed information about the composition of biological membranes shifts the study of these domains into the focus of classical molecular dynamics simulations. In this chapter, we present a versatile yet robust analysis pipeline that can be easily implemented and adapted for a wide range of lipid compositions. It employs Gaussian-based Hidden Markov Models to predict the hidden order states of individual lipids by describing their structure through the area per lipid and the average SCC order parameters per acyl chain. Regions of the membrane with a high correlation between ordered lipids are identified by employing the Getis-Ord local spatial autocorrelation statistic on a Voronoi tessellation of the lipids. As an example, the approach is applied to two distinct systems at a coarse-grained resolution, demonstrating either a strong tendency towards phase separation (1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DIPC), cholesterol) or a weak tendency toward phase separation (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (PUPC), cholesterol). Explanations of the steps are complemented by coding examples written in Python, providing both a comprehensive understanding and practical guidance for a seamless integration of the workflow into individual projects.

Serotonin Signaling through Lipid Membranes

Serotonin (5-HT) is a vital modulatory neurotransmitter responsible for regulating most behaviors in the brain. An inefficient 5-HT synaptic function is often linked to various mental disorders. Primarily, membrane proteins controlling the expression and activity of 5-HT synthesis, storage, release, receptor activation, and inactivation are critical to 5-HT signaling in synaptic and extra-synaptic sites. Moreover, these signals represent information transmission across membranes. Although the lipid membrane environment is often viewed as fairly stable, emerging research suggests significant functional lipid-protein interactions with many synaptic 5-HT proteins. These protein-lipid interactions extend to almost all the primary lipid classes that form the plasma membrane. Collectively, these lipid classes and lipid-protein interactions affect 5-HT synaptic efficacy at the synapse. The highly dynamic lipid composition of synaptic membranes suggests that these lipids and their interactions with proteins may contribute to the plasticity of the 5-HT synapse. Therefore, this broader protein-lipid model of the 5-HT synapse necessitates a reconsideration of 5-HT's role in various associated mental disorders.

The intricate link between membrane lipid structure and composition and membrane structural properties in bacterial membranes

It is now evident that the cell manipulates lipid composition to regulate different processes such as membrane protein insertion, assembly and function. Moreover, changes in membrane structure and properties, lipid homeostasis during growth and differentiation with associated changes in cell size and shape, and responses to external stress have been related to drug resistance across mammalian species and a range of microorganisms. While it is well known that the biomembrane is a fluid self-assembled nanostructure, the link between the lipid components and the structural properties of the lipid bilayer are not well understood. This perspective aims to address this topic with a view to a more detailed understanding of the factors that regulate bilayer structure and flexibility. We describe a selection of recent studies that address the dynamic nature of bacterial lipid diversity and membrane properties in response to stress conditions. This emerging area has important implications for a broad range of cellular processes and may open new avenues of drug design for selective cell targeting.

Different membrane order measurement techniques are not mutually consistent

"Membrane order" is a term commonly used to describe the elastic and mechanical properties of the lipid bilayer, though its exact meaning is somewhat context- and method dependent. These mechanical properties of the membrane control many cellular functions and are measured using various biophysical techniques. Here, we ask if the results obtained from various techniques are mutually consistent. Such consistency cannot be assumed a priori because these techniques probe different spatial locations and different spatial and temporal scales. We evaluate the change of membrane order induced by serotonin using nine different techniques in lipid bilayers of three different compositions. Serotonin is an important neurotransmitter present at 100s of mM concentrations in neurotransmitter vesicles, and therefore its interaction with the lipid bilayer is biologically relevant. Our measurement tools include fluorescence of lipophilic dyes (Nile Red, Laurdan, TMA-DPH, DPH), whose properties are a function of membrane order; atomic force spectroscopy, which provides a measure of the force required to indent the lipid bilayer; 2H solid-state NMR spectroscopy, which measures the molecular order of the lipid acyl chain segments; fluorescence correlation spectroscopy, which provides a measure of the diffusivity of the probe in the membrane; and Raman spectroscopy, where spectral intensity ratios are affected by acyl chain order. We find that different measures often do not correlate with each other and sometimes even yield conflicting results. We conclude that no probe provides a general measure of membrane order and that any inference based on the change of membrane order measured by a particular probe may be unreliable.

Computational Advances of Protein/Neurotransmitter-membrane Interactions Involved in Vesicle Fusion and Neurotransmitter Release

Vesicle fusion is of crucial importance to neuronal communication at neuron terminals. The exquisite but complex fusion machinery for neurotransmitter release is tightly controlled and regulated by protein/neurotransmitter-membrane interactions. Computational 'microscopies', in particular molecular dynamics simulations and related techniques, have provided notable insight into the physiological process over the past decades, and have made enormous contributions to fields such as neurology, pharmacology and pathophysiology. Here we review the computational advances of protein/neurotransmitter-membrane interactions related to presynaptic vesicle-membrane fusion and neurotransmitter release, and outline the in silico challenges ahead for understanding this important physiological process.

Serotonergic drugs modulate the phase behavior of complex lipid bilayers

Serotonin is an endogenous neurotransmitter involved in both physiological and pathophysiological processes. Traditionally, serotonin acts as a ligand for G protein-coupled receptors (GPCRs) leading to subsequent cell signaling. However, serotonin can also bind to lipid membranes with high affinity and modulate the phase behavior in 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC)/N-palmitoyl-D-erythro-sphingosylphosphorylcholine (PSM)/cholesterol model membranes mimicking the outer leaflet of the plasma membrane. Here, we investigated if serotonergic drugs containing the pharmacophore from serotonin would also modulate phase behavior in lipid membranes in a similar fashion. We used ²H NMR spectroscopy to explore the phase behavior of POPC/PSM/cholesterol (4/4/2 molar ratio) mixtures in the presence of the serotonergic drugs aripiprazole, BRL-54443, BW-723C86, and CP-135807 at a lipid to drug molar ratio of 10:1. POPC and PSM were perdeuterated in the palmitoyl chain, respectively, and prepared in individual samples. Numerical lineshape simulations of the ²H NMR spectra were used to calculate the order parameter profiles and projected lengths of the saturated acyl chains. All serotonergic drugs induce two components in ²H NMR spectra, indicating that they increased the hydrophobic mismatch between the thickness of the coexisting lipid phases leading to larger domain sizes, relatively similarly to serotonin. AFM force indentation and Raman spectral studies, which interrogate membrane mechanical properties, also indicate changes in membrane order in the presence of these drugs. These findings highlight how serotonergic drugs alter membrane phase behavior and could modulate both target and other membrane proteins, possibly explaining the side effects observed for serotonergic and other clinically relevant drugs.

Magic mushroom extracts in lipid membranes

The active hallucinogen of magic mushrooms, psilocin, is being repurposed to treat nicotine addiction and treatment-resistant depression. Psilocin belongs to the tryptamine class of psychedelic compounds which include the hormone serotonin. It is believed that psilocin exerts its effect by binding to the serotonin 5-HT_2A receptor. However, recent in-vivo evidence suggests that psilocin may employ a different mechanism to exert its effects. Membrane-mediated receptor desensitization of neurotransmitter receptors is one such mechanism. We compare the impact of the neutral and charged versions of psilocin and serotonin on the properties of zwitterionic and anionic lipid membranes using molecular dynamics simulations and calorimetry. Both compounds partition to the lipid interface and induce membrane thinning. The tertiary amine in psilocin, as opposed to the primary amine in serotonin, limits psilocin's impact on the membrane although more psilocin partitions into the membrane than serotonin. Calorimetry corroborates that both compounds induce a classical melting point depression like anesthetics do. Our results also lend support to a membrane-mediated receptor-binding mechanism for both psilocin and serotonin and provide physical insights into subtle chemical changes that can alter the membrane-binding of psychedelic compounds.

py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD

py-MCMD, an open-source Python software, provides a robust workflow layer that manages communication of relevant system information between the simulation engines NAMD and GOMC and generates coherent thermodynamic properties and trajectories for analysis. To validate the workflow and highlight its capabilities, hybrid Monte Carlo/molecular dynamics (MC/MD) simulations are performed for SPC/E water in the isobaric-isothermal (NPT) and grand canonical (GC) ensembles as well as with Gibbs ensemble Monte Carlo (GEMC). The hybrid MC/MD approach shows close agreement with reference MC simulations and has a computational efficiency that is 2 to 136 times greater than traditional Monte Carlo simulations. MC/MD simulations performed for water in a graphene slit pore illustrate significant gains in sampling efficiency when the coupled-decoupled configurational-bias MC (CD-CBMC) algorithm is used compared with simulations using a single unbiased random trial position. Simulations using CD-CBMC reach equilibrium with 25 times fewer cycles than simulations using a single unbiased random trial position, with a small increase in computational cost. In a more challenging application, hybrid grand canonical Monte Carlo/molecular dynamics (GCMC/MD) simulations are used to hydrate a buried binding pocket in bovine pancreatic trypsin inhibitor. Water occupancies produced by GCMC/MD simulations are in close agreement with crystallographically identified positions, and GCMC/MD simulations have a computational efficiency that is 5 times better than MD simulations. py-MCMD is available on GitHub at https://github.com/GOMC-WSU/py-MCMD.

Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations

Numerous health benefits are associated with omega-3 polyunsaturated fatty acids (n-3 PUFA) consumed in fish oils. An understanding of the mechanism remains elusive. The plasma membrane as a site of action is the focus in this study. With large-scale all-atom MD simulations run on a model membrane (1050 lipid molecules), we observed the evolution over time (6 μs) of a circular (raft-like) domain composed of N-palmitoylsphingomyelin (PSM) and cholesterol embedded into a surrounding (non-raft) patch composed of polyunsaturated 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) (1:1:1 mol). A supervised machine learning algorithm was developed to characterize the migration of each lipid based on molecular conformation and the local environment. PDPC molecules were seen to infiltrate the ordered raft-like domain in a small amount, while a small concentration of PSM and cholesterol molecules was seen to migrate into the disordered non-raft region. Enclosing the raft-like domain, a narrow (∼2 nm in width) interfacial zone composed of PDPC, PSM, and cholesterol that buffers the substantial difference in order (ΔS_CD ≈ 0.12) between raft-like and non-raft environments was seen to form. Our results suggest that n-3 PUFA regulate the architecture of lipid rafts enriched in sphingolipids and cholesterol with a minimal effect on order within their interior in membranes.

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

Altered Membrane Mechanics Provides a Receptor-Independent Pathway for Serotonin Action

Serotonin, an important signaling molecule in humans, has an unexpectedly high lipid membrane affinity. The significance of this finding has evoked considerable speculation. Here we show that membrane binding by serotonin can directly modulate membrane properties and cellular function, providing an activity pathway completely independent of serotonin receptors. Atomic force microscopy shows that serotonin makes artificial lipid bilayers softer, and induces nucleation of liquid disordered domains inside the raft-like liquid-ordered domains. Solid-state NMR spectroscopy corroborates this data at the atomic level, revealing a homogeneous decrease in the order parameter of the lipid chains in the presence of serotonin. In the RN46A immortalized serotonergic neuronal cell line, extracellular serotonin enhances transferrin receptor endocytosis, even in the presence of broad-spectrum serotonin receptor and transporter inhibitors. Similarly, it increases the membrane binding and internalization of oligomeric peptides. Our results uncover a mode of serotonin-membrane interaction that can potentiate key cellular processes in a receptor-independent fashion.