Structure predictions of membrane proteins are not that bad.

A simple generalization of the well-known hydrophobicity analysis is sufficient to predict membrane-spanning amphiphilic alpha-helices and beta-strands. The use of this method is illustrated for bacteriorhodopsin, OmpA protein and the photosynthetic reaction centre.

Electrostatic interactions at charged lipid membranes. Kinetics of the electrostatically triggered phase transition.

Charged lipid membranes of dimyristoylmethylphosphatidic acid were mixed rapidly in a stopped-flow cell with protons or Ca2+ to compensate the charges and thereby trigger the ordered-fluid phase transition. The kinetics of the transition was studied by following the time development of the fluorescence anisotropy of diphenylhexatriene. A relaxation process was observed with a characteristic time in the range 10-200 ms. By comparison with existing theories of non-equilibrium relaxation it was concluded that the relaxation process is governed by a nucleation step.

The orientation of melittin in lipid membranes. A polarized infrared spectroscopy study.

Polarized infrared spectra of melittin incorporated into macroscopically oriented lipid membranes are reported. From the linear dichroism of the amide I and amide II vibrational bands, the spatial orientation of the melittin helices was determined as being preferentially parallel to the membrane normal, under our experimental condition of low water content and an ordered lipid phase. Considering the various models for the orientation of melittin in lipid membranes proposed in the literature, we conclude that our data are in accord with an arrangement whereby the hydrophobic part of the polypeptide either spans the bilayer in the form of two bent helix segments, or is folded back within one monolayer in the form of a wedge.

Studies on lung surfactant replacement in respiratory distress syndrome. Rapid film formation from binary mixed liposomes.

Binary mixed liposomes were prepared from dipalmitoylphosphatidylcholine (DPPC) and a minor compound, e.g., egg phosphatidylglycerol (PG) at a ratio of 9:1. Using different preparative techniques, large unilamellar vesicles (LUV), small unilamellar vesicles (SUV) or multilamellar vesicles (MLV) were obtained and were studied with an electron microscope for morphology, with a Wilhelmy balance for spreading and surface tension lowering potential, and in the surfactant-depleted isolated rat lung for their ability to restore expiratory lung capacity. Only the simultaneous investigation of phospholipids by negative staining and thin sectioning allows unequivocal classification of liposomes. The surface-active structures prepared with the technique of Bangham et al. (Bangham, A.D., Hill, M.W. and Miller, N.G.A. (1974) in Methods in Membrane Biology (Korn, E., ed.), Vol. 1, pp. 1-68, Plenum Press, New York) at room temperature are LUV. LUV containing DPPC:PG at a ratio of 9:1 rapidly spread to a film with high surface tension lowering potential. Within 5 min after injection into the subphase they rise to the surface and form a film at the air/liquid interface able to lower the surface tension to less than 1 mN/m at compression. SUV of the same chemical composition, however, are immediately surface-active only when spread directly onto the surface. MLV exhibit poor surface activity. LUV or pure DPPC, applied onto the surface, are weakly surface active within 5 min. DPPC vesicles injected into the subphase at 37 degrees C do not adsorb to any film with surface tension lowering potential in this time. The minor compounds PE, PI, PS, PA, lysoPC enable DPPC to form surface-active films after application on saline at 37 degrees C. Removal of surfactant decreases the expiratory lung capacity of the isolated rat lung from 49.7 to 12.4% at 4 cmH2O. After substitution with natural surfactant, the expiratory lung capacity is twice that of the washed lung (25.9%), but the original distensibility of the native lung is not restituted. The effect of LUV containing DPPC:PG at a ratio of 9:1 is also remarkable (21.2%).

Localization of the galactoside binding site in the lactose carrier of Escherichia coli.

The location of flurophores specifically bound to the lactose/H+ carrier of Escherichia coli was ascertained by the use of various collisional quenchers. The reporter groups were (1) the pyrenyl residue of N-(1-pyrenyl)maleimide attached to the essential cysteine residue 148, which is presumably at or near the galactoside binding site, and (2) the dansyl moieties of a series of fluorescent substrate molecules. The accessibility of these fluorophores from the lipid phase was assessed by nitroxyl-labelled fatty acids and phospholipids. By using a series of nitroxyl-labelled fatty acids carrying the quencher at different positions in the acyl chain, the position of a quenchable fluorophore with respect to the membrane normal can be determined. The accessibility of fluophores from the aqueous phase was assessed by using a water-soluble quencher, the N-methylpicolinium ion. The results of quenching studies suggest that the galactoside binding site is located within the carrier and that this binding site communicates with the aqueous phase through a pore.

Models for the structure of outer-membrane proteins of Escherichia coli derived from raman spectroscopy and prediction methods.

The secondary structure of porin, maltoporin and OmpA protein reconstituted in lipid membranes is determined by Raman spectroscopy. The three proteins have similar structures consisting of 50 to 60% beta-strand, about 20% beta-turn, and less than 15% alpha-helix. Employing a method for structural prediction that accounts for amphipathic beta-strands, folding models are developed for porin and for the segment of OmpA protein incorporated into the membrane. In the model, the OmpA fragment consists of eight amphipathic membrane-spanning beta-strands that form a beta-barrel. Similarly, porin is folded into ten amphipathic membrane-spanning beta-strands that are located at the surface of the trimer towards the lipids and eight predominantly hydrophilic strands in the interior.

Modeling of the structure of bacteriorhodopsin. A molecular dynamics study.

Secondary structure predictions for membrane proteins are relatively reliable and permit the construction of model structures that may serve as initial conformations for molecular dynamics simulations. This might provide a scheme to predict the three-dimensional structures of membrane proteins. The feasibility of such an approach is tested for bacteriorhodopsin. We were not able to fully predict the kidney-shaped structure of bacteriorhodopsin. However, features compatible with this structure developed in a simulation starting from a circular arrangement of the seven predicted helices. When instead we started from the kidney shape, assigning the seven predicted helices in different ways to those on the structure, we could distinguish between the different assignments on the basis of energy and tilt of the helices. In this way we could select the correct assignment from a few others. For the correct assignment, the helices spontaneously adopted a tilt that agrees remarkably well with the experimental model structure derived by others. The root-mean-square deviation between our best molecular dynamics structure and the experimental model structure is 3.8 A, caused mainly by deviations in the internal degrees of freedom of the helices.

Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study.

Molecular dynamics simulations on bacteriorhodopsin were performed starting from the model structure described by Henderson et al. The simulations were gradually improved by first treating a monomer in vacuum and then adding further monomers, lipids, and water to finally simulate a unit cell of the hexagonal lattice of the purple membrane containing a trimer and lipids and water on both sides. During all simulations, the protein structure moved away from the model structure to reach a root-mean-square (r.m.s.) deviation of 2 to 3 A. In the simulations with the trimer, the structures of the three monomers differed by about the same amount and averaging over them led to an average structure with a considerably smaller r.m.s. deviation. The best average structure obtained had an r.m.s. deviation from the model structure of 1.3 A. Fluctuations of the protein, the lipids, and water were analyzed in detail. As expected, the membrane-spanning helices of the protein fluctuate less than the peripheral loops. Unexpected, however, was the finding that the fluctuations of the protein are asymmetric with respect to the midplane of the membrane. The fluctuations of the loops and the ends of the helices on the inner side of the membrane are much stronger than on the outer side. This asymmetry is also reflected by the fluctuations for the lipids, the lipids of the inner leaflet fluctuating more strongly than those of the outer leaflet. The asymmetry was observed only in the presence of water on both sides of the membrane. On the average, nine water molecules were found inside the protein, most of them undergoing exchange with external water.

Enhanced internal dynamics of a membrane transport protein during substrate translocation.

Conformational changes are essential for the activity of many proteins. If, or how fast, internal fluctuations are related to slow conformational changes that mediate protein function is not understood. In this study, we measure internal fluctuations of the transport protein lactose permease in the presence and absence of substrate by tryptophan fluorescence spectroscopy. We demonstrate that nanosecond fluctuations of alpha-helices are enhanced when the enzyme transports substrate. This correlates with previously published kinetic data from transport measurements showing that millisecond conformational transitions of the substrate-loaded carrier are faster than those in the absence of substrate. These findings corroborate the hypothesis of the hierarchical model of protein dynamics that predicts that slow conformational transitions are based on fast, thermally activated internal motions.

Secondary structure of the promastigote surface protease of Leishmania.

By Raman spectroscopic analysis we have determined the secondary structure of the promastigote surface protease, named PSP or gp63, of Leishmania major. It consist of nearly 50% antiparallel beta-strand, and less than 20% alpha-helix. These results are contrasted with the predominantly alpha-helical VSGs of the African trypanosomes and the alpha-helical metalloprotease thermolysin. The PSP of Leishmania thus represents a novel kind of membrane-anchored protease.

Predicted structure of tail-fiber proteins of T-even type phages.

The sequences of the tail fiber protein 36 of the phages T4, T2, K3, and Ox2 were analyzed for homologies and for folding patterns using structure prediction methods. No repeating motif was found. A model for the fiber structure is proposed in which beta-strands of about 6 amino acids are separated by turns. In the beta-strand, hydrophobic amino acids are found alternating with hydrophilic ones. Such amphipathic beta-strands can be stabilized by dimer formation. The dimerization occurs in a parallel fashion so that both N-termini are at one end of the dimer. This structure represents a rigid fiber. Our model is consistent with electron microscopic data and electron diffraction patterns for the T4 tail fiber. The observation that all fiber components are found as dimers supports our model. Sequences of the receptor recognition proteins 38 of T-even type phages reveal an architecture different from the architecture of the fiber proteins 36 and 37 of these phages.

Secondary structure of the variant surface glycoproteins of trypanosomes.

The secondary structure of seven variant surface glycoproteins (VSGs) of trypanosomes has been determined by Raman spectroscopy. They are all predominantly alpha-helical, the alpha-helix content varying between 50 and 60%. The beta-strand content varies between 20 and 25%, and the content of beta-turn and nonregular structures is about 25%. For three VSGs the N-terminal domain obtained by proteolytic cleavage was found to have essentially the same secondary structure as the complete VSGs. For three VSGs a secondary structure prediction has been performed applying the rules of Chou and Fasman. In all cases, two long alpha-helices extending over about 50 residues or 80 A are predicted in agreement with the X-ray diffraction data of Freymann et al. [(1984) Nature 311, 167-169] and Metcalf et al. [(1987) Nature 325, 84-86]. The region between the two alpha-helical segments exhibits a high potential of beta-turns, suggesting that this segment may be exposed on the cell surface and carry major antigenic determinants.

Biosensors based on membrane transport proteins.

We propose a novel class of biosensors based on membrane bound receptors or transport proteins as the sensing element. The protein is incorporated in a planar lipid bilayer which covers the transducer. The transducer may detect an electric current, a voltage, or a change in fluorescence. A prototype lactose sensor is presented which consists of a quartz slide covered by a lipid membrane containing the protein lactose permease from Escherichia coli. This protein is a lactose/H+ cotransporter, hence lactose in the external medium initiates lactose/H+ cotransport across the lipid membrane. This leads to a rise in proton concentration in the small volume between the lipid membrane and the quartz surface which can be detected by a pH-sensitive fluorescence dye.

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 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 membranes. The results confirm the interpretation of experimental data as given by Träuble et al. in the accompanying paper.

The structure of a membrane-spanning polypeptide studied by molecular dynamics.

We have performed a molecular dynamics simulation of a 46-residue segment of glycophorin which includes the hydrophobic membrane-spanning region of this protein. The presence of a membrane and of water is taken into account in a continuum approximation which makes use of phenomenological hydrophobic energies. The initial alpha-helical conformation and the membrane incorporation of the hydrophobic segment remain stable for the length of the simulation which is 100 ps. Moreover, when the hydrophobic segment is partially shifted out of the membrane, it moves back into the membrane. Superimposed on these deterministic effects one also observes thermal fluctuations in the form of bending and tilting of the membrane-spanning helix.

No need for a new membrane model.

Schindler et al. recently reported lateral diffusion measurements in reconstituted membranes of phospholipid (PL), lipoplysaccharide (LPS) and Escherichia coli matrix protein (P), using the technique of fluorescence recovery after photobleaching (FRAP). Evaluation of their data led Schindler et al. to conclude that the fluid mosaic model is an inadequate description of the membrane and to propose a new membrane model. Their conclusion was based on identifying the fluid mosaic model with a particular binding behaviour of LPS to matrix protein. I present here a more general model for the association of membrane components, and demonstrate the use of lateral diffusion data in elucidating membrane structure. The data of Schindler et al. are shown to be reasonably interpretable on the basis of an association of LPS and matrix protein, which obviates the necessity for postulating a new membrane model.

Critical effects from lipid-protein interaction in membranes. II. Interpretation of experimental results.

The effects arising from lipid-protein and lipid-cholesterol interaction are discussed within the framework of a general theoretical description presented in the preceding paper. Available experimental results are interpreted, and new experiments are proposed. In the fluid lipid phase proteins and cholesterol increase the lipid orientational order in their neighborhood, in the ordered phase they decrease it. This leads to a decrease of the latent heat at the ordered-fluid transition, which vanishes at a critical concentration of protein or cholesterol. Theoretical predictions for the critical concentrations agree with results from calorimetry. The approach to the critical point is accompanied by an increase of thermal fluctuations of the lipid order and an increase of the lipid response on small perturbations. Thus proteins and cholesterol increase the lipid specific heat, lateral compressibility, permeability, and lateral diffusion on both sides of the phase transition. Notions such as decrease of cooperativity or fluidity due to protein or cholesterol are reviewed in this context.