Enzyme peptide synthesis and semisynthesis: Kinetic and thermodynamic aspects

The hydrolysis/synthesis equilibrium of the peptide bond is governed by the relative magnitudes of the corresponding Gibbs' energies of hydrolysis to non-ionized products and of their ionization. The positive energy change in peptide hydrolysis to non-ionized products is the thermodynamic basis for the acyl and leaving group specificity of proteinases. With a proteinase of suitable specificity, some peptide bonds can be synthesized by a thermodynamically controlled enzyme aminolysis of specific acylamino or peptide acids; any peptide bond can be formed by a kinetically controlled enzyme aminolysis of the corresponding acylamino or peptide esters.     

Comparative and evolutionary aspects of macromolecular translocation across membranes

Membrane barriers preserve the integrity of organelles of eukaryotic cells, yet the genesis and ongoing functions of the same organelles requires that their limiting membranes allow import and export of selected macromolecules. Multiple distinct mechanisms are used for this purpose, only some of which have been traced to prokaryotes. Some can accomodate both monomeric and also large heterooligomeric cargos. The best characterized of these is nucleocytoplasmic transport. This synthesis compares the unidirectional and bidirectional mechanisms of macromolecular transport of the endoplasmic reticulum, mitochondria, peroxisomes and the nucleus, calls attention to the powerful experimental approaches which have been used for their elucidation, discusses their regulation and evolutionary origins, and highlights relatively unexplored areas.     

Kinetic models and phenomenological analysis of passive lipid translocation in single-file

Passive movement of lipids through a membrane-embedded pore is analysed with kinetic equations of transport in single-file. The number of lipids arranged along the translocation coordinate in the pore is not limited in the calculations. The assumption is made that the energetic state of a pore is independent of the sequence of lipids contained in it. The results are valid for an arbitrary number of species with identical kinetic constants. It is shown that infinitely fast diffusion of one vacant site is equivalent to the filled pore approximation, which has been used here. We introduce the concept of non-strict single-file, which allows also for exchanges of neighbouring lipids inside the pore at specified rates. The model successfully simulates the redistribution of lipids between the monolayers of red blood cell plasma membranes under operation of an active aminophospholipid translocase. Kinetic equations are related to linear flux force relations. Phenomenological coefficients are expressed and analysed in terms of kinetic constants. Plausible kinetic pore model parameters are derived from comparison with a reference simulation of a thermodynamic model of the erythrocyte transmembrane lipid distribution. Mechanical forces due to differences in compressions of the lipid molecules between the monolayers are incorporated in kinetic rate constants. It is seen how the active inward transport of aminophospholipids causes an unsymmetrical passive redistribution of the other components due to mechanical effects and cross-coupling of fluxes.     

Mechanism for translocation of fluoroquinolones across lipid membranes

Classical atom-scale molecular dynamics simulations, constrained free energy calculations, and quantum mechanical (QM) calculations are employed to study the diffusive translocation of ciprofloxacin (CPFX) across lipid membranes. CPFX is considered here as a representative of the fluoroquinolone antibiotics class. Neutral and zwitterionic CPFX coexist at physiological pH, with the latter being predominant. Simulations reveal that only the neutral form permeates the bilayer, and it does so through a novel mechanism that involves dissolution of concerted stacks of zwitterionic ciprofloxacins. Subsequent QM analysis of the observed molecular stacking shows the important role of partial charge neutralization in the stacks, highlighting how the zwitterionic form of the drug is neutralized for translocation. The findings propose a translocation mechanism in which zwitterionic CPFX molecules approach the membrane in stacks, but they diffuse through the membrane as neutral CPFX monomers due to intermolecular transfer of protons favored by partial solvation loss. The mechanism is expected to be of importance in the permeation and translocation of a variety of ampholitic drugs with stacking tendencies.     

Relay model of lipid peroxidation in biological membranes

The present study examines the evidence for the important role of free radicals, localized on carbon atoms of the hydrocarbon chains, in lipid peroxidation. These radicals show a great inter- and intramolecular mobility in membranes by the way of relay-transfer (isomerisation). The sequence of intermediate steps of shift of free radicals in membranes with correction for molecular organization of the hydrocarbon zone of membranes, the intramembrane localization of unsaturated links and the gradient of mobility of the hydrocarbon chains are described. The effect of inhibitors in lipid peroxidation are interpreted in terms of decay of hydrocarbon free radicals as a result of its interaction with the antioxidant molecules. The natural antioxidants having a side chain (such as tocopherols) may be regarded as a some kind of "channel" through which free radicals leave the hydrocarbon moiety of the membrane. The processes of lipid peroxidation in membranes are subjected to a great extent to the requirements of the theory of oxidation of solid polymers and hydrocarbons.     

A critical reassessment of penetratin translocation across lipid membranes

Penetratin is a short, basic cell-penetrating peptide able to induce cellular uptake of a vast variety of large, hydrophilic cargos. We have reassessed the highly controversial issue of direct permeation of the strongly cationic peptide across negatively charged lipid membranes. Confocal laser scanning microscopy on rhodamine-labeled giant vesicles incubated with carboxyfluorescein-labeled penetratin yielded no evidence of transbilayer movement, in contradiction to previously reported results. Confocal fluorescence spectroscopy on black lipid membranes confirmed this finding, which was also not affected by application of a transmembrane electric potential difference. A novel dialysis assay based on tryptophan absorbance and fluorescence spectroscopy demonstrated that the permeability of small and large unilamellar vesicles to penetratin is <10(-13) m/s. Taken together, the results show that penetratin is not capable of overcoming model membrane systems irrespective of the bilayer curvature or the presence of a transmembrane voltage. Thus, direct translocation across the hydrophobic core of the plasma membrane cannot account for the efficient uptake of penetratin into live cells, which is in accord with recent in vitro studies underlining the importance of endocytosis in the internalization process of cationic cell-penetrating peptides.     

Vesicle size-dependent translocation of penetratin analogs across lipid membranes

The recent discoveries of serious artifacts associated with the use of cell fixation in studies of the cellular uptake of cell-penetrating peptides (CPPs) have prompted a reevaluation of the current understanding of peptide-mediated cellular delivery. Following a report on the differential cellular uptake of a number of penetratin analogs in unfixed cells, we here investigate their membrane translocation abilities in large and giant unilamellar vesicles (LUVs and GUVs, respectively). Surprisingly, in contrast to the behavior in living cells, all peptides readily entered the giant vesicles (>1 microm) as proved by confocal microscopy, while none of them could cross the membranes of LUVs (100 nm). For determination of the location of the peptides in the LUVs, a new concept was introduced, based on sensitive resonance energy transfer (RET) measurements of the enhanced fluorescence of acceptor fluorophores present solely in the inner leaflet. An easily adopted method to prepare such asymmetrically labeled liposomes is described. The membrane insertion depths of the tryptophan moieties of the peptides were determined by use of brominated lipids and found to be very similar for all of the peptides studied. We also demonstrate that infrared spectroscopy on the lipid carbonyl stretch vibration peak is a convenient technique to determine phospholipid concentration.     

Sphingomyelinase activity causes transbilayer lipid translocation in model and cell membranes

Ceramide is known to induce structural rearrangements in membrane bilayers, including the formation of ceramide-rich and -poor domains and the efflux of aqueous solutes. This report describes a novel effect of ceramide, namely the induction of transbilayer lipid movements. This effect was demonstrated in both model (large unilamellar vesicles) and cell (erythrocyte ghost) membranes in which ceramide generation took place in situ through the action of an externally added sphingomyelinase. Two different novel assays were developed to detect transbilayer lipid movement. One of the assays required the preparation of vesicles containing a ganglioside only in the outer monolayer and entrapped neuraminidase. Sphingomyelinase activity induced ganglioside hydrolysis under conditions in which no neuraminidase was released from the vesicles. The second assay involved the preparation of liposomes or erythrocyte ghosts labeled with a fluorescent energy donor in their inner leaflets. Sphingomyelin hydrolysis was accompanied by fluorescence energy transfer to an impermeable acceptor in the outer aqueous medium. Ceramide-induced transbilayer lipid movement is explained in terms of another well known property of ceramide, namely the facilitation of lamellar to non-lamellar lipid-phase transitions. Thus, sphingomyelinase generates ceramide on one side of the membrane; ceramide then induces the transient formation of non-lamellar structural intermediates, which cause the loss of lipid asymmetry in the bilayer, i.e. the transbilayer movement of ceramide together with other lipids. As direct targets for ceramide tend to be intracellular, these observations may be relevant to the mechanism of transmembrane signaling by means of the sphingomyelin pathway.     

C-NMR detection of lipid polymorphism in model and biological membranes

1. 1. The application of the ¹³C-NMR technique to the study of lipid polymorphism is described for various model and biological membranes.

2. 2. The ¹³C-NMR line-width of various resonances of the lipid molecule are sensitive to the bilayer hexagonal and the bilayer ‘isotropic’ phase transition. The latter transition in some cases is accompanied by the occurrence of lipidic particles as detected by freeze-fracturing. Thus, specific ¹³C-labeling experiments allow the study of the individual phase behaviour of lipids in mixed lipid systems.

3. 3. In diet experiments using rats, the choline group of phosphatidylcholine present in erythrocyte, endoplasmic and sarcoplasmic reticulum membranes could be specifically ¹³C-labeled. The ¹³C line-widths of the resonance from the erythrocyte are typical for a lamellar arrangement of the membrane lipids. In strong contrast, the line-width observed at 37°C for the endoplasmic and sarcoplasmic reticulum membranes is much smaller, typical of the isotropic phases observed in model membranes. In isolated rat liver microsomes and liver slices, the ¹³C line-width is strongly temperature dependent. At lower temperatures the line-widths strongly increase towards values typical of lipids in a bilayer structure.

Interaction between lanthanum and lipid moieties of biological membranes

The binding of colloidal lanthanum to isolated biological membranes and lipid vesicles was studied by optical and X-ray spectroscopy, and by electron microscopy. Excellent correlation was observed using these techniques. The increase in turbidity and electron density appeared to be directly proportional to the extent of negative charge in the system. X-ray microanalysis confirmed the presence of lanthanum on the lipid vesicles. Among the negatively charged phospholipids, phosphatidylinositol showed the greatest affinity for lanthanum.     

Measuring translocation of fluorescent lipid derivatives across yeast Golgi membranes

Phospholipid asymmetry is a fundamental feature of the plasma membrane of most eukaryotic cells and its regulation is linked to diverse physiological processes such as apoptosis and blood clotting [P. Williamson, R.A. Schlegel, Biochim. Biophys. Acta 1585 (2002) 53-63; R.F. Zwaal, A.J. Schroit, Blood 89 (1997) 1121-1132]. In addition, the phospholipid translocases (flippases) that are thought to establish asymmetry are also implicated in vesicle-mediated protein transport throughout the secretory and endocytic pathways [T.R. Graham, Trends Cell Biol. 14 (2004) 670-677]. However, the biochemical properties of phospholipid translocases in membranes of the Golgi complex and endosomes have received much less attention than translocases in the plasma membrane. We describe here a method for purifying yeast Golgi membranes and assaying an ATP-dependent phospholipid translocase activity in these membranes using fluorescent lipid analogues. This assay detects ATP-dependent translocation of labeled phosphatidylserine across late Golgi membranes, which requires the activity of a P-type ATPase called Drs2p [P. Natarajan, J. Wang, Z. Hua, T.R. Graham, Proc. Natl. Acad. Sci. USA 101 (2004) 10614-10619].     

Charge-dependent translocation of the Trojan peptide penetratin across lipid membranes

We studied the interaction of the cell-penetrating peptide penetratin with mixed dioleoylphosphatidylcholine/dioleoylphoshatidylglycerol (DOPC/DOPG) unilamellar vesicles as a function of the molar fraction of anionic lipid, X(PG), by means of isothermal titration calorimetry. The work was aimed at getting a better understanding of factors that affect the peptide binding to lipid membranes and its permeation through the bilayer. The binding was well described by a surface partitioning equilibrium using an effective charge of the peptide of z(P) approximately 5.1 +/- 0.5. The peptide first binds to the outer surface of the vesicles, the effective binding capacity of which increases with X(PG). At X(PG) approximately 0.5 and a molar ratio of bound peptide-to-lipid of approximately 1/20 the membranes become permeable and penetratin binds also to the inner monolayer after internalization. The results were rationalized in terms of an "electroporation-like" mechanism, according to which the asymmetrical distribution of the peptide between the outer and inner surfaces of the charged bilayer causes a transmembrane electrical field, which alters the lateral and the curvature stress acting within the membrane. At a threshold value these effects induce internalization of penetratin presumably via inversely curved transient structures.     

Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.

A statistical thermodynamic approach is used to analyze the various contributions to the free energy change associated with the insertion of proteins and protein fragments into lipid bilayers. The partition coefficient that determines the equilibrium distribution of proteins between the membrane and the solution is expressed as the ratio between the partition functions of the protein in the two phases. It is shown that when all of the relevant degrees of freedom (i.e., those that change their character upon insertion into the membrane) can be treated classically, the partition coefficient is fully determined by the ratio of the configurational integrals and thus does not involve any mass-dependent factors, a conclusion that is also valid for related processes such as protein adsorption on a membrane surface or substrate binding to proteins. The partition coefficient, and hence the transfer free energy, depend only on the potential energy of the protein in the membrane. Expressing this potential as a sum of a "static" term, corresponding to the equilibrium (minimal free energy) configuration of the protein in the membrane, and a "dynamical" term representing fluctuations around the equilibrium configuration, we show that the static term contains the "solvation" and "lipid perturbation" contributions to the transfer free energy. The dynamical term is responsible for the "immobilization" free energy, reflecting the loss of translational and rotational entropy of the protein upon incorporation into the membrane. Based on a recent molecular theory of lipid-protein interactions, the lipid perturbation and immobilization contributions are then expressed in terms of the elastic deformation free energy resulting from the perturbation of the lipid environment by the foreign (protein) inclusion. The model is formulated for cylindrically shaped proteins, and numerical estimates are given for the insertion of an alpha-helical peptide into a lipid bilayer. The immobilization free energy is shown to be considerably smaller than in previous estimates of this quantity, and the origin of the difference is discussed in detail.     

Free radical lipid oxidation and physical properties of lipid layer of biological membranes

The results obtained mainly by the author and coworkers are summarized. One efficient method to detect free radicals in biological samples is chemiluminescence (CL). In the absence of activators CL of membraneous systems is due to lipid peroxide free radicals, whereas in the presence of luminol it is initiated by oxygen radicals. Low levels of free radicals in the cells and blood plasma are maintained by antioxidants, enzymes included. Ferrous ions increase free radical concentrations in the cells and tissues. Deleterious action of hydroxyl radicals is the result of the breakage of DNA strains and of lipid peroxidation (LPO). The latter reaction brings about the damage of the membrane barriers due to a decrease of the electrical stability of the membrane lipid bilayer and "self-breakdown" of the membranes by potential differences produced in the living cells.     

Cobaltous ion inhibition of lipid peroxidation in biological membranes.

The effect of cobalt on lipid peroxidation in biological membranes, phospholipid liposomes and fatty acid micelles was investigated. Cobaltous ion, at micromolar concentrations, inhibited iron-ascorbate induced lipid peroxidation in erythrocyte ghosts, microsomes and phosphatidylserine liposomes at pH 7.4. The pH seemed to be important for the anti-peroxidative effect of cobalt, because under slightly acidic conditions cobalt did not inhibit peroxidation. Cobalt was less effective in inhibiting peroxidation stimulated by organic hydroperoxides. Iron-ascorbate induced lipid peroxidation was also inhibited by EDTA. However, certain ratios of EDTA: cobalt in the reaction mixture stimulated peroxidation. Cobalt did not inhibit lipid peroxidation in linoleic acid micelles and phosphatidylethanolamine liposomes. The presence of phosphatidylserine, however, rendered these micelles and liposomes to cobalt inhibition. We conclude that the cobaltous ion is a potent inhibitor of lipid peroxidation in biological membranes and that the binding of cobalt to phosphatidylserine is necessary for the inhibitory effect of this metal ion.     

A model for phase transitions in lipid bilayers and biological membranes

We wish to present an order-disorder model for the observed phase transitions in lipid bilayers and biological membranes. We show that the model may, under certain circumstances, exhibit two phase transitions, one corresponding to positional disordering of entire lipid molecules, and the other corresponding to orientational disordering in the hydrocarbon chains. We then give results of our numerical analysis of the model and compare them with experimental data. Shortcomings of the model and future directions for analyses of this type are also discussed.     

Structural changes in lipid bilayers and biological membranes caused hydrostatic pressure

By use of neutron diffraction, the structural parameters of oriented multilayers of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine with deuteriocarbon chains/cholesterol (molar ratio 70:30), multilamellar lipid vesicles composed of pure lipids and lipid/cholesterol mixtures, and crystalline purple membrane patches from Halobacterium halobium have been measured at pressures up to 2 kbar. Pressurization of the oriented 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine/cholesterol multilayers results in an in-plane compression with the mean deuteriocarbon chain spacing of 4.44 A obtained under ambient conditions decreasing by 3-7% at 1.9 kbar. The thickness for this bilayer increases by approximately equal to 1.5 A, but the net bilayer volume decreases and the isothermal compressibility is estimated to be in the range (-0.1 to -0.6) X 10(-4)/bar at 19.0 degrees C. The d spacings for multilamellar vesicles composed of lipids in the liquid crystalline state and lipid/cholesterol mixtures increase linearly as a function of pressure, suggesting that these bilayers are also compressed in the membrane plane. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine and 1,2-distearoyl-sn-glycero-3-phosphatidylcholine MLVs in the gel state, the d spacing decreases with pressure. For 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine, the hexagonally packed chains are anisotropically compressed in the bilayer plane, resulting in a pseudohexagonal chain packing at 1.9 kbar. The bilayer compressibility is (-0.4 or -0.5) X 10(-4)/bar depending on whether the chain tilt increases with pressure or terminal methyl groups of apposing lipid monolayers approach each other.(ABSTRACT TRUNCATED AT 250 WORDS)