The ins and outs in membrane dynamics: tubulation and vesiculation

Living cells constantly adjust the composition and size of their membrane systems to accommodate the demands for the housekeeping activities, to expand and reduce cell size, and to commit the cell for division. Although it is well known that vesicles are the vehicles to deliver and retrieve lipids and proteins to and from the membranes, the mechanisms allowing vesicles to pinch off from membranes or fuse into a flat lipid bilayer have been poorly understood, particularly in plants. Recent studies on dynamins and dynamin-related proteins in animals and plants now allow new concepts in membrane dynamics to be considered.     

Properties influencing fluorophore lifetime distributions in lipid bilayers

The fluorescence lifetime of the membrane fluorophore 1,6-diphenyl-1,3,5-hexatriene has been analyzed according to the distributional approach in a number of lipid bilayer systems. The systems included vesicles of 16:0/18:1-phosphatidylcholine (POPC), egg phosphatidylcholine (EYPC), microsomal phospholipids, and also intact microsomal membranes. With increasing complexity of composition, an increasingly broader width was found in the major component of a bimodal Lorentzian fluorescence lifetime distribution. In order to explain these findings, we propose a model based on environmental heterogeneity and environmental sampling, where the environment is defined as the lipid molecules immediately surrounding the fluorophore. Environmental heterogeneity is thought of as arising from organizational, compositional, and solvent factors. Environmental sampling pertains to the ability of a fluorophore to detect environments in a system and is a function of the fluorophore lifetime and the lipid dynamics. If the fluorescence lifetime is sufficiently short, the fluorophore will only sample a particular environment, and great compositional complexity will mean that each fluorophore in an ensemble will decay to the ground state with a different time. This appears to explain why in our results with DPH a narrow width is obtained for POPC, where vesicles are composed of a single phospholipid molecular species, compared to EYPC and microsomal phospholipid vesicles having complex molecular species composition. This model should serve as a basis for understanding the interrelationships of environmental complexity and lipid dynamics in membranes.     

ICMRBS founder’s medal 2006: Biological solid-state NMR,methods and applications

Solid-state NMR (ssNMR) provides increasing possibilities to study structure and dynamics of biomolecular systems. Our group has been interested in developing ssNMR-based approaches that are applicable to biomolecules of increasing molecular size and complexity without the need of specific isotope-labelling. Methodological aspects ranging from spectral assignments to the indirect detection of proton–proton contacts in multi-dimensional ssNMR are discussed and applied to (membrane) protein complexes.     

Cholesterol interactions with phospholipids in membranes.

Mammalian cell membranes are composed of a complex array of glycerophospholipids and sphingolipids that vary in head-group and acyl-chain composition. In a given cell type, membrane phospholipids may amount to more than a thousand molecular species. The complexity of phospholipid and sphingolipid structures is most likely a consequence of their diverse roles in membrane dynamics, protein regulation, signal transduction and secretion. This review is mainly focused on two of the major classes of membrane phospholipids in eukaryotic organisms, sphingomyelins and phosphatidylcholines. These phospholipid classes constitute more than 50% of membrane phospholipids. Cholesterol is most likely to associate with these lipids in the membranes of the cells. We discuss the synthesis and distribution in the cell of these lipids, how they are believed to interact with each other, and what cellular consequences such interactions may have. We also include a discussion about findings in the recent literature regarding cholesterol/phospholipid interactions in model membrane systems. Finally, we look at the recent trends in computer and molecular dynamics simulations regarding phospholipid and cholesterol/phospholipid behavior in bilayer membranes.     

Three-Dimensional Cell Geometry Controls Excitable Membrane Signaling in Dictyostelium Cells

Phosphatidylinositol (3–5)-trisphosphate (PtdInsP3) is known to propagate as waves on the plasma membrane and is related to the membrane-protrusive activities in Dictyostelium and mammalian cells. Although there have been a few attempts to study the three-dimensional (3D) dynamics of these processes, most studies have focused on the dynamics extracted from single focal planes. However, the relation between the dynamics and 3D cell shape remains elusive because of the lack of signaling information about the unobserved part of the membrane. Here, we show that PtdInsP3 wave dynamics are directly regulated by the 3D geometry (i.e., size and shape) of the plasma membrane. By introducing an analysis method that extracts the 3D spatiotemporal activities on the entire cell membrane, we show that PtdInsP3 waves self-regulate their dynamics within the confined membrane area. This leads to changes in speed, orientation, and pattern evolution, following the underlying excitability of the signal transduction system. Our findings emphasize the role of the plasma membrane topology in reaction-diffusion-driven biological systems and indicate its importance in other mammalian systems.     

The utility of a digital simulation language for ecological modeling

Summary Dynamic modeling of ecological phenomena has been greatly facilitated by the recent development of continuous system simulator programs. This paper illustrates the application of one of these programs, S/360 Continuous System Modeling Program (S/360 CSMP), to four systems of graduated complexity. The first is a two species system, with one feeding on the other, using differential equations with constant coefficients. The second and third systems involve two competing plant species in which the coefficients of the differential equations are varying with time. The final example considers the management of a postulated buffalo herd in which the dynamics of the herd population and composition by sex and age is combined with various strategies to control its size and to optimize buffalo production.     

Applying the resource dispersion hypothesis to a fission–fusion society: A case study of the African lion (Panthera leo)

The relationship between the spatiotemporal distribution of resources and patterns of sociality is widely discussed. While the resource dispersion hypothesis (RDH) was formulated to explain why animals sometimes live in groups from which they derive no obvious benefits, it has also been successfully applied to species that benefit from group living. Some empirical tests have supported the RDH, but others have not, so conclusions remain equivocal and further research is required to determine the extent to which RDH predictions hold in natural systems. Here, we test four predictions of the RDH in an African lion population in the context of their fission–fusion society. We analyzed data on group composition of GPS‐collared lions and patterns of prey availability. Our results supported the first and second predictions of the RDH: Home range size (a) was independent of group size and (b) increased with distance between encounters with prey herds. Nonetheless, the third and fourth RDH predictions were not supported: (c) The measure of resource heterogeneity and (d) resource patch richness measured through prey herd size and body size had no significant effect on lion group size. However, regarding the fourth prediction, we added an adaptation to account for dynamics of fission–fusion society and found that the frequency of pride fission increased as group size increased. Our data set restricted us from going on to explore the effect of fission–fusion dynamics on the relationship between group size and patch richness. However, this should be investigated in future studies as including fission–fusion dynamics provides a more nuanced, realistic appreciation of lion society. Our study emphasizes the importance of understanding the complexity of a species' behavioral ecology within the framework of resource dispersion. Whatever larger theoretical framework may emerge to explain lion society, incorporating fission–fusion dynamics should allow the RDH to be refined and improved.     

Preparing giant unilamellar vesicles (GUVs) of complex lipid mixtures on demand: Mixing small unilamellar vesicles of compositionally heterogeneous mixtures

Giant unilamellar vesicles (GUVs) are simple model membrane systems of cell-size, which are instrumental to study the function of more complex biological membranes involving heterogeneities in lipid composition, shape, mechanical properties, and chemical properties. We have devised a method that makes it possible to prepare a uniform sample of ternary GUVs of a prescribed composition and heterogeneity by mixing different populations of small unilamellar vesicles (SUVs). The validity of the protocol has been demonstrated by applying it to ternary lipid mixture of DOPC, DPPC, and cholesterol by mixing small unilamellar vesicles (SUVs) of two different populations and with different lipid compositions. The compositional homogeneity among GUVs resulting from SUV mixing is quantified by measuring the area fraction of the liquid ordered–liquid disordered phases in giant vesicles and is found to be comparable to that in GUVs of the prescribed composition produced from hydration of dried lipids mixed in organic solvent. Our method opens up the possibility to quickly increase and manipulate the complexity of GUV membranes in a controlled manner at physiological buffer and temperature conditions. The new protocol will permit quantitative biophysical studies of a whole new class of well-defined model membrane systems of a complexity that resembles biological membranes with rafts.     

Increasing community size and connectance can increase stability in competitive communities

The relationship between community complexity and stability has been the subject of an enduring debate in ecology over the last 50 years. Results from early model communities showed that increased complexity is associated with decreased local stability. I demonstrate that increasing both the number of species in a community and the connectance between these species results in an increased probability of local stability in discrete-time competitive communities, when some species would show unstable dynamics in the absence of competition. This is shown analytically for a simple case and across a wider range of community sizes using simulations, where individual species have dynamics that can range from stable point equilibria to periodic or more complex. Increasing the number of competitive links in the community reduces per-capita growth rates through an increase in competitive feedback, stabilising oscillating dynamics. This result was robust to the introduction of a trade-off between competitive ability and intrinsic growth rate and changes in species interaction strengths. This throws new light on the discrepancy between the theoretical view that increased complexity reduces stability and the empirical view that more complex systems are more likely to be stable, giving one explanation for the relative lack of complex dynamics found in natural systems. I examine how these results relate to diversity-biomass stability relationships and show that an analytical solution derived in the region of stable equilibrium dynamics captures many features of the change in biomass fluctuations with community size in communities including species with oscillating dynamics.     

In Vitro Reconstitution of the Initial Stages of the Bacterial Cell Division Machinery

Fission of many prokaryotes as well as some eukaryotic organelles depends on the self-assembly of the FtsZ protein into a membrane-associated ring structure early in the division process. Different components of the machinery are then sequentially recruited. Although the assembly order has been established, the molecular interactions and the understanding of the force-generating mechanism of this dividing machinery have remained elusive. It is desirable to develop simple reconstituted systems that attempt to reproduce, at least partially, some of the stages of the process. High-resolution studies of Escherichia coli FtsZ filaments’ structure and dynamics on mica have allowed the identification of relevant interactions between filaments that suggest a mechanism by which the polymers could generate force on the membrane. Reconstituting the membrane-anchoring protein ZipA on E. coli lipid membrane on surfaces is now providing information on how the membrane attachment regulates FtsZ polymer dynamics and indicates the important role played by the lipid composition of the membrane.     

Fission-fusion dynamics, behavioral flexibility, and inhibitory control in primates

The Machiavellian Intelligence or Social Brain Hypothesis explains the evolution of increased brain size as mainly driven by living in complex organized social systems in which individuals represent "moving targets" who can adopt multiple strategies to respond to one another. Frequently splitting and merging in subgroups of variable composition (fission-fusion or FF dynamics) has been proposed as one aspect of social complexity ( compare with) that may be associated with an enhancement of cognitive skills like inhibition, which allows the suppression of prepotent but ineffective responses in a changing social environment. We compared the performance of primates experiencing high levels of FF dynamics (chimpanzees, bonobos, orangutans, and spider monkeys) to that of species living in more cohesive groups (gorillas, capuchin monkeys, and long-tailed macaques) on five inhibition tasks. Testing species differing in diet, phylogenetic relatedness, and levels of FF dynamics allowed us to contrast ecological, phylogenetic, and socioecological explanations for interspecific differences. Spider monkeys performed at levels comparable to chimpanzees, bonobos, and orangutans, and better than gorillas. A two-cluster analysis grouped all species with higher levels of FF dynamics together. These findings confirmed that enhanced inhibitory skills are positively associated with FF dynamics, more than to phylogenetic relations or feeding ecology.     

Lipid-induced conformation and lipid-binding properties of cytolytic and antimicrobial peptides: determination and biological specificity

While antimicrobial and cytolytic peptides exert their effects on cells largely by interacting with the lipid bilayers of their membranes, the influence of the cell membrane lipid composition on the specificity of these peptides towards a given organism is not yet understood. The lack of experimental model systems that mimic the complexity of natural cell membranes has hampered efforts to establish a direct correlation between the induced conformation of these peptides upon binding to cell membranes and their biological specificities. Nevertheless, studies using model membranes reconstituted from lipids and a few membrane-associated proteins, combined with spectroscopic techniques (i.e. circular dichroism, fluorescence spectroscopy, Fourier transform infra red spectroscopy, etc.), have provided information on specific structure-function relationships of peptide-membrane interactions at the molecular level. Reversed phase-high performance chromatography (RP-HPLC) and surface plasmon resonance (SPR) are emerging techniques for the study of the dynamics of the interactions between cytolytic and antimicrobial peptides and lipid surfaces. Thus, the immobilization of lipid moieties onto RP-HPLC sorbent now allows the investigation of peptide conformational transition upon interaction with membrane surfaces, while SPR allows the observation of the time course of peptide binding to membrane surfaces. Such studies have clearly demonstrated the complexity of peptide-membrane interactions in terms of the mutual changes in peptide binding, conformation, orientation, and lipid organization, and have, to a certain extent, allowed correlations to be drawn between peptide conformational properties and lytic activity.     

Peptides in lipid bilayers: the power of simple models

Interactions between proteins and lipids lie at the heart of virtually all membrane processes, but on a molecular level they are still poorly understood. Nowadays, simple model systems comprising designed transmembrane peptides in synthetic lipid bilayers are increasingly being recognized as powerful tools to uncover basic principles of protein-lipid interactions. Such model systems enable detailed analysis of how the properties of lipids influence the structure and dynamics of transmembrane helices, how these helices are anchored at the lipid-water interface, and how the length and composition of transmembrane segments influence the organization and dynamics of membrane lipids. In addition, well-characterized model systems have proven useful to refine computational approaches and to develop new techniques for studies of protein-lipid interactions.     

Odefy - From discrete to continuous models

Background  

Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable.     

Influence of the extracellular domain size on the dynamic behavior of membrane proteins

The dynamic behavior of plasma membrane proteins mediates various cellular processes such as cellular motility, communication, and signaling. It is widely accepted that the dynamics of the membrane proteins is determined either by the interactions of the transmembrane domain with the surrounding lipids or by the interactions of the intracellular domain with cytosolic components such as cortical actin. Although initiation of different cellular signaling events at the plasma membrane has been attributed to the extracellular domain (ECD) properties recently, the impact of ECDs on the dynamic behavior of membrane proteins is rather unexplored. Here, we investigate how ECD properties influence protein dynamics in the lipid bilayer by reconstituting ECDs of different sizes or glycosylation in model membrane systems and analyzing ECD-driven protein sorting in lipid domains as well as protein mobility. Our data show that increasing the ECD mass or glycosylation leads to a decrease in ordered domain partitioning and diffusivity. Our data reconcile different mechanisms proposed for the initiation of cellular signaling by linking the ECD size of membrane proteins with their localization and diffusion dynamics in the plasma membrane.     

跨膜蛋白CD3ε与磷脂酰肌醇二磷酸在脂筏域体系中蛋白质-脂质相互作用的粗粒化模拟研究

细胞膜局部区域可形成富含饱和脂质、胆固醇、鞘脂的脂筏域作为其信号转导调控平台。传统实验手段在研究脂筏及其功能时受到系统复杂度高及区域结构瞬时性强等制约。近年来,分子动力学模拟技术为细胞膜的组织原则提供了重要的理论支撑,从简单的单一组分模型到多组分系统转变,最终形成了越来越多的细胞膜仿真模型。其中,粗粒化模拟由于其简化模型,可大副拓展模拟体系的复杂程度与模拟时间,在细胞膜以及蛋白质-脂质相互作用相关研究中得到了广泛应用。本文采用MARTINI粗粒化力场模拟,构建了一种含有阴离子脂质磷脂酰肌醇二磷酸(phosphatidylinositol diphosphate, PIP2)的混合膜体系。模拟结果表明,该体系在适当温度及饱和度条件下,能自发分层形成脂筏域;膜厚度、膜组分分布、膜组分流动性等多种参数均表明,脂筏结构形成且符合其结构特征;少量PIP2添加不影响分层特性且PIP2对脂筏具有显著亲和性。此外,利用该模型以跨膜信号蛋白CD3ε为例研究了脂筏域体系中蛋白质-脂质相互作用。结果表明,PIP2-CD3ε胞内区相互作用可能是脂筏招募CD3ε的驱动力,且该过程可受钙离子调控。本工作体现了粗粒化模拟在仿真膜相关研究中的巨大优势及良好应用前景。     

Bicelles: A natural ‘molecular goniometer’ for structural,dynamical and topological studies of molecules in membranes

Major biological processes occur at the biological membrane. One of the great challenges is to understand the function of chemical or biological molecules inside the membrane; as well of those involved in membrane trafficking. This requires obtaining a complete picture of the in situ structure and dynamics as well as the topology and orientation of these molecules in the membrane lipid bilayer. These led to the creation of several innovative models of biological membranes in order to investigate the structure and dynamics of amphiphilic molecules, as well as integral membrane proteins having single or multiple transmembrane segments. Because the determination of the structure, dynamics and topology of molecules in membranes requires a macroscopic alignment of the system, a new membrane model called ‘bicelles’ that represents a crossover between lipid vesicles and classical micelles has become very popular due to its property of spontaneous self-orientation in magnetic fields. In addition, crucial factors involved in mimicking natural membranes, such as sample hydration, pH and salinity limits, are easy to control in bicelle systems. Bicelles are composed of mixtures of long chain (14–18 carbons) and short chain phospholipids (6–8 carbons) hydrated up to 98% with buffers and may adopt various morphologies depending on lipid composition, temperature and hydration. We have been developing bicelle systems under the form of nano-discs made of lipids with saturated or biphenyl-containing fatty acyl chains. Depending on the lipid nature, these membranous nano-discs may be macroscopically oriented with their normal perpendicular or parallel to the magnetic field, providing a natural ‘molecular goniometer’ for structural and topological studies, especially in the field of NMR. Bicelles can also be spun at the magic angle and lead to the 3D structural determination of molecules in membranes.     

Monitoring the organization and dynamics of bovine hippocampal membranes utilizing Laurdan generalized polarization

Organization and dynamics of cellular membranes in the nervous system are crucial for the function of neuronal membrane receptors. The lipid composition of neuronal cells is unique and has been correlated with the increased complexity in the organization of the nervous system during evolution. Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors such as the G-protein coupled serotonin_1A receptor. In this paper, we have explored the organization and dynamics of bovine hippocampal membranes using the amphiphilic environment-sensitive fluorescent probe Laurdan. Our results show that the emission spectra of Laurdan display an additional red shifted peak as a function of increasing temperature in native as well as cholesterol-depleted membranes and liposomes made from lipid extracts of the native membrane. Interestingly, wavelength dependence of Laurdan generalized polarization (GP) in native membranes indicates the presence of an ordered gel-like phase at low temperatures, whereas characteristics of the liquid-ordered phase are observed at high temperatures. Similar experiments performed using cholesterol-depleted membranes show fluidization of the membrane with increasing cholesterol depletion. In addition, results from fluorescence polarization of DPH indicate that the hippocampal membrane is fairly ordered even at physiological temperature. The temperature dependence of Laurdan excitation GP provides a measure of the apparent thermal transition temperature and extent of cooperativity in these membranes. Analysis of time-resolved fluorescence measurements of Laurdan shows reduction in mean fluorescence lifetime with increasing temperature due to change in environmental polarity. These results constitute novel information on the dynamics of hippocampal membranes and its modulation by cholesterol depletion monitored using Laurdan fluorescence.     

Size constraints and the evolution of display complexity: why do large lizards have simple displays?

Social, environmental, and perceptual factors have been suggested to account for the evolution of visual signal diversity in lizards. Previous investigations have inferred that signal complexity may also be related to body size. In this study, we use three complementary comparative analyses to investigate whether body size has influenced macro-evolutionary trends in display modifier repertoire size for 110 species of iguanian lizards. We found evidence that signal complexity, as measured by repertoire size, is negatively associated with body size. However, this relationship was not strictly linear. Rather, body size seems to impose a threshold on signal evolution. Specifically, the evolution of large repertoire size appears to be less likely above a particular size threshold, which results in large-bodied lizards having a significantly lower probability of evolving elaborate displays. This relationship may reflect the influence of body size on resource use and the emergent social dynamics it promotes. Large lizards tend to be herbivorous and typically do not defend foraging patches. Consistent with this hypothesis is the previously reported finding of a similar size threshold dividing herbivorous from insectivorous lizards. We suggest to fully understand the evolutionary processes acting on communicative systems, it is important that we identify both the selective forces involved and the nature of their influence. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 145–161.     

Balance between Noise and Information Flow Maximizes Set Complexity of Network Dynamics

Boolean networks have been used as a discrete model for several biological systems, including metabolic and genetic regulatory networks. Due to their simplicity they offer a firm foundation for generic studies of physical systems. In this work we show, using a measure of context-dependent information, set complexity, that prior to reaching an attractor, random Boolean networks pass through a transient state characterized by high complexity. We justify this finding with a use of another measure of complexity, namely, the statistical complexity. We show that the networks can be tuned to the regime of maximal complexity by adding a suitable amount of noise to the deterministic Boolean dynamics. In fact, we show that for networks with Poisson degree distributions, all networks ranging from subcritical to slightly supercritical can be tuned with noise to reach maximal set complexity in their dynamics. For networks with a fixed number of inputs this is true for near-to-critical networks. This increase in complexity is obtained at the expense of disruption in information flow. For a large ensemble of networks showing maximal complexity, there exists a balance between noise and contracting dynamics in the state space. In networks that are close to critical the intrinsic noise required for the tuning is smaller and thus also has the smallest effect in terms of the information processing in the system. Our results suggest that the maximization of complexity near to the state transition might be a more general phenomenon in physical systems, and that noise present in a system may in fact be useful in retaining the system in a state with high information content.