X-ray diffraction analysis of matrix porin, an integral membrane protein from Escherichia coli outer membranes

Folding patterns of porin and bacteriorhodopsin

Porin spans the outer membrane of Escherichia coli with most of the protein embedded within the membrane. It lacks pronounced hydrophobic domains and consists predominantly of beta-pleated sheet. These observations require the accommodation of polar and ionizable residues in an environment that has a low dielectric constant. Owing to a currently limited understanding of the constraints governing membrane protein structure, a minimal approach to structure prediction is proposed that identifies segments causing polypeptides to reverse their direction (turn identification). The application of this procedure avoids hydrophobicity parameters and yields a model of porin which is in good agreement with all experimental data available. The presence of polar and ionizable residues within membrane boundaries implies a dense (saturating) network of hydrogen bond donor and acceptor groups. Application to a paradigm of hydrophobic membrane proteins, bacteriorhodopsin, reveals a pattern consistent with its alpha-helical folding. The postulated structure includes significantly more polar residues in the membrane domain than have been assumed previously, suggesting that there are also hydrogen bonding networks in bacteriorhodopsin. Extensive networks permeating protein interior and surfaces would explain the extraordinary stability and the tight interactions between functional units in the formation of crystalline arrays of both proteins.

New biophysical techniques and their application to the study of membranes

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Projected structure of the pore-forming OmpC protein from Escherichia coli outer membrane

A single-projection structure analysis of a bacterial outer membrane protein, OmpC, has been carried out by electron microscopy of frozen hydrated specimens. Two distinct crystal polymorphs have been observed in the frozen-hydrated samples, and projection structures of both forms have been obtained to a resolution of 13.5 A. Preliminary examination of negatively stained samples revealed the expected, trimeric appearance of pores in the OmpC specimens. Electron microscopy of unstained, frozen-hydrated OmpC reveals the trimeric pore structure with equal clarity. In addition, the overall molecular envelope of the protein is readily discerned, and a major lipid-containing domain can also be seen. Because of the small coherent patch size, mosaic disorder, and unpredictable polymorphism of the presently available specimens, three-dimensional reconstruction of frozen-hydrated OmpC has not been carried out.

Ion selectivity of gram-negative bacterial porins

Twelve different porins from the gram-negative bacteria Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, and Yersinia pestis were reconstituted into lipid bilayer membranes. Most of the porins, except outer membrane protein P, formed large, water-filled, ion-permeable channels with a single-channel conductance between 1.5 and 6 nS in 1 M KCl. The ions used for probing the pore structure had the same relative mobilities while moving through the porin pore as they did while moving in free solution. Thus the single-channel conductances of the individual porins could be used to estimate the effective channel diameters of these porins, yielding values ranging from 1.0 to 2.0 nm. Zero-current potential measurements in the presence of salt gradients across lipid bilayer membranes containing individual porins gave results that were consistent with the conclusions drawn from the single-channel experiments. For all porins except protein P, the channels exhibited a greater cation selectivity for less mobile anions and a greater anion selectivity for less mobile cations, which again indicated that the ions were moving inside the pores in a fashion similar to their movement in the aqueous phase. Three porins, PhoE and NmpC of E. coli and protein P of P. aeruginosa, formed anion-selective pores. PhoE and NmpC were only weakly anion selective, and their selectivity was dependent on the mobility of the ions. In contrast, cations were unable to enter the selectivity filter of the protein P channel. This resulted in a high anion selectivity for all salts tested in this study. The other porins examined, including all of the known constitutive porins of the four gram-negative bacteria studied, were cation selective with a 3- to 40-fold preference for K+ ions over Cl- ions.

Secondary structure and assembly mechanism of an oligomeric channel protein

The alpha-toxin of Staphylococcus aureus is secreted as a water-soluble, monomeric polypeptide (Mr 33 182) that can assemble into an oligomeric membrane channel. By chemical cross-linking, we have confirmed that the major form of the channel is a hexamer. The circular dichroism spectrum of this hexamer in detergent revealed that it contains a high proportion of beta-sheet that we deduce must lie within the lipid bilayer when the protein is associated with membranes. The circular dichroism spectrum of the monomeric toxin in the presence or absence of detergent was closely similar to the spectrum of the hexamer, suggesting that the secondary structure of the polypeptide is little changed on assembly. Results of experiments involving limited proteolysis of the monomer and hexamer are consistent with the idea that assembly involves the movement of two rigid domains about a hinge located near the midpoint of the polypeptide chain. The hydrophilic monomer is thereby converted to an amphipathic rod that becomes a subunit of the hexamer.

Porin from bacterial and mitochondrial outer membranes

The outer membrane of gram-negative bacteria acts as a molecular filter with defined exclusion limit for hydrophilic substances. The exclusion limit is dependent on the type of bacteria and has for enteric bacteria like Escherichia coli and Salmonella typhimurium a value between 600 and 800 Daltons, whereas molecules with molecular weights up to 6000 can penetrate the outer membrane of Pseudomonas aeruginosa. The molecular sieving properties result from the presence of a class of major proteins called porins which form trimers of identical subunits in the outer membrane. The porin trimers most likely contain only one large but well-defined pore with a diameter between 1.2 and 2 nm. Mitochondria are presumably descendents of gram-negative bacteria. The outer membrane of mitochondria contains in agreement with this hypothesis large pores which are permeable for hydrophilic substances with molecular weights up to 6000. The mitochondrial porins are processed by the cell and have molecular weights around 30,000 Daltons. There exists some evidence that the pore is controlled by electric fields and metabolic processes.

X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis

X-ray analysis of three-dimensional crystals of the photosynthetic reaction center from the purple bacterium Rhodopseudomonas viridis led to an electron density distribution at 3 A resolution calculated with phases from multiple isomorphous replacement. The protein subunits of the complex were identified. An atomic model of the prosthetic groups of the reaction center complex (4 bacteriochlorophyll b, 2 bacteriopheophytin b. 1 non-heme iron, 1 menaquinone, 4 heme groups) was built. The arrangement of the ring systems of the bacteriochlorophyll b and bacteriopheophytin b molecules shows a local 2-fold rotation symmetry; two bacteriochlorophyll b form a closely associated, non-covalently linked dimer ("special pair"). A different local 2-fold symmetry axis is observed for the heme groups of the cytochrome part.

Biochemical and immunological analyses of the cell surface of Bordetella bronchiseptica isolates with special reference to atrophic rhinitis in swine

The guinea-pig skintest was used to test the pathogenic character of nine Bordetella bronchiseptica isolates derived from a number of different animals. One isolate was non-pathogenic, one showed a doubtful reaction whereas the others were pathogenic. Analysis of the cell envelope protein patterns by sodium dodecyl sulphate polyacrylamide gel electrophoresis revealed only minor differences. Two major protein bands and at least thirty five minor bands were observed. The major protein with an apparent molecular weight of 37000 has properties similar to those of pore proteins of Enterobacteriaceae. Lipopolysaccharides (LPS), analysed by the same technique, could be separated into two fractions, LPS-I and LPS-II. The electrophoretic mobilities of the LPS of the strains were indistinguishable from each other with the exception of that of the non-pathogenic strain, which also differed serologically from that of the other strains. All sera of animals which had been successfully vaccinated with whole B. bronchiseptica cells showed a positive reaction with LPS-I whereas antibodies against the 37000 dalton protein, LPS-II as well as against several other proteins, were also detected in several sera. These results strongly suggest that LPS-I is a protective antigen. LPS-I and the 37000 dalton protein are accessible to antibodies in whole cells. This protein as well as a 28000 dalton protein were found to be located at the cell surface using iodination of whole cells with Iodo-Gen.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriophage T5 gene A2 protein alters the outer membrane of Escherichia coli

Evidence for changes in Escherichia coli envelope structure caused by the bacteriophage T5 gene A2 protein was obtained by the use of mutant bacteriophages, envelope fractionation procedures, electrophoretic analysis, and in vitro binding studies with purified gene A2 protein. The results suggested that the T5 gene A2 protein perturbs the host envelope as it functions to promote DNA transfer.

Crystallization of reaction center from Rhodopseudomonas sphaeroides: preliminary characterization

Reaction centers (RCs), integral membrane proteins that mediate the conversion of light into chemical energy, were crystallized by two different vapor diffusion techniques. In one method, small amphipathic molecules (1,2,3-heptanetriol and triethylammonium phosphate) were added to the RCs that had been solubilized in detergent. In the second method, crystallization occurred near the phase boundaries of a two-phase system created by the addition of polyethylene glycol and NaCl to RCs in octyl beta-D-glucoside. Several different crystal forms were obtained; two were analyzed by x-ray diffraction. One was monoclinic (space group P2) with beta = 105 degrees, and a = 70 A, b = 105 A, and c = 85 A, two RCs per unit cell, and one RC per asymmetric unit; the crystal diffracted to 3.5 A at 17 degrees C. The other crystal form was orthorhombic (space group C222) with a = 185 A, b = 170 A, and c = 105 A, with eight RCs per unit cell and one RC per asymmetric unit. Reversible light-induced EPR signals of the primary donor (bacteriochlorophyll dimer) showed that the RCs in the crystal were fully active. From the angular dependence of the EPR signal the molecular g anisotropy of the bacteriochlorophyll dimer was deduced to be g perpendicular - g parallel = (64 +/- 3) X 10(-5). Linear dichroism measurements were performed on the monoclinic crystal. The two bands at 535 and 544 nm assigned to the Qx transitions of the bacteriopheophytins were resolved and preliminary orientations of some of the pigments were obtained.

Structural transitions of porin, a transmembrane protein

Conformational transitions of porin were monitored using 3 independent criteria: (i) oligomeric state as observed by SDS-polyacrylamide gel electrophoresis; (ii) spectroscopic titrations (ultraviolet and circular dichroism) and (iii) chemical modifications. Four pH-dependent transitions were observed with half-maximal changes occurring at pH values of 1.6, 3.5, 11.2 and 12.4. Two of these pH values differ significantly from intrinsic pK values of the constituent amino acids of this membrane protein. Since porin is very polar despite its location predominantly within the outer membranes, this may be due to ion pair formation in the hydrophobic environment of the membrane.

Outer-membrane protein PhoE from Escherichia coli forms anion-selective pores in lipid-bilayer membranes

Porin PhoE of the outer membrane of Escherichia coli was isolated and purified. Reconstitution experiments with lipid bilayer membranes showed that this protein formed pores which had a single channel conductance of 210 pS at 0.1 M KCl. The PhoE pores were obviously not voltage-controlled or regulated. In contrast to pores formed by the OmpF porin from E. coli the PhoE channel was found to be anion-selective at neutral pH. Chloride is about three to ten times more permeable through the pore than alkali ions. On the basis of the observed pH dependence of the permeability ratio of anions and cations, this anionic selectivity is explained by the assumption that the PhoE pore contains an excess of fixed positive charges.

Dynamical electron scattering from negatively stained protein microcrystals

Multislice n-beam dynamical calculations have been carried out at 20 and 15.6 A resolution to simulate the electron scattering from a negatively-stained protein microcrystal using a model based on the crystal structure of E. coli matrix porin. Images at t = 100 A, i.e. the thickness of reconstituted vesicle preparation, correspond to the projected potential of the kinematical structure. The kinematical model is valid at least to t = 500 A, beyond which the projected-image symmetry does not correspond to the actual structure. If a crystallographic residual limit R = 0.20 is imposed, the electron diffraction intensity data correspond to the kinematical data up to t = 700 and 1000 A, respectively, for 15.6 and 20 A resolution.

3D reconstruction from electron micrographs: its potential and practical limitations

The 3D structure of stain-penetrated transmembrane channels of E. coli outer membrane porin has been reconstructed from electron microscopic projections. The averaged unit cells of the projected hexagonal porin lattices were calculated by correlation averaging. Amplitude and phase values along the continuous lattice lines were obtained from the unit cell transforms, and continuous curves were fitted using either a cubic spline-fit or by convolution with an appropriate sinc function. The reconstructed model shows that the three channels of a porin triplet merge to a single channel while traversing the membrane. This is in excellent agreement with results of functional studies. Some technical difficulties and limitations as well as the potential of the reconstruction process are discussed.

A genetic approach to defining the sites of interaction of a membrane protein with different external agents

In addition to a role in maintaining outer membrane structural integrity, the OmpA protein of Escherichia coli serves as a receptor for different phages, is required in the recipient cell for efficient conjugation, and functions in the internalization of receptor-bound colicins. To determine whether the same or different sites of OmpA protein are needed for these different functions, this paper presents the properties of a collection of ompA mutants selected as being defective in phage receptor function, but containing normal amounts of OmpA protein. Of 44 mutants examined, most were affected in more than one OmpA protein function, showing that there is considerable overlap in sites needed for different functions. The pattern of this overlap can be represented in a phenotypic map of OmpA protein functions.

Two-dimensional crystal packing of matrix porin. A channel forming protein in Escherichia coli outer membranes

Two-dimensional crystalline porin sheets were obtained by reconstitution of monodisperse protein trimers and phospholipids (dimyristoylphosphatidylcholine) by detergent dialysis, analogous to the reconstitution method used for functional tests (Schindler & Rosenbusch, 1981). Three different packing arrangements were observed: two were hexagonal (with p3 symmetry and lattice constants of 9.3 nm and 7.9 nm), and one rectangular (a = 7.9 nm, b = 13.9 nm). The different crystals could be correlated to phospholipid-to-protein weight ratios of 0.16 to 0.72. At the higher ratio, large hexagonal lattices predominated. Higher lipid ratios did not reveal other crystal forms. The packing arrangement of the large hexagonal form appears very similar to the hexagonal habit of three-dimensional crystal forms (Garavito et al., 1983). The shape of the stain-penetrated triplet indentations appeared conserved in the crystal forms to a resolution of 2.2 nm. The mass distribution between triplets, however, were significantly different. They are likely to correspond primarily to lipids. Mass determinations of unstained porin by scanning transmission electron microscopy showed that unit cells consisted of single trimers. The mass found (100,000 daltons) is in good agreement with the value obtained by sedimentation equilibrium analysis.