Biology subjects

Lyman, E.

Publications and source records attributed to Lyman, E..

14 recordsLinked to original sources

bioRxiv2026

Spatial Organization of Lipids Drives GPCR Conformational Equilibria

Despite the widespread use of lipid nanodiscs for structure-function studies of membrane proteins, little is known about how lipids are spatially organized within nanodiscs and how this organization influences embedded proteins. The activity and conformational equilibria of the human A2A adenosine receptor, a class A G protein-coupled receptor, are highly sensitive to anionic lipids that directly interact with the receptor. We leverage this lipid-dependent sensitivity to probe the accessibility of anionic lipids across nanodiscs of varying sizes. We identify a threshold concentration of anionic lipids required to fully populate active receptor conformations that is higher for POPS than for POPG. Computational simulations reveal that POPS and POPG each form lipid clusters reducing the effective availability of anionic lipids to interact with the receptor. This effect is stronger for POPS and scales with increasing nanodisc size, correlating with experimental biophysical and biochemical measurements. Simulations further identify positively charged residues within the membrane scaffold protein that coordinate anionic lipid headgroups. Targeted protein engineering reduces the threshold concentration of anionic lipids required for receptor activation, supporting strategies to control lipid accessibility within nanodiscs. Because membrane scaffold proteins are derived from apolipoprotein A-I, similar lipid-protein interactions may also influence lipid organization within biological systems such as HDL particles.

biophysics↗

bioRxiv2026

Ether linkages in phospholipids provide modular control of membrane mechanics

The structures of phospholipid headgroups and chains are well-established determinants of membrane elastic properties, but functions for different chemistries that join these moieties together are poorly understood. While common phospholipids feature ester linkages, alkyl ether- and plasmenyl-linked species emerged in prokaryotes, are highly abundant in metazoans, and have been implicated in neurodegeneration and aging. Multiple pathways for ether lipid synthesis evolved convergently, suggesting conserved functions for ether linkage chemistry in the structure of cell membranes. Here we combine experiments and molecular simulations to show that backbone linkage chemistry provides modular control of membrane mechanics and topology through a set of discrete drivers. Alkyl linkages provide the first of these by additively promoting negative intrinsic curvature, which destabilizes bilayers. Ethers also decouple membrane stiffness from viscosity, softening membranes while maintaining packing in the hydrophobic core. The plasmenyl C=C bond represents a second, distinct driver that stabilizes the inverted hexagonal phase by relieving interstitial packing frustration. These results explain the fusogenicity of ether lipids, show how they regulate membrane topology through multiple physical mechanisms, and provide a rationale for convergent evolution of the complex plasmenyl linkage moiety.

biophysics↗

bioRxiv2026

Investigator-blind discovery of structural elements controlling GPCR function

With the advance of hardware and software for molecular dynamics simulation it has become routine to obtain trajectories that are tens of microseconds in duration for all kinds of protein machinery. This shifts the burden of work onto analysis of the simulation data and opens opportunities for more rigorous and reproducible observations on mechanism. Toward this end we developed an investigator-blind analysis pipeline which operates on featurized simulation data, performs unsupervised clustering, and then identifies which input features are most discriminatory of cluster identity. Application of this pipeline to a large set of G-protein coupled receptor simulation data shows that it identifies several well-known microswitches. Inspection of these structural elements reveals changes in conformation that are known to accompany functional transitions of the receptor. In addition to these known structural elements the analysis also identifies two possibly new structural motifs: the kink in transmembrane helix 2, and a coupled "piston-like" motion of TM2 and TM3.

biophysics↗

bioRxiv2024

Signatures of glassy dynamics in highly ordered lipid bilayers with emergence of soft dynamic channels

Over the last few decades, extensive investigations on spatial and dynamic heterogeneity have been performed on carefully reconstituted biological lipid membranes. Characterising the molecular features in heterogeneous membranes is extremely challenging due to experimentally inaccessible time- and length-scales of these emergent systems. In this context, simulations can provide important insights into molecular-level interactions leading to membrane heterogeneity and associated functions. To that end, we use the non-affine displacement (NAD) framework (a concept borrowed from Physics of granular material) to faithfully capture molecular-scale local membrane order in simulated heterogeneous bilayers. In our latest application of NAD, we investigate the temperature-dependent spatial and temporal organisation on microseconds trajectories of liquid-ordered bilayer systems at all-atom resolution (DPPC/DOPC/CHOL: 0.55:0.15:0.30; 40 nm x 40 nm with a total of 5600 lipids and 2 million atoms). Lateral organisation in these large bilayer patches show noticeable dynamic heterogeneity despite their liquid-ordered nature. Moreover, our NAD analyses reveal soft fluid channels within the tightly packed membrane reminiscent of the classical two-component Kob-Andersen glass-forming binary mixture. Hence, we characterised these systems using classical glass physics markers for dynamic heterogeneities such as Overlap, Four-point Susceptibility, van Hove, and Intermediate Scattering functions to quantify the multiple time scales underlying the lipid dynamics. Our analyses reveal that highly ordered membrane systems can have glass-like dynamics with distinct soft fluid channels inside them. Biologically, these dynamic channels could act as conduits for facilitating molecular encounters for biological functions even in highly ordered phases such as lipid nanodomains and rafts. SignificanceLiquid-ordered lipid membrane offers a reliable representation of the cholesterolrich outer leaflet of the plasma membrane. We show that dynamic heterogeneity is present even in highly ordered phases of lipid membrane, which arise at equilibrium merely from thermal fluctuations. Membranes in this state act as strong glass formers, and are hence less susceptible to temperature fluctuations. The dynamics is faster than actin or proteinmediated reorganisation and presence of passive but dynamic "soft channels" amidst the highly ordered lipid environment suggests a new exciting possibility that these channels could act as fast conduits for molecular encounters on the robust membrane surface.

biophysics↗

bioRxiv2023

Membrane Mimetic-Dependence of GPCR Energy Landscapes

Protein function strongly depends on temperature, which is related to temperature-dependent changes in the equilibria of protein conformational states. We leveraged variable-temperature 19F-NMR spectroscopy to interrogate the temperature dependence of the conformational landscape of the human A2A adenosine receptor (A2AAR), a class A GPCR. Temperature-induced changes in the conformational equilibria of A2AAR in lipid nanodiscs were markedly dependent on the efficacy of bound drugs. While antagonist complexes displayed only modest changes as the temperature rose, both full and partial agonist complexes exhibited substantial increases in the active state population. Importantly, the temperature-dependent response of complexes with both full and partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. In striking contrast to observations within lipid nanodiscs, in detergent micelles the active state population exhibited different behavior for A2AAR complexes with both full and partial agonists. This underscores the importance of the protein environment in understanding the thermodynamics of GPCR activation. HighlightsO_LIActive A2AAR population increases with increasing temperature in lipid nanodiscs C_LIO_LIActive A2AAR population exhibits different temperature dependence in detergents C_LIO_LIPartial agonist complexes present a unique conformational state in nanodiscs C_LIO_LITemperature dependence of partial agonist equilibria depends on membrane mimetic C_LI

biophysics↗

bioRxiv2023

Varying the position of phospholipid acyl chain unsaturation modulates hopanoid and sterol ordering

The cell membrane must balance mechanical stability with fluidity to function as both a barrier and an organizational platform. Key to this balance is the thermodynamic ordering of lipids. Most Eukaryotes employ sterols, which are uniquely capable of modulating lipid order to decouple membrane stability from fluidity. Ancient sterol analogues known as hopanoids are found in many bacteria and are proposed as ancestral ordering lipids. The juxtaposition of sterols and hopanoids in extant organisms prompts us to ask why both pathways persist, especially in light of their convergent ability to order lipids. We reveal that both hopanoids and sterols order unsaturated phospholipids differently based on the position of double bonds in the phospholipids acyl chain. We find that cholesterol and diplopterols methyl group distributions lead to distinct effects on unsaturated lipids. In Mesoplasma florum, diplopterols constrained ordering capacity reduces membrane resistance to osmotic stress, unlike cholesterol. These findings suggest cholesterols broader lipid ordering ability may have facilitated the exploration of a more diverse lipidomic landscape in eukaryotic membranes.

biophysics↗

bioRxiv2023

Cell Membranes Sustain Phospholipid Imbalance Via Cholesterol Asymmetry

Membranes are molecular interfaces that compartmentalize cells to control the flow of nutrients and information. These functions are facilitated by diverse collections of lipids, nearly all of which are distributed asymmetrically between the two bilayer leaflets. Most models of biomembrane structure and function often include the implicit assumption that these leaflets have similar abundances of phospholipids. Here, we show that this assumption is generally invalid and investigate the consequences of lipid abundance imbalances in mammalian plasma membranes (PM). Using quantitative lipidomics, we discovered that cytoplasmic leaflets of human erythrocyte membranes have >50% overabundance of phospholipids compared to exoplasmic leaflets. This imbalance is enabled by an asymmetric interleaflet distribution of cholesterol, which regulates cellular cholesterol homeostasis. These features produce unique functional characteristics, including low PM permeability and resting tension in the cytoplasmic leaflet that regulates protein localization. These largely overlooked aspects of membrane asymmetry represent an evolution of classic paradigms of biomembrane structure and physiology.

biophysics↗

bioRxiv2023

Anionic Phospholipids Control Mechanisms of GPCR-G Protein Recognition

G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we visualized the impact of anionic lipids on the function-related conformational equilibria of the human A2A adenosine receptor (A2AAR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids primed the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeded through a less favorable induced fit mechanism. In computational models, anionic lipids mimicked interactions between a G protein and positively charged residues in A2AAR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly altered the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.

biophysics↗

bioRxiv2021

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.

Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cells organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1s life cycle.

biophysics↗

bioRxiv2020

Activation of G-protein coupled receptors is thermodynamically linked to lipid solvation

Preferential lipid solvation of the G-protein coupled A2A adenosine receptor (A2AR) is evaluated from 35 sec of all-atom molecular dynamics simulation. A coarse-grained transition matrix algorithm is developed to overcome slow equilibration of the first solvation shell, obtaining statistically robust estimates of the free energy of solvation by different lipids for the receptor in different activation states. Results indicate preference for solvation by unsaturated chains, which favors the active receptor. A model for lipid-dependent GPCR activity is proposed in which the chemical potential of lipids in the bulk membrane modulates receptor activity. The enthalpy and entropy associated with moving saturated vs. unsaturated lipids from bulk to A2ARs first solvation shell are compared. In the simulated mixture, saturated chains are disordered (i.e., obtain a favorable entropic contribution) when partitioning to the receptor surface, but this is outweighed by a favorable enthalpic contribution for unsaturated chains to occupy the first solvation shell.

biophysics↗

bioRxiv2020

Changes in weak pair-wise correlations during running reshapes network state in the main olfactory bulb

Neural codes for sensory representations are thought to reside in a broader space defined by the patterns of spontaneous activity that occur when stimuli are not being presented. To understand the structure of this spontaneous activity in the olfactory system, we performed high-density recordings of population activity in the main olfactory bulb of awake mice. We found that spontaneous activity patterns of ensembles of mitral and tufted (M/T) cells in the main olfactory bulb changed dramatically during locomotion, including decreases in pairwise correlations between neurons and increases in the entropy of the population. Maximum entropy models of the ensemble activity revealed that pair-wise interactions were better at predicting patterns of activity when the animal was stationary than while running, suggesting that higher order (3rd, 4th order) interactions between neurons shape activity during locomotion. Taken together, we found that locomotion influenced the structure of spontaneous population activity at the earliest stages of olfactory processing, 1 synapse away from the sensory receptors in the nasal epithelium. New and NoteworthyThe organization and structure of spontaneous population activity in the olfactory system places constraints of how odor information is represented. Using high-density electrophysiological recordings of mitral and tufted cells, we found that running increases the dimensionality of spontaneous activity, implicating higher-order interactions among neurons during locomotion. Behavior thus flexibly alters neuronal activity at the earliest stages of sensory processing.

neuroscience↗

bioRxiv2019

The Molecular and Structural Asymmetry of the Plasma Membrane

A fundamental feature of cellular plasma membranes (PM) is asymmetric lipid distribution between the bilayer leaflets. However, neither the detailed, comprehensive compositions of individual PM leaflets, nor how these contribute to structural membrane asymmetries have been defined. We report the distinct lipidomes and biophysical properties of both monolayers in living mammalian PMs. Phospholipid unsaturation is dramatically asymmetric, with the cytoplasmic leaflet being [~]2-fold more unsaturated than the exoplasmic. Atomistic simulations and spectroscopy of leaflet-selective fluorescent probes reveal that the outer PM leaflet is more packed and less diffusive than the inner leaflet, with this biophysical asymmetry maintained in the endocytic system. The structural asymmetry of the PM is reflected in asymmetric structures of protein transmembrane domains (TMD). These structural asymmetries are conserved throughout Eukaryota, suggesting fundamental cellular design principles.

cell biology↗

bioRxiv2019

Nanoscale dynamics of cholesterol in the cell membrane

Cholesterol constitutes approximately 30-40% of the mammalian plasma membrane -- a larger fraction than any other single component. It is a major player in numerous signalling processes as well as molecular membrane architecture. However, our knowledge on dynamics of cholesterol in the plasma membrane is limited which restricts our understanding of the mechanisms regulating its involvement in cell signalling. Here, advanced fluorescence imaging and spectroscopy approaches were applied on in vitro (model membranes) and in vivo (live cells and embryos) membranes to systematically study the nanoscale dynamics of cholesterol in biological membranes. The results show that cholesterol diffuses faster than phospholipids in live membranes, but not in model membranes. The data indicate that diffusion of cholesterol and phospholipids is not correlated with membrane domain partitioning. Instead, our data show that the fast diffusion of cholesterol is due to its nanoscale interactions and localization in the membrane.

biophysics↗

bioRxiv2018

The Organization of Membranes Below 100 nm: Experimental Breakthroughs Occasion a Modeling Manifesto

New experimental techniques reveal the plasma membrane to be heterogeneous and \"scale-rich,\" from nanometers to microns, and from microseconds to seconds. This is critical information, as heterogeneous, scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich, and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity to the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the \"manifesto\". Together with the experimental data, simulations which satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches which aim to meet them are detailed.

biophysics↗