Kinetics of bimolecular reactions in model bilayers and biological membranes. A critical review

Location of dopamine in lipid bilayers and its relevance to neuromodulator function

Dopamine (DA) is a neurotransmitter that also acts as a neuromodulator, with both functions being essential to brain function. Here, we present the first experimental measurement of DA location in lipid bilayers using x-ray diffuse scattering, solid-state deuterium NMR, and electron paramagnetic resonance. We find that the association of DA with lipid headgroups as seen in electron density profiles leads to an increase of intermembrane repulsion most likely due to electrostatic charging. DA location in the lipid headgroup region also leads to an increase of the cross-sectional area per lipid without affecting the bending rigidity significantly. The order parameters measured by solid-state deuterium NMR decrease in the presence of DA for the acyl chains of PC and PS lipids, consistent with an increase in the area per lipid due to DA. Most importantly, these results support the hypothesis that three-dimensional diffusion of DA to target membranes could be followed by relatively more efficient two-dimensional diffusion to receptors within those membranes.

The Impact of Membrane Protein Diffusion on GPCR Signaling

Spatiotemporal signal shaping in G protein-coupled receptor (GPCR) signaling is now a well-established and accepted notion to explain how signaling specificity can be achieved by a superfamily sharing only a handful of downstream second messengers. Dozens of Gs-coupled GPCR signals ultimately converge on the production of cAMP, a ubiquitous second messenger. This idea is almost always framed in terms of local concentrations, the differences in which are maintained by means of spatial separation. However, given the dynamic nature of the reaction-diffusion processes at hand, the dynamics, in particular the local diffusional properties of the receptors and their cognate G proteins, are also important. By combining some first principle considerations, simulated data, and experimental data of the receptors diffusing on the membranes of living cells, we offer a short perspective on the modulatory role of local membrane diffusion in regulating GPCR-mediated cell signaling. Our analysis points to a diffusion-limited regime where the effective production rate of activated G protein scales linearly with the receptor–G protein complex’s relative diffusion rate and to an interesting role played by the membrane geometry in modulating the efficiency of coupling.

Picosecond to Second Fluorescence Correlation Spectroscopy for Studying Solute Exchange and Quenching Dynamics in Micellar Media

Numerous studies have been devoted to understand the reaction kinetics in micelles, where the accessible kinetic time window is often limited by the dynamic range of the employed spectroscopic technique. This is usually accompanied by a selection of probes that comfortably explore time scales where slow solute exchange kinetics is negligible, as compared to the fast excited state reactions. This has led to an undervaluation of the role played by dynamic partitioning of hydrophilic solutes in microheterogeneous media. Here, we employ fluorescence correlation spectroscopy (FCS) and the zwitterionic dye Rhodamine 110 to quantitatively explore the impact of solute exchange on the photoinduced electron transfer between this dye and N,N-dimethylaniline in micellar media. Our study elucidates the coupling and interplay between the kinetics of photophysics, quenching, and solute exchange through a quantitative unified molecular-state quenching-kinetic model that describes the steady-state ensemble and FCS data from subnanosecond photon antibunching to millisecond diffusions.

Molecular Crowding and Diffusion-Capture in Synapses

Cell membranes often contain domains with important physiological functions. A typical example are neuronal synapses, whose capacity to capture receptors for neurotransmitters is central to neuronal functions. Receptors diffuse in the membrane until they are stabilized by interactions with stable elements, the scaffold. Single particle tracking experiments demonstrated that these interactions are rather weak and that lateral diffusion is strongly impaired in the post-synaptic membrane due to molecular crowding. We investigated how the distribution of scaffolding molecules and molecular crowding affect the capture of receptors. In particle-based Monte Carlo simulations, based on experimental data of molecular diffusion and organization, crowding enhanced the receptor-scaffold interaction but reduced the capture of new molecules. The distribution of scaffolding sites in several clusters reduced crowding and fostered the exchange of molecules accelerating synaptic plasticity. Synapses could switch between two regimes, becoming more stable or more plastic depending on the internal distribution of molecules.

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The good: molecular crowding enhances the interaction receptors-scaffold

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The bad: the exchange of molecules with extrasynaptic areas is reduced by crowding

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Molecular crowding helps synapses to be stable

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Nanoclusters of scaffold sites reduce crowding effects and favor synaptic plasticity

Modeling Thrombin Generation in Plasma under Diffusion and Flow

We investigate the capacity of published numerical models of thrombin generation to reproduce experimentally observed threshold behavior under conditions in which diffusion and/or flow are important. Computational fluid dynamics simulations incorporating species diffusion, fluid flow, and biochemical reactions are compared with published data for thrombin generation in vitro in 1) quiescent plasma exposed to patches of tissue factor and 2) plasma perfused through a capillary coated with tissue factor. Clot time is correctly predicted in individual cases, and some models qualitatively replicate thrombin generation thresholds across a series of tissue factor patch sizes or wall shear rates. Numerical results suggest that there is not a genuine patch size threshold in quiescent plasma-clotting always occurs given enough time-whereas the shear rate threshold observed under flow is a genuine physical limit imposed by flow-mediated washout of active coagulation factors. Despite the encouraging qualitative results obtained with some models, no single model robustly reproduces all experiments, demonstrating that greater understanding of the underlying reaction network, and particularly of surface reactions, is required. In this direction, additional simulations provide evidence that 1) a surface-localized enzyme, speculatively identified as meizothrombin, is significantly active toward the fluorescent thrombin substrate used in the experiments or, less likely, 2) thrombin is irreversibly inhibited at a faster-than-expected rate, possibly explained by a stimulatory effect of plasma heparin on antithrombin. These results highlight the power of simulation to provide novel mechanistic insights that augment experimental studies and build our understanding of complex biophysicochemical processes. Further validation work is critical to unleashing the full potential of coagulation models as tools for drug development and personalized medicine.

Imaging of intermittent lipid-receptor interactions reflects changes in live cell membranes upon agonist-receptor binding

Protein-lipid interactions in cellular membranes modulate central cellular functions, are often transient in character, but occur too intermittently to be readily observable. We introduce transient state imaging (TRAST), combining sensitive fluorescence detection of fluorophore markers with monitoring of their dark triplet state transitions, allowing imaging of such protein-lipid interactions. We first determined the dark state kinetics of the biomembrane fluorophore 7-nitrobenz-2-oxa-1,3-diazole-4-yl (NBD) in lipid vesicles, and how its triplet state is quenched by spin-labels in the same membranes. We then monitored collisional quenching of NBD-lipid derivatives by spin-labelled stearic acids in live cell plasma membranes, and of NBD-lipid derivatives by spin-labelled G-Protein Coupled Receptors (GPCRs). We could then resolve transient interactions between the GPCRs and different lipids, how these interactions changed upon GPCR activation, thereby demonstrating a widely applicable means to image and characterize transient molecular interactions in live cell membranes in general, not within reach via traditional fluorescence readouts.

Diffusion-influenced reaction rates in the presence of pair interactions

The kinetics of bimolecular reactions in solution depends, among other factors, on intermolecular forces such as steric repulsion or electrostatic interaction. Microscopically, a pair of molecules first has to meet by diffusion before the reaction can take place. In this work, we establish an extension of Doi's volume reaction model to molecules interacting via pair potentials, which is a key ingredient for interacting-particle-based reaction-diffusion (iPRD) simulations. As a central result, we relate model parameters and macroscopic reaction rate constants in this situation. We solve the corresponding reaction-diffusion equation in the steady state and derive semi-analytical expressions for the reaction rate constant and the local concentration profiles. Our results apply to the full spectrum from well-mixed to diffusion-limited kinetics. For limiting cases, we give explicit formulas, and we provide a computationally inexpensive numerical scheme for the general case, including the intermediate, diffusion-influenced regime. The obtained rate constants decompose uniquely into encounter and formation rates, and we discuss the effect of the potential on both subprocesses, exemplified for a soft harmonic repulsion and a Lennard-Jones potential. The analysis is complemented by extensive stochastic iPRD simulations, and we find excellent agreement with the theoretical predictions.

Surface reaction-diffusion kinetics on lattice at the microscopic scale

Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method (MLM) can model these processes at the microscopic scale by tracking individual molecules, represented as hard spheres, on fine lattice voxels. Although MLM is simple to implement and is generally less computationally demanding than off-lattice approaches, its accuracy and consistency in modeling surface reactions have not been fully verified. Using the Spatiocyte scheme, we study the accuracy of MLM in diffusion-influenced surface reactions. We derive the lattice-based bimolecular association rates for two-dimensional (2D) surface-surface reaction and one-dimensional (1D) volume-surface adsorption according to the Smoluchowski-Collins-Kimball model and random walk theory. We match the time-dependent rates on lattice with off-lattice counterparts to obtain the correct expressions for MLM parameters in terms of physical constants. The expressions indicate that the voxel size needs to be at least 0.6% larger than the molecule to accurately simulate surface reactions on triangular lattice. On square lattice, the minimum voxel size should be even larger, at 5%. We also demonstrate the ability of MLM-based schemes such as Spatiocyte to simulate a reaction-diffusion model that involves all dimensions: three-dimensional (3D) diffusion in the cytoplasm, 2D diffusion on the cell membrane, and 1D cytoplasm-membrane adsorption. With the model, we examine the contribution of the 2D reaction pathway to the overall reaction rate at different reactant diffusivity, reactivity, and concentrations.

The influence of cholesterol on melittin lipidation in neutral membranes

Cholesterol inclusion in membranes influences the rate and selectivity of acyl transfer from lipids to a membrane-embedded peptide.

Toward a systems approach to the human cytochrome P450 ensemble: interactions between CYP2D6 and CYP2E1 and their functional consequences

Functional cross-talk among human drug-metabolizing cytochrome P450 through their association is a topic of emerging importance. Here, we studied the interactions of human CYP2D6, a major metabolizer of psychoactive drugs, with one of the most prevalent human P450 enzymes, ethanol-inducible CYP2E1. Detection of P450-P450 interactions was accomplished through luminescence resonance energy transfer between labeled proteins incorporated into human liver microsomes and the microsomes of insect cells containing NADPH-cytochrome P450 reductase. The potential of CYP2D6 to form oligomers in the microsomal membrane is among the highest observed with human cytochrome P450 studied up to date. We also observed the formation of heteromeric complexes of CYP2D6 with CYP2E1 and CYP3A4, and found a significant modulation of these interactions by 3,4-methylenedioxymethylamphetamine, a widespread drug of abuse metabolized by CYP2D6. Our results demonstrate an ample alteration of the catalytic properties of CYP2D6 and CYP2E1 caused by their association. In particular, we demonstrated that preincubation of microsomes containing co-incorporated CYP2D6 and CYP2E1 with CYP2D6-specific substrates resulted in considerable time-dependent activation of CYP2D6, which presumably occurs via a slow substrate-induced reorganization of CYP2E1-CYP2D6 hetero-oligomers. Furthermore, we demonstrated that the formation of heteromeric complexes between CYP2E1 and CYP2D6 affects the stoichiometry of futile cycling and substrate oxidation by CYP2D6 by means of decreasing the electron leakage through the peroxide-generating pathways. Our results further emphasize the role of P450-P450 interactions in regulatory cross-talk in human drug-metabolizing ensemble and suggest a role of interactions of CYP2E1 with CYP2D6 in pharmacologically important instances of alcohol-drug interactions.

Effect of Spatial Inhomogeneities on the Membrane Surface on Receptor Dimerization and Signal Initiation

Important signal transduction pathways originate on the plasma membrane, where microdomains may transiently entrap diffusing receptors. This results in a non-random distribution of receptors even in the resting state, which can be visualized as “clusters” by high resolution imaging methods. Here, we explore how spatial in-homogeneities in the plasma membrane might influence the dimerization and phosphorylation status of ErbB2 and ErbB3, two receptor tyrosine kinases that preferentially heterodimerize and are often co-expressed in cancer. This theoretical study is based upon spatial stochastic simulations of the two-dimensional membrane landscape, where variables include differential distributions and overlap of transient confinement zones (“domains”) for the two receptor species. The in silico model is parameterized and validated using data from single particle tracking experiments. We report key differences in signaling output based on the degree of overlap between domains and the relative retention of receptors in such domains, expressed as escape probability. Results predict that a high overlap of domains, which favors transient co-confinement of both receptor species, will enhance the rate of hetero-interactions. Where domains do not overlap, simulations confirm expectations that homo-interactions are favored. Since ErbB3 is uniquely dependent on ErbB2 interactions for activation of its catalytic activity, variations in domain overlap or escape probability markedly alter the predicted patterns and time course of ErbB3 and ErbB2 phosphorylation. Taken together, these results implicate membrane domain organization as an important modulator of signal initiation, motivating the design of novel experimental approaches to measure these important parameters across a wider range of receptor systems.

How spatial heterogeneity shapes multiscale biochemical reaction network dynamics

Spatial heterogeneity in cells can be modelled using distinct compartments connected by molecular movement between them. In addition to movement, changes in the amount of molecules are due to biochemical reactions within compartments, often such that some molecular types fluctuate on a slower timescale than others. It is natural to ask the following questions: how sensitive is the dynamics of molecular types to their own spatial distribution, and how sensitive are they to the distribution of others? What conditions lead to effective homogeneity in biochemical dynamics despite heterogeneity in molecular distribution? What kind of spatial distribution is optimal from the point of view of some downstream product? Within a spatially heterogeneous multiscale model, we consider two notions of dynamical homogeneity (full homogeneity and homogeneity for the fast subsystem), and consider their implications under different timescales for the motility of molecules between compartments. We derive rigorous results for their dynamics and long-term behaviour, and illustrate them with examples of a shared pathway, Michaelis-Menten enzymatic kinetics and autoregulating feedbacks. Using stochastic averaging of fast fluctuations to their quasi-steady-state distribution, we obtain simple analytic results that significantly reduce the complexity and expedite simulation of stochastic compartment models of chemical reactions.

Pivotal role of P450-P450 interactions in CYP3A4 allostery: the case of α-naphthoflavone

We investigated the relationship between oligomerization of CYP3A4 (cytochrome P450 3A4) and its response to ANF (α-naphthoflavone), a prototypical heterotropic activator. The addition of ANF resulted in over a 2-fold increase in the rate of CYP3A4-dependent debenzylation of 7-BFC [7-benzyloxy-4-(trifluoromethyl)coumarin] in HLM (human liver microsomes), but failed to produce activation in BD Supersomes or Baculosomes containing recombinant CYP3A4 and NADPH-CPR (cytochrome P450 reductase). However, incorporation of purified CYP3A4 into Supersomes containing only recombinant CPR reproduced the behaviour observed with HLM. The activation in this system was dependent on the surface density of the enzyme. Although no activation was detectable at an L/P (lipid/P450) ratio ≥750, it reached 225% at an L/P ratio of 140. To explore the relationship between this effect and CYP3A4 oligomerization, we probed P450-P450 interactions with a new technique that employs LRET (luminescence resonance energy transfer). The amplitude of LRET in mixed oligomers of the haem protein labelled with donor and acceptor fluorophores exhibited a sigmoidal dependence on the surface density of CYP3A4 in Supersomes™. The addition of ANF eliminated this sigmoidal character and increased the degree of oligomerization at low enzyme concentrations. Therefore the mechanisms of CYP3A4 allostery with ANF involve effector-dependent modulation of P450-P450 interactions.

Phosphoryl transfers of the phospholipase D superfamily: a quantum mechanical theoretical study

The HKD-containing Phospholipase D superfamily catalyzes the cleavage of the headgroup of phosphatidylcholine to produce phosphatidic acid and choline. The mechanism of this cleavage process is studied theoretically. The geometric basis of our models is the X-ray crystal structure of the five-coordinate phosphohistidine intermediate from Streptomyces sp . Strain PMF (PDB Code = 1V0Y ). Hybrid ONIOM QM:QM methodology with Density Functional Theory (DFT) and semiempirical PM6 (DFT:PM6) is used to acquire thermodynamic and kinetic data for the initial phosphoryl transfer, subsequent hydrolysis, and finally, the formation of the experimentally observed ″dead-end″ phosphohistidine product (PDB Code = 1V0W ). The model contains nineteen amino acid residues (including the two highly conserved HKD-motifs), four explicit water molecules, and the substrate. Via computations, the persistence of the short-lived five-coordinate phosphorane intermediate on the minutes times scale is rationalized. This five-coordinate phosphohistidine intermediate energetically exists between the hydrolysis event and ″substrate reorganization″ (the reorganization of the in vitro model substrate within the active site). Computations directly support the thermodynamic favorability of the in vitro four-coordinate phosphohistidine product. In vivo, the activation energy of substrate reorganization is too high, perhaps due to a combination of substrate immobility when embedded in the lipid bilayer, as well as its larger steric bulk compared to the compound used in the in vitro substrate soaks. On this longer time scale, the enzyme will migrate along the lipid membrane toward its next substrate target, rather than promote the formation of the dead-end product.

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

For cells to function properly, membrane proteins must be able to diffuse within biological membranes. The functions of these membrane proteins depend on their position and also on protein-protein and protein-lipid interactions. However, so far, it has not been possible to study simultaneously the structure and dynamics of biological membranes. Here, we show that the motion of unlabelled membrane proteins can be characterized using high-speed atomic force microscopy. We find that the molecules of outer membrane protein F (OmpF) are widely distributed in the membrane as a result of diffusion-limited aggregation, and while the overall protein motion scales roughly with the local density of proteins in the membrane, individual protein molecules can also diffuse freely or become trapped by protein-protein interactions. Using these measurements, and the results of molecular dynamics simulations, we determine an interaction potential map and an interaction pathway for a membrane protein, which should provide new insights into the connection between the structures of individual proteins and the structures and dynamics of supramolecular membranes.

Confining domains lead to reaction bursts: reaction kinetics in the plasma membrane

Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity.

Reaction kinetics in the plasma membrane

A great puzzle in science is establishing a bottom up understanding of life by revealing how a collection of molecules gives rise to a living cell that can survive, communicate, and reproduce. In the confines of physics, chemistry, or material science laboratories where it possible to study complex interactions between molecules in a well-defined environment, our understanding of collective behavior is substantially developed. However, the environment in which molecules of a biological cell perform their functions is far from ideal or controllable. The environment inside cellular regions such as the plasma membrane is heterogeneous and dynamic, and functional molecules such as proteins are both dynamic and promiscuous, as they interact with countless other molecules. This makes it extremely challenging to grasp the inner mechanism of the cells, both experimentally and theoretically. On the bright side, this presents scientists with a colorful playground that waits to be explored: the mesoscopic world inside the cell. This review covers some of the recent experimental and theoretical developments in the study of molecular interactions in the plasma membrane, viewed as a heterogeneous medium where the number of reactants can be small, sometimes countable, and its implications for biological function.

Quenching of triplet state fluorophores for studying diffusion-mediated reactions in lipid membranes

An approach to study bimolecular interactions in model lipid bilayers and biological membranes is introduced, exploiting the influence of membrane-associated electron spin resonance labels on the triplet state kinetics of membrane-bound fluorophores. Singlet-triplet state transitions within the dye Lissamine Rhodamine B (LRB) were studied, when free in aqueous solutions, with LRB bound to a lipid in a liposome, and in the presence of different local concentrations of the electron spin resonance label TEMPO. By monitoring the triplet state kinetics via variations in the fluorescence signal, in this study using fluorescence correlation spectroscopy, a strong fluorescence signal can be combined with the ability to monitor low-frequency molecular interactions, at timescales much longer than the fluorescence lifetimes. Both in solution and in membranes, the measured relative changes in the singlet-triplet transitions rates were found to well reflect the expected collisional frequencies between the LRB and TEMPO molecules. These collisional rates could also be monitored at local TEMPO concentrations where practically no quenching of the excited state of the fluorophores can be detected. The proposed strategy is broadly applicable, in terms of possible read-out means, types of molecular interactions that can be followed, and in what environments these interactions can be measured.

Iodide as a fluorescence quencher and promoter--mechanisms and possible implications

In this work, fluorescence correlation spectroscopy (FCS) was used to investigate the effects of potassium iodide (KI) on the electronic-state population kinetics of a range of organic dyes in the visible wavelength range. Apart from a heavy atom effect promoting intersystem crossing to the triplet states in all dyes, KI was also found to enhance the triplet-state decay rate by a charge-coupled deactivation. This deactivation was only found for dyes with excitation maximum in the blue range, not for those with excitation maxima at wavelengths in the green range or longer. Consequently, under excitation conditions sufficient for triplet state formation, KI can promote the triplet state buildup of one dye and reduce it for another, red-shifted dye. This anticorrelated, spectrally separable response of two different dyes to the presence of one and the same agent may provide a useful readout for biomolecular interaction and microenvironmental monitoring studies. In contrast to the typical notion of KI as a fluorescence quencher, the FCS measurements also revealed that when added in micromolar concentrations KI can act as an antioxidant, promoting the recovery of photo-oxidized fluorophores. However, in millimolar concentrations KI also reduces intact, fluorescently viable fluorophores to a considerable extent. In aqueous solutions, for the dye Rhodamine Green, an optimal concentration of KI of approximately 5 mM can be defined at which the fluorescence signal is maximized. This concentration is not high enough to allow full triplet state quenching. Therefore, as a fluorescence enhancement agent, it is primarily the antioxidative properties of KI that play a role.

Tyrosine-lipid peroxide adducts from radical termination: para coupling and intramolecular Diels-Alder cyclization

Free radical co-oxidation of polyunsaturated lipids with tyrosine or phenolic analogues of tyrosine gave rise to lipid peroxide-tyrosine (phenol) adducts in both aqueous micellar and organic solutions. The novel adducts were isolated and characterized by 1D and 2D NMR spectroscopy as well as by mass spectrometry (MS). The spectral data suggest that the polyunsaturated lipid peroxyl radicals give stable peroxide coupling products exclusively at the para position of the tyrosyl (phenoxy) radicals. These adducts have characteristic (13)C chemical shifts at 185 ppm due to the cross-conjugated carbonyl of the phenol-derived cyclohexadienone. The primary peroxide adducts subsequently undergo intramolecular Diels-Alder (IMDA) cyclization, affording a number of diastereomeric tricyclic adducts that have characteristic carbonyl (13)C chemical shifts at ~198 ppm. All of the NMR HMBC and HSQC correlations support the structure assignments of the primary and Diels-Alder adducts, as does MS collision-induced dissociation data. Kinetic rate constants and activation parameters for the IMDA reaction were determined, and the primary adducts were reduced with cuprous ion to give a phenol-derived 4-hydroxycyclohexa-2,5-dienone. No products from adduction of peroxyls at the phenolic ortho position were found in either the primary or cuprous reduction product mixtures. These studies provide a framework for understanding the nature of lipid-protein adducts formed by peroxyl-tyrosyl radical-radical termination processes. Coupling of lipid peroxyl radicals with tyrosyl radicals leads to cyclohexenone and cyclohexadienone adducts, which are of interest in and of themselves since, as electrophiles, they are likely targets for protein nucleophiles. One consequence of lipid peroxyl reactions with tyrosyls may therefore be protein-protein cross-links via interprotein Michael adducts.

Phase-dependent lateral diffusion of α-tocopherol in DPPC liposomes monitored by fluorescence quenching

The temperature-dependent fluorescence quenching of an amphiphilic palmitoyl derivative of 2,3-diazabicyclo[2.2.2]oct-2-ene (Fluorazophore-L) by α-tocopherol (α-Toc) has been determined in liposomes composed of a saturated lipid, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The mutual lateral diffusion coefficients (D(L)) were extracted according to a laterally diffusion-controlled dynamic quenching model. Three distinct temperature regimes were identified: one between 65 and 39 °C, where the lateral diffusion coefficients were in the range of 10(-7) cm(2) s(-1) and the lifetime of the probe was monoexponential in the absence of α-Toc, a second one between 39 and 30 °C, where the lateral diffusion coefficients were in the range of 10(-8) cm(2) s(-1) and the lifetime of the probe was biexponential in the absence of α-Toc, and a third one below 30 °C, in which no diffusion was detectable, suggesting D(L) < 10(-9) cm(2)s (-1). These temperature domains were assigned, supported by differential scanning calorimetry (DSC) measurements, to the liquid-crystalline, ripple, and solid-gel phases of DPPC liposomes in the presence of the two additives. The absolute values of the individual lateral diffusion coefficients (taken as (1)/(2) of the D(L) values) of the Fluorazophore-L/α-Toc (ca. 2.5 × 10(-7) cm(2) s(-1) at 52 °C) couple demonstrates that α-Toc does not diffuse at an unexpectedly high rate in comparison to the self-diffusion of DPPC (1.5 × 10(-7) cm(2) s(-1) at 52 °C). However, diffusion in DPPC liposomes is distinctly slower than that in POPC ones (e.g., D(L) = 4.9 × 10(-7) cm(2) s(-1) versus 6.4 × 10(-7) cm(2) s(-1) at 50 °C), with an activation energy of 49 ± 5 kJ mol(-1) (value for POPC: 47 ± 5 kJ mol(-1)), in the temperature range of the liquid-crystalline phase. Diffusion in the ripple phase, that is, below the main phase transition temperature, was found to be non-negligible, with an apparent activation energy of 175 ± 50 kJ mol(-1).

Fast on-rates allow short dwell time ligands to activate T cells

Two contrasting theories have emerged that attempt to describe T-cell ligand potency, one based on the t(1/2) of the interaction and the other based on the equilibrium affinity (K(D)). Here, we have identified and studied an extensive set of T-cell receptor (TCR)-peptide-MHC (pMHC) interactions for CD4(+) cells that have differential K(D)s and kinetics of binding. Our data indicate that ligands with a short t(1/2) can be highly stimulatory if they have fast on-rates. Simple models suggest these fast kinetic ligands are stimulatory because the pMHCs bind and rebind the same TCR several times. Rebinding occurs when the TCR-pMHC on-rate outcompetes TCR-pMHC diffusion within the cell membrane, creating an aggregate t(1/2) (t(a)) that can be significantly longer than a single TCR-pMHC encounter. Accounting for t(a), ligand potency is K(D)-based when ligands have fast on-rates (k(on)) and t(1/2)-dependent when they have slow k(on). Thus, TCR-pMHC k(on) allow high-affinity short t(1/2) ligands to follow a kinetic proofreading model.

Membrane promotes tBID interaction with BCL(XL)

Two important questions on the molecular mechanism of the B cell CLL/lymphoma 2 (BCL2) proteins involve the interaction network between pro- and antiapoptotic members and the role of their translocation to the mitochondrial membrane during apoptosis. We used fluorescence correlation spectroscopy to quantify the molecular interactions of BH3-interacting domain death agonist (BID) and its truncated form tBID with the B cell lymphoma extra-large protein truncated at the C terminus (BCL(XL)DeltaCt) in solution and in membranes, and we found that (i) only the active form tBID binds to BCL(XL)DeltaCt and (ii) that the membrane strongly promotes binding between them. Particularly, a BH3 peptide from BID disrupts the tBID-BCL(XL) complex in solution, but only partially in lipid bilayers. These data indicate that tBID-BCL(XL) interactions in solution and lipid membranes are distinct, and they support a model in which BCL(XL) inhibition of tBID takes place predominantly at the membrane. Our findings imply an active role of the membrane in modulating the interactions between BCL2 proteins that has so far been underestimated.

Electrodes modified with lipid membranes to study quinone oxidoreductases

Quinone oxidoreductases are a class of membrane enzymes that catalyse the oxidation or reduction of membrane-bound quinols/quinones. The conversion of quinone/quinol by these enzymes is difficult to study because of the hydrophobic nature of the enzymes and their substrates. We describe some biochemical properties of quinones and quinone oxidoreductases and then look in more detail at two model membranes that can be used to study quinone oxidoreductases in a native-like membrane environment with their native lipophilic quinone substrates. The results obtained with these model membranes are compared with classical enzyme assays that use water-soluble quinone analogues.

A biological interpretation of transient anomalous subdiffusion. II. Reaction kinetics

Reaction kinetics in a cell or cell membrane is modeled in terms of the first passage time for a random walker at a random initial position to reach an immobile target site in the presence of a hierarchy of nonreactive binding sites. Monte Carlo calculations are carried out for the triangular, square, and cubic lattices. The mean capture time is expressed as the product of three factors: the analytical expression of Montroll for the capture time in a system with a single target and no binding sites; an exact expression for the mean escape time from the set of lattice points; and a correction factor for the number of targets present. The correction factor, obtained from Monte Carlo calculations, is between one and two. Trapping may contribute significantly to noise in reaction rates. The statistical distribution of capture times is obtained from Monte Carlo calculations and shows a crossover from power-law to exponential behavior. The distribution is analyzed using probability generating functions; this analysis resolves the contributions of the different sources of randomness to the distribution of capture times. This analysis predicts the distribution function for a lattice with perfect mixing; deviations reflect imperfect mixing in an ordinary random walk.

Bilayer polarity and its thermal dependency in the l(o) and l(d) phases of binary phosphatidylcholine/cholesterol mixtures

Diverse variations in membrane properties are observed in binary phosphatidylcholine/cholesterol mixtures. These mixtures are nonideal, displaying single or phase coexistence, depending on chemical composition and other thermodynamic parameters. When compared with pure phospholipid bilayers, there are changes in water permeability, bilayer thickness and thermomechanical properties, molecular packing and conformational freedom of phospholipid acyl chains, in internal dipolar potential and in lipid lateral diffusion. Based on the phase diagrams for DMPC/cholesterol and DPPC/cholesterol, we compare the equivalent polarity of pure bilayers with specific compositions of these mixtures, by using the Py empirical scale of polarity. Besides the contrast between pure and mixed lipid bilayers, we find that liquid-ordered (l(o)) and liquid-disordered (l(d)) phases display significantly different polarities. Moreover, in the l(o) phase, the polarities of bilayers and their thermal dependences vary with the chemical composition, showing noteworthy differences for cholesterol proportions at 35, 40, and 45 mol%. At 20 degrees C, for DMPC/cholesterol at 35 and 45 mol%, the equivalent dielectric constants are 21.8 and 23.8, respectively. Additionally, we illustrate potential implications of polarity in various membrane-based processes and reactions, proposing that for cholesterol containing bilayers, it may also go along with the occurrence of lateral heterogeneity in biological membranes.