Membrane composition determines pardaxin's mechanism of lipid bilayer disruption

Pardaxin is a membrane-lysing peptide originally isolated from the fish Pardachirus marmoratus. The effect of the carboxy-amide of pardaxin (P1a) on bilayers of varying composition was studied using (15)N and (31)P solid-state NMR of mechanically aligned samples and differential scanning calorimetry (DSC). (15)N NMR spectroscopy of [(15)N-Leu(19)]P1a found that the orientation of the peptide's C-terminal helix depends on membrane composition. It is located on the surface of lipid bilayers composed of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and is inserted in lipid bilayers composed of 1,2-dimyristoyl-phosphatidylcholine (DMPC). The former suggests a carpet mechanism for bilayer disruption whereas the latter is consistent with a barrel-stave mechanism. The (31)P chemical shift NMR spectra showed that the peptide significantly disrupts lipid bilayers composed solely of zwitterionic lipids, particularly bilayers composed of POPC, in agreement with a carpet mechanism. P1a caused the formation of an isotropic phase in 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) lipid bilayers. This, combined with DSC data that found P1a reduced the fluid lamellar-to-inverted hexagonal phase transition temperature at very low concentrations (1:50,000), is interpreted as the formation of a cubic phase and not micellization of the membrane. Experiments exploring the effect of P1a on lipid bilayers composed of 4:1 POPC:cholesterol, 4:1 POPE:cholesterol, 3:1 POPC:1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG), and 3:1 POPE:POPG were also conducted, and the presence of anionic lipids or cholesterol was found to reduce the peptide's ability to disrupt bilayers. Considered together, these data demonstrate that the mechanism of P1a is dependent on membrane composition.     

Membrane lipid fluidity and its effect on the activation energy of membrane-associated enzymes.

1. The fatty acid composition of mitochondrial membranes from sheep and rats was altered by feeding these animals diets which were rich in unsaturated fatty acids. Changes in membrane lipid fluidity resulting from the altered membrane lipid composition were assessed by determining the upper temperature limit of the disorder-order transition (Tf) and the Arrhenius activation energy (Ea) of succinate oxidase. 2. After feeding the unsaturated fatty acid-rich diet to sheep the Ea, in the temperature range above Tf, increased from 8 to 63 kJ . mol-1 while Tf decreased from 32 to 15 degrees C. Rats fed an unsaturated fatty acid-rich diet exhibited an increase in Ea from 17 to 63 kJ . mol-1 and a decrease in Tf from 23 to 4 degrees C. 3. This decrease in Tf was related to an increase in the ratio of linoleic acid to stearic acid in the membrane lipid. Tf was not related to the proportion of unsaturated fatty acids in the membrane lipids, although an increase in unsaturation usually led to a decrease in Tf. 4. The results show that membrane lipid fluidity has a direct influence on the conformation of the active site of some membrane-associated enzymes, with the result that such enzymes display a higher Ea when the membrane lipids are comparatively more fluid. The increase in Ea of membrane-associated enzymes which accompanies changes in the physical state of membrane suggests that some proteins may phase separate with the more fluid lipids at low temperatures.     

Simulating the free energy of passive membrane permeation for small molecules

Abstract

Computer simulations of passive membrane permeation provide important microscopic insights into the molecular mechanism of this important biological process that are complementary to experimental data. Our review focuses on the main approaches for calculating the free energy, or potential of mean force, for permeation of small molecules through lipid bilayers. The theoretical background for most currently used methods for potential of mean force calculation is described, including particle insertion, thermodynamic integration, umbrella sampling, metadynamics, adaptive biasing force and milestoning. A brief comparison of strengths and weaknesses of the competing approaches is presented. This is followed by a survey of results obtained by the different methods, with special attention to describing the mechanistic insights generated by modelling and illustrating capabilities of the different techniques. We conclude with a discussion of recent advances and future directions in modelling membrane permeation, including latest methodological enhancements, consideration of multiple slow variables and memory effects.     

Membrane potential of E. coli recipient cells determines the rate of linear transport of DNA during conjugation

The rate of conjugal DNA transport from donor to recipient cells has been shown to depend on the membrane potential (delta psi) value in the DNA recipient cell. On the other hand, delta psi in the DNA donor cells is required for the formation of stable aggregates of conjugating cells, but not for the RNA transport. Both components of the electrochemical proton gradient on the cytoplasmic membrane of the recipient cells, the delta psi and the pH gradient are equivalent in the conjugal process.     

Membrane glycoprotein and surface free energy changes in hypoxic fibroblast cells

Hypoxia affects the biochemistry of mammalian cells and thus alters their sensitivity to subsequent chemo- and radiotherapy. When V79 Chinese hamster lung fibroblasts were grown under conditions of extreme hypoxia (less than 10 ppm O2) there was a significant shift in the membrane glycoprotein composition. Scanning electron microscopy revealed altered cell surface morphology including loss of pseudopodial projections. Experiments to determine changes in interfacial free energy of these cells using equilibrium two phase systems of poly(ethylene glycol) (PEG) and dextran were carried out. Test fluid droplets of the denser dextran-rich phase were formed on layers of cells in the PEG-rich phase as the bathing medium, and the contact angles the droplets made with the cell layers were measured from photomicrographs. The contact angles on cells in the plateau phase increased significantly with time of exposure to hypoxia, from 25 degrees (zero time) to 35 degrees (6 h) to 60 degrees (9 h). Contact angles on cells in the exponential phase increased from 80 degrees (zero time) to 150 degrees after 20 h of hypoxia. It appears that the altered contact angles reflect changes in cell surface hydrophobicity that may, in part, reflect alterations in the membrane glycoprotein composition.     

High free energy of lipid/protein interaction in biological membranes

The free energy of lipid/protein interaction in biological membranes is still unknown although extensive partitioning and modelling studies have revealed many partial energetic increments. Multiple site binding kinetics are now applied to four well-studied functional membrane proteins, and mean free energy values (+/-S.D.) of -4.23+/-0.49 kcal/mol for single lipid binding sites and of -89.7+/-35.4 kcal/mol for complete lipid substitution are obtained. These high free energy values point to an important bioenergetic role of lipid/protein interaction in membrane functions.     

Electrostatic free energy and shift of the phase transition for charged lipid membranes

For a charged membrane in an electrolyte solution the electrostatic free energy is derived treating the system as a diffuse double layer. The dependence of the free energy on external parameters like surface charge density and temperature is obtained and the physical basis discussed. As an application the charges are shown to exert an electrostatic surface pressure on the lipid chain packing which leads to a shift in the phase transition of lipid membranes. The results confirm the interpretation of experimental data as given by Träuble et al. in the accompanying paper.     

The role of lipid radicals in electron transport and energy transformation

Data given propose two regimes of lipid radicals and oxygen utilization realized in microsomal and mitochondrial membranes. The first one, lipid peroxidation, i.e. interaction of lipid radicals and oxygen is an empty step. In converting this regime to the functional one NADPH-dependent lipid peroxidation is inhibited. A change of this regime to the functional one in microsome demand the presence of hydroxylation substrates. Setting lipid radical-dependent coupling apparatus on phosphorylation in mitochondria occur in the presence of ADP and Pi-phosphorylation substrates.     

Kinetics and free energy profiles of spermine transport in liver mitochondria

In the present study, the voltage-dependent mechanism of spermine transport in liver mitochondria [Toninello, A., Dalla Via, L., Siliprandi, D., and Garlid, K. D. (1992) J. Biol. Chem. 267, 18393-18397] was further characterized by determining the rate constants J(max) and K(m) as functions of membrane potential. An increase in mitochondrial membrane potential from 150 to 210 mV promoted spermine transport, as reflected by an approximate 4-fold increase in J(max) and 25% decrease in K(m). The mechanism for the voltage dependence of transport was examined using the beta value, i. e., the slope of ln(flux) vs FDeltaPsi/RT plots. Flux-voltage analyses performed at very high and very low spermine concentrations yielded beta values of 0.125 and 0.25, for J(max) and J(max)/K(m), respectively. The physical significance of these beta values was analyzed by means of a theory relating the enzyme reaction rate to the free energy profiles [Yagisawa, S. (1985) Biochem. J. 303, 305-311]. Depending on the nature of K(m), two possible models could be proposed to describe the location and shape of the barriers in the membrane. Analysis of previous data concerning spermine binding [Dalla Via, L., Di Noto, V., Siliprandi, D., and Toninello, A. (1996) Biochim. Biophys. Acta 1284, 247-252] by a new rationale provided evidence for an asymmetrical energy profile composed of two peaks with the binding site near the membrane surface followed by a rate-determining energy barrier for the movement of the bound spermine toward the internal region of the membrane.     

DNA supercoiling determines the activation energy barrier for site specific recombination by Tn21 resolvase.

A kinetic analysis of site specific recombination by Tn21 resolvase has been carried out using DNA substrates of varying superhelicities. The rates for the formation of the recombinant product increased with increasing superhelicity up to a maximum value, after which further increases in superhelicity caused no further increase in rate. The reactions with DNA of reduced superhelicity were extremely slow, yet they eventually led to virtually all of the substrate being converted to product. Hence, the level of DNA superhelicity must determine the activation energy barrier for at least one of the steps within the reaction pathway that can be rate-limiting. In the presence (but not in the absence) of Mg2+ ions, the DNA was fully saturated with resolvase whenever the protein was in stoichiometric excess over resolvase binding sites on the DNA. Thus the process affected by DNA supercoiling cannot be coupled to the binding of resolvase. Instead, the step whose rate is determined by supercoiling seems to be located within the reaction pathway after the synapse. However, these reactions may involve two forms of the synaptic complex that are converted to the recombinant product at different rates.     

Membrane transport of fatty acylcarnitine and free L-carnitine by rat liver microsomes.

Recent studies have suggested that parts of the hepatic activities of diacylglycerol acyltransferase and acyl cholesterol acyltransferase are expressed in the lumen of the endoplasmic reticulum (ER). However the ER membrane is impermeable to the long-chain fatty acyl-CoA substrates of these enzymes. Liver microsomal vesicles that were shown to be at least 95% impermeable to palmitoyl-CoA were used to demonstrate the membrane transport of palmitoylcarnitine and free L-carnitine - processes that are necessary for an indirect route of provision of ER luminal fatty acyl-CoA through a luminal carnitine acyltransferase (CAT). Experimental conditions and precautions were established to permit measurement of the transport of [14C]palmitoylcarnitine into microsomes through the use of the luminal CAT and acyl-CoA:ethanol acyltransferase as a reporter system to detect formation of luminal [14C]palmitoyl-CoA. Rapid, unidirectional transport of free L-[3H]carnitine by microsomes was measured directly. This process, mediated either by a channel or a carrier, was inhibited by mersalyl but not by N-ethylmaleimide or sulfobetaine - properties that differentiate it from the mitochondrial inner membrane carnitine/acylcarnitine exchange carrier. These findings are relevant to the understanding of processes for the reassembly of triacylglycerols that lipidate very low density lipoprotein particles as part of a hepatic triacylglycerol lipolysis/re-esterification cycle.     

Homeostasis of free cholesterol in the blood: a preliminary evaluation and modeling of its passive transport

The rate of noncatalyzed transfer of cholesterol (Chol) among lipoproteins and cells in the blood is of fundamental importance as a baseline to assess the role of active transport mechanisms, but remains unknown. Here we address this gap by characterizing the associa­tion of the Chol analog, ergosta-5,7,9(11),22-tetraen-3β-ol (DHE), with the lipoproteins VLDL, LDL, HDL₂, and HDL₃. Combining these results with data for the association of DHE with liposomes, we elaborated a kinetic model for the noncatalyzed exchange of free Chol among blood compartments. The computational results are in good agreement with experimental values. The small deviations are explained by the nonequilibrium distribution of unesterified Chol in vivo, due to esterification and entry of new unesterified Chol, and eventual effects introduced by incubations at low temperatures. The kinetic profile of the homeostasis of unesterified Chol in the blood predicted by the model developed in this work is in good agreement with the observations in vivo, highlighting the importance of passive processes.     

Role of hydrophobicity in the binding of coenzymes. Appendix. Translational and rotational contribution to the free energy of dissociation.

We calculate the loss of surface area accessible to solvent associated with coenzyme binding in Clostridium flavodoxin, in dogfish lactate dehydrogenase, and in lobster glyceraldehyde-3-phosphate dehydrogenase. The coenzymes are nearly buried in the complexes and lose on the order of 600 A2, while the proteins lose a similar amount of accessible surface area. Some of the loss can be attributed to conformation changes in the protein, at least in the case of lactate dehydrogenase, where we show that the apoenzyme has a larger accessible surface area than the holoenzyme. Using known correlations with the hydrophobic contribution to the free energy, we demonstrate that hydrophobicity is the major source of stabilization free energy in FMN binding to flavodoxin and in NAD binding to the two dehydrogenases: it contributes 25 to 30 kcal/mol to the free energy of dissociation, more than required in order to compensate for the loss of six degrees of translational/rotational freedom by the coenzyme.     

Membrane lipid changes during formation of a functional electron transport system in Staphylococcus aureus

Addition of oxygen to a culture of anaerobically growing Staphylococcus aureus results in the formation of a membrane-bound, functional electron transport system. With the shift to aerobic growth, there is at least a 15-fold increase in cytochrome a and at least a 55-fold increase in cytochrome oxidase o. At the completion of the shift to aerobic growth, the cytochrome levels equal those found in bacteria grown with aeration throughout the entire growth cycle. Cytochromes b(1) and o are formed first. Their synthesis slows when cytochrome a becomes detectable. Concentrations of cytochromes b(1) and sometimes cytochrome a increase late in the adaptive period. Concomitant with this is a decrease in the oxygen tension at which the rate of oxygen utilization becomes dependent on the oxygen concentration. During the shift to aerobic growth, the protoheme content increases ninefold, and all the protoheme can be accounted for in enzymatically reducible cytochrome b(1) and cytochrome oxidase o. Protoheme, but not a functional cytochrome system, is synthesized by anaerobically growing S. aureus. Heme a appears only after a period of aerobic growth. During the shift to aerobic growth, there is a 1.6-fold increase in the vitamin K(2) content, with an alteration in the ratios of the 35 and 45 carbon side chain isoprenologues. A twofold increase in phosphatidyl glycerol and a 1.6-fold increase in cardiolipin occur with the shift to aerobic growth. Lysyl-phosphtidyl glycerol remains essentially constant in this period. Concentrations of mono- and diglucosyl diglycerides increase coordinately 1.3-fold during the shift to aerobic growth at a 2.5 to 1 m ratio.     

Membrane fusogenic lysine type lipid assemblies possess enhanced NLRP3 inflammasome activation potency

Lysine (K) type cationic lipid with a propyl spacer and ditetradecyl hydrophobic moieties composing liposomes, K3C14, previously studied for gene delivery, were reported to activate the NLRP3 inflammasomes in human macrophages via the conventional phagolysosomal pathway. In this study, K3C16, a propyl spacer bearing lysine type lipids with dihexadecyl moieties (an extension of two hydrocarbon tail length) were compared with K3C14 as liposomes. Such a small change in tail length did not alter the physical properties such as size distribution, zeta potential and polydispersity index (PDI). The NLRP3 activation potency of K3C16 was shown to be 1.5-fold higher. Yet, the toxicity was minimal, whereas K3C14 has shown to cause significant cell death after 24 h incubation. Even in the presence of endocytosis inhibitors, cytochalasin D or dynasore, K3C16 continued to activate the NLRP3 inflammasomes and to induce IL-1β release. To our surprise, K3C16 liposomes were confirmed to fuse with the plasma membrane of human macrophages and CHO-K1 cells. It is demonstrated that the change in hydrophobic tail length by two hydrocarbons drastically changed a cellular entry route and potency in activating the NLRP3 inflammasomes.     

Estimating the voltage-dependent free energy change of ion channels using the median voltage for activation

Voltage-gated ion channels are crucial for electrical activity and chemical signaling in a variety of cell types. Structure-activity studies involving electrophysiological characterization of mutants are widely used and allow us to quickly realize the energetic effects of a mutation by measuring macroscopic currents and fitting the observed voltage dependence of conductance to a Boltzmann equation. However, such an approach is somewhat limiting, principally because of the inherent assumption that the channel activation is a two-state process. In this analysis, we show that the area delineated by the gating charge displacement curve and its ordinate axis is related to the free energy of activation of a voltage-gated ion channel. We derive a parameter, the median voltage of charge transfer (V(m)), which is proportional to this area, and prove that the chemical component of free energy change of a system can be obtained from the knowledge of V(m) and the maximum number of charges transferred. Our method is not constrained by the number or connectivity of intermediate states and is applicable to instances in which the observed responses show a multiphasic behavior. We consider various models of ion channel gating with voltage-dependent steps, latent charge movement, inactivation, etc. and discuss the applicability of this approach in each case. Notably, our method estimates a net free energy change of approximately -14 kcal/mol associated with the full-scale activation of the Shaker potassium channel, in contrast to -2 to -3 kcal/mol estimated from a single Boltzmann fit. Our estimate of the net free energy change in the system is consistent with those derived from detailed kinetic models (Zagotta et al. 1994. J. Gen. Physiol. doi:10.1085/jgp.103.2.321). The median voltage method can reliably quantify the magnitude of free energy change associated with activation of a voltage-dependent system from macroscopic equilibrium measurements. This will be particularly useful in scanning mutagenesis experiments.