Existence and purification of porin heterotrimers of Escherichia coli K12 OmpC, OmpF, and PhoE proteins

Porin is a trimeric membrane protein that functions as a diffusion pore in the outer membrane of Escherichia coli. We report the existence and purification of porin heterotrimers between the ompC, ompF, and phoE porin gene products. Separation was achieved using a high resolution anion exchange column. The amount of each heterotrimer species present depended on the level of expression of the subunits and was consistent with random mixing of trimer subunits. A strong effect of bacterial lipopolysaccharide on the chromatography of porin was also detected. These results imply that assembly of porin trimers occurs between subunits synthesized on different polysomes and that subunit contacts between the porin subunits occur in conserved regions of the primary sequence.     

Subunit structure of functional porin oligomers that form permeability channels in the other membrane of Escherichia coli.

Oligomers of a protein, porin, form permeability channels in the outer membrane of Escherichia coli B. A functional porin oligomer was identified and was purified to homogeneity by gel filtration in the presence of salts and sodium dodecyl sulfate. Molecular weights of purified porin oligomer and heat-dissociated monomer appeared to be 102,900 and 32,600, respectively, when determined by sedimentation equilibrium in the presence of sodium dodecyl sulfate. We concluded that the porin oligomer thus consists of three identical subunits. These data and results from other laboratories suggest porin trimers exist also in the outer membrane of intact cells, and participate in the formation of permeability channels. It was found that porin trimer bound less sodium dodecyl sulfate than the porin monomer.     

Outer membrane porin protein of Haemophilus influenzae type b: pore size and subunit structure

The 40-kDa porin protein of Haemophilus influenzae type b was reconstituted into proteoliposomes. The relative rates of diffusion of small uncharged sugars across the channels formed by this protein were determined by measuring the rates of osmotic swelling of the liposomes. From these rates, a pore diameter of 1.8 nm was estimated using the Renkin equation. A chemical cross-linking technique was used to investigate the oligomeric structure of the 40-kDa porin. Sodium dodecyl sulfate - polyacrylamide gel electrophoresis revealed the presence of porin dimers and trimers after reaction of the protein with dithio-bis-(succinimidyl propionate). These results confirmed that the porin of H. influenzae forms large water-filled channels and indicated that it probably exists as trimers in the outer membrane.     

Permeability properties of chemically modified porin trimers from Escherichia coli B

The pore-forming protein of the outer membrane of Escherichia coli, porin, was chemically modified with acetic anhydride, succinic anhydride, and glycinamide. Extensive modification of amino groups of the functional porin trimers caused reduced diffusion rates of the negatively charged solutes such as p-nitrophenyl phosphate and AMP, but did not reduce significantly the diffusion of positively charged molecules carbobenzoxy-glycyl-prolyl-arginine-p-nitranilide and tosyl-glycyl-prolyl-arginine-p-nitranilide. Modification of carboxyl groups of trimers caused decreased diffusion rates of the positively charged solutes more significantly than the diffusion rates of negatively charged solutes. The results suggest that the ionic interactions play an important role for the diffusion of charged solutes through the porin pore. The diffusion of p-nitrophenyl alpha-D-glucoside, an uncharged solute, ws not influenced significantly by modification of either amino or carboxyl groups. This observation suggests that modifications only occurred in areas outside of the narrowest portion of the pore or, alternatively, that amino and carboxyl groups are exclusively located at noncylindrical area of the pore. The structural integrity of the acetylated and the succinylated trimers seemed well preserved. On the other hand, modification of carboxyl groups decreased the thermal stability of trimers and extensive modifications caused the dissociation of trimers into monomers at 37 degrees C.     

Structural and functional analyses of the major outer membrane protein of Chlamydia trachomatis

Chlamydia trachomatis is a major pathogen throughout the world, and preventive measures have focused on the production of a vaccine using the major outer membrane protein (MOMP). Here, in elementary bodies and in preparations of the outer membrane, we identified native trimers of the MOMP. The trimers were stable under reducing conditions, although disulfide bonds appear to be present between the monomers of a trimer and between trimers. Cross-linking of the outer membrane complex demonstrated that the MOMP is most likely not in a close spatial relationship with the 60- and 12-kDa cysteine-rich proteins. Extraction of the MOMP from Chlamydia isolates under nondenaturing conditions yielded the trimeric conformation of this protein as shown by cross-linking and analysis by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis with different concentrations of acrylamide. Using circular dichroism spectroscopy, we determined that the trimers were formed mainly of beta-pleated sheet structures in detergent micelles. Using a liposomal swelling assay, the MOMP was found to have porin activity, and the size of the pore was estimated to be approximately 2 nm in diameter. The trimers were found to be stable in SDS at temperatures ranging from 4 to 37 degrees C and over a pH range of 5.0 to 8.0. In addition, the trimers of MOMP were found to be resistant to digestion with trypsin. In conclusion, these results show that the native conformation of the MOMP of C. trachomatis is a trimer with predominantly a beta-sheet structure and porin function.     

Effects of pH on structural and functional properties of porin from the outer membrane of Yersinia pseudotuberculosis. II. Characterization of pH-induced conformational intermediates of yersinin

pH-Induced intermediates of Omp F-like porin from the outer membrane of Yersinia pseudotuberculosis (yersinin) were characterized by fluorescence and fluorescent probe spectroscopy and circular dichroism. The most dramatic changes in the intrinsic fluorescence of the protein induced by pH titration correlated with different conformational states of the porin molecule. pH-induced conformational transitions of yersinin can be described in terms of a three-state model: (1) disordering of porin associates and formation of porin trimers structurally similar to the native protein; (2) unfolding of individual porin domains followed by cooperative dissociation of trimers into monomers; (3) formation of two loosely structured forms of monomer intermediates. It is assumed that one of these monomeric forms (at pH 3.0) corresponds to the molten-globule state of porin with native secondary structure, while the other one (at 2.0) represents a partly denatured (misfolded) monomer, which retains no more than 50% of the regular secondary structure. The putative mechanism of low pH-induced β-barrel unfolding is discussed in terms of a theoretical model of yersinin spatial structure.     

Effect of structural modifications on the assembly of a glycinin subunit.

A Gy4 glycinin cDNA was modified and used to produce structurally altered 11S storage protein subunits. We evaluated these modified subunits for their ability to assemble into oligomers. Alterations made in the acidic polypeptide changed the subunit solubility characteristics but did not eliminate assembly. Modifications in the basic polypeptide usually eliminated assembly of subunits into trimers. A region exhibiting high natural variability located at the COOH terminus of the acidic polypeptide that we have designated the hypervariable region was also studied. Extensive deletions and insertions were tolerated in the hypervariable region without perturbing subunit assembly. Some of the insertions significantly increased the methionine content in the Gy4 glycinin subunit. Together, our results indicated that the structure of the basic polypeptide was more critical for assembly of trimers than that of the acidic polypeptide, an observation that implies that the basic polypeptides direct trimer formation. The assembly assays described here will be useful in efforts to improve seed quality. Using them, the effects of modifications to the storage protein subunits can be rapidly evaluated before introducing the mutated genes into plants.     

Associations of Escherichia coli K-12 OmpF trimers with rough and smooth lipopolysaccharides.

The associations of both rough and smooth lipopolysaccharides (LPS) with the OmpF porin of Escherichia coli K-12 were examined in galE strains deleted for ompC. Transformation with pSS37 and growth with galactose conferred the ability to assemble a Shigella dysenteriae O antigen onto the core oligosaccharide of E. coli K-12 LPS. The association of LPS with OmpF trimers was assessed by staining, autoradiography of LPS specifically labeled with [1-14C]galactose, and Western immunoblotting with a monoclonal antibody specific for OmpF trimers. These techniques revealed that the migration distances and multiple banding patterns of OmpF porin trimers in sodium dodecyl sulfate-polyacrylamide gels were dictated by the chemotype of associated LPS. Expression of smooth LPS caused almost all of the trimeric OmpF to run in gels with a slower mobility than trimers from rough strains. The LPS associated with trimers from a smooth strain differed from the bulk-phase LPS by consisting almost exclusively of molecules with O antigen.     

Isolation and preliminary characterization of wild-type OmpC porin dimers from Escherichia coli K-12

Escherichia coli K-12 strain PLB3255 contains a mutation in the ompF gene that results in a 15 amino acid deletion in the porin protein. The mutation (dex) appears to increase the OmpF channel size, allowing the PLB3255 cells to grow on maltodextrins in the absence of a functional maltoporin. Porin isolated from strain PLB3255, which contains a wild-type ompC gene, was separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and shown to contain 50-60% trimer aggregates and 35-40% of a 50-kDa "dimer". When the porin isolate was heated to 100 degrees C and separated on SDS gels containing 8 M urea, both the trimer and the "dimer" were recovered in a single band at 36 kDa that corresponded in mobility to wild-type OmpC porin. An analysis of the temperature stability of the isolate showed that the OmpC "dimer" was less stable and denatured at 66 degrees C compared to 81 degrees C for the trimer. To separate these aggregates, the unheated porin was suspended in 30% SDS, applied to a Sephadex G-200 gel filtration column, and eluted with 0.5% sodium deoxycholate. Two peaks were recovered containing separated trimers and "dimers". Circular dichroism spectra of isolated dimers and trimers indicated similar amounts of beta-structure. The isolated dimers and trimers were reconstituted into artificial membranes. Electrical conductance across planar bilayer lipid membranes and liposome swelling assays showed that the two isolates had similar channel-forming activity. Four other ompF deletion mutants of the same phenotype were also shown to produce 50-kDa OmpC porin "dimers".(ABSTRACT TRUNCATED AT 250 WORDS)     

The voltage-dependent activity of Escherichia coli porins in different planar bilayer reconstitutions

Because of conflicting results from differing techniques, the degree of voltage sensitivity of Escherichia coli porins in planar bilayers is still a matter of debate. In order to provide the first comparative study, OmpF porin was purified in three ways; firstly as native outer membrane vesicles, secondly as salt-extracted porin trimers in sodium dodecyl sulphate and thirdly as solubilised trimers extracted with octyl-polyoxyethylene (Octyl-POE). These methods represent the major approaches to porin isolation and purification. All three were reconstituted into Schindler-type bilayers. Detergent-solubilised OmpF was also reconstituted into Montal-Mueller- and Mueller-Rudin-type bilayers. In all cases voltage-dependent closing of OmpF was observed. Octyl-POE-extracted PhoE porin was similarly investigated in all three types of planar bilayer. Two membrane-formation techniques appeared genuinely to alter the voltage sensitivity of the porins they contained. Firstly, porins in membranes formed by the Montal-Mueller technique sometimes showed an increase in voltage sensitivity during the first 30 min after bilayer formation. Secondly, membranes formed by the Mueller-Rudin technique on thick polyethylene septa showed both poor solvent drainage and a significantly reduced porin voltage sensitivity.     

A novel OmpY porin from Yersinia pseudotuberculosis: structure, channel-forming activity and trimer thermal stability

A novel OmpY porin was predicted based on the Yersinia pseudotuberculosis genome analysis. Whereas it has the different genomic annotation such as "outer membrane protein N" (ABS46310.1) in str. IP 31758 or "outer membrane protein C2, porin" (YP_070481.1) in str. IP32953, it might be warranted to rename the OmpN/OmpC2 to OmpY, "outer membrane protein Y", where letter "Y" pertained to Yersinia. Both phylogenetic analysis and genomic localization clearly support that the OmpY porin belongs to a new group of general bacterial porins. The recombinant OmpY protein with its signal sequence was overexpressed in porin-deficient Escherichia coli strain. The mature rOmpY was shown to insert into outer membrane as a trimer. The OmpY porin, isolated from the outer membrane, was studied employing spectroscopic, electrophoretic and bilayer lipid membranes techniques. The far UV CD spectrum of rOmpY was essentially identical to that of Y. pseudotuberculosis OmpF. The near UV CD spectrum of rOmpY was weaker and smoother than that of OmpF. The rOmpY single-channel conductance was 180 ± 20 pS in 0.1 M NaCl and was lower than that of the OmpF porin. As was shown by electrophoretic and bilayer lipid membrane experiments, the rOmpY trimers were less thermostable than the OmpF trimers. The porins differed in the trimer-monomer transition temperature by about 20°C. The three-dimensional structural models of the Y. pseudotuberculosis OmpY and OmpF trimers were generated and the intra- and intermonomeric interactions stabilizing the porins were investigated. The difference in the thermal stability of OmpY and OmpF trimers was established to correlate with the difference in intermonomeric polar contacts.     

A Structural Analysis of the Regularly Arranged Porin on the Outer Membrane of Campylobacter jejuni Based on Correlation Averaging

A negatively stained electron micrograph of regularly arranged porin proteins of Campylobacter jejuni on the isolated outer membrane of bacteria was analyzed in detail by the correlation averaging method using a computer-assisted program. The results showed that the porin of C. jejuni had a trimeric structure separated by about 10.4±0.15 nm. In addition, the pores in the trimers were also separated by about 4.3 ±0.1 nm.     

Characterization of porins from the outer membrane of Salmonella typhimurium. 2. Physical properties of the functional oligomeric aggregates.

We have purified to homogeneity, from mutant strains of Salmonella typhimurium, the small oligomers of porin that confer permeability channels to artificial vesicle membranes reconstituted from phospholipids and lipopolysaccharide. The molecular weights of the porin oligomers from the strains SH5551 and SH6017 appeared to be 130000 and 125000, respectively, and those of the monomers were 41000 and 37500, respectively, when determined by sedimentation equilibrium in the presence of dodecylsulfate. It was thus concluded that the functional porin oligomers consisted of three identical subunits. The Stokes' radius of the trimer . dodecylsulfate complex was around 5 nm. The trimer bound less dodecylsulfate than the monomer. The trimer . dodecylsulfate complex retained at room temperature the native conformation of porin, which is rich in beta-structure. When the trimers were dissociated further by various treatments, only the porin monomers were recovered in significant amounts, and the permeability-conferring activity was lost simultaneously. We propose, therefore, that the trimer is the minimal functional unit of porin that is capable of forming permeability channels in the outer membrane of Salmonella typhimurium.     

The Binding Protein Associates with Monomeric Phaseolin

The association of the binding protein (BiP) with newly synthesized proteins in the endoplasmic reticulum (ER) of developing bean (Phaseolus vulgaris) cotyledonary cells was investigated. ATP-sensitive association with many polypeptides was detected. The fraction of newly synthesized polypeptides associated with BiP varies among different proteins. The relationship between subunit assembly and binding to BiP was investigated in the case of the vacuolar trimeric glycoprotein phaseolin. In spite of the presence of a significant pool of phaseolin trimers in the ER, only monomeric phaseolin is found in association with BiP. On the whole, our results point to a general role of BiP in the synthesis of plant secretory proteins and indicate that, in the case of phaseolin, BiP binding sites are concealed during structural maturation in the ER, either before or upon formation of trimers. Our results also indicate that trimerization does not constitute a rate-limiting step in the transport of phaseolin to the protein storage vacuoles.     

Reproducible acquisition of Escherichia coli porin surface topographs by atomic force microscopy.

Crystalline membranes reconstituted from Escherichia coli OmpF porin and phospholipids were adsorbed to freshly cleaved mica and imaged in solution by the atomic force microscope. The extracellular as well as the periplasmic side of the porin trimers could be identified and the conditions to record topographs at 1-nm lateral and 0.1-nm vertical resolution were established.     

Properties of chemically modified porin from Escherichia coli in lipid bilayer membranes

Purified porin OmpF from Escherichia coli outer membrane was chemically modified by acetylation and succinylation of amino groups and by amidation of the carboxyl groups. Native and chemically modified porins were incorporated into lipid bilayer membranes and the permeability properties of the pores were studied. Acetylation and succinylation of the porin trimers had almost no influence on the single channel conductance in the presence of small cations and anions and the cation selectivity remained essentially unchanged as compared with the native porin. Amidation had also only little influence on the single channel conductance and changed the pore conductance at maximum by less than 50%, whereas the cation selectivity of the porin is completely lost after amidation. The results suggest that the structure of the porin pore remains essentially unchanged after chemical modification of the pores and that their cation selectivity is caused by an excess of negatively charged groups inside the pore and/or on the surface of the protein. Furthermore, it seems very unlikely that the pore contains any positively charged group at neutral pH.     

Homology models of the Yersinia pseudotuberculosis and Yersinia pestis general porins and comparative analysis of their functional and antigenic regions

The amino acid sequences of the Yersinia pseudotuberculosis porin (YPS) and Y. pestis porin (YPT) have recently deduced but their three-dimensional structures were not known. These sequences were analyzed using the servers 3D-PSSM and PredPort. The YPS and YPT porins were shown to have a high degree of identity (above 50%) in primary and secondary structures. The three-dimensional models of the Yersinia pseudotuberculosis porin (YPS) and Y. pestis porin (YPT) were obtained using the homology modeling approach, SWISS-MODEL Protein Modeling Server and 3-D structure of PhoE porin from E. coli as template. The superposition of the Calpha-atoms of the monomers of the Yersinia porins and PhoE porin gave a root mean square deviations of 0.47 A and 0.43 A for YPS and YPT respectively. Yersinia porins were found to be very similar in their three-dimensional structure to other non-specific enterobacterial porins, having the same features of overall fold and disposition of loop L3. The intrinsic structures of the monomer pores of YPS and YPT were investigated and their conductances were predicted with the program HOLE. The good correspondence between the theoretical and experimental magnitudes of YPS conductance was found. The Yersinia porins were determined to be unusual in containing the substitution, Glu replaced by Val, in a highly conserved pentapeptide (Pro-Glu-Phe-Gly-Gly-Asp), located in the loop L3 tip that disturbs the functionally important cluster of the acidic amino acids in the constriction site. Comparative analysis of structural organization of YPS and E. coli OmpF porin in the regions involved in subunit association and pore lumen was performed. The YPS porin functional properties were predicted. The differences between these porins in polar interactions playing a significant role in stabilization of the porin trimers were found and discussed in term of the variations in trimer stability. The Yersinia porins were shown to have the highest degree of the structural similarity. The differences between the porins were observed in their external loops. Their loops L6 and loops L8 showed 71.4 and 52.9% of sequence identity, respectively. The arrangement of charged residues clustered in the channel external vestibule of these porins was found to be also different suggesting the possible differences in their functional properties. The surface exposed regions of Yersinia porins involved in their potential sequential antigenic determinants were compared. The structural basis of their cross reactivity and antigenic differences is discussed.     

High-resolution electron diffraction of reconstituted PhoE porin

PhoE porin has been reconstituted with phospholipid, forming large membrane patches. Electron diffraction shows that the reconstituted PhoE porin forms highly coherent crystalline arrays, giving structural information to a resolution of 3.4 A. The crystal form is of the orthorhombic space group P2(1)2(1)2, with unit cell dimensions a = 150 A and b = 129 A. Images of negatively stained PhoE crystalline patches show that there are four PhoE porin trimers in a unit cell.     

Accessibility of lysyl residues of Escherichia coli B/r porin (OmpF) to covalent labeling reagents of different sizes. An approach for a three-dimensional structure of a channel-forming protein

The three-dimensional structure of Escherichia coli B/r porin (OmpF) was studied by chemical modification using activated sugars of different size. Galactose and galactosides of different penetration properties through the porin channel were oxidized by galactose oxidase, and the 6-aldehydes formed were linked to amino groups in porin by reduction with NaBH3CN. Tryptic fragments of modified and unmodified porin were separated by reversed-phase high pressure liquid chromatography and identified by amino acid and amino-terminal analysis from the known primary structure of OmpF. Modification of purified native porin trimers in beta-octylglucoside revealed three classes of amino groups: (i) those not modified by any sugars; (ii) those modified only by small sugars that diffuse rapidly through the pore, such as galactose or melibiose; and (iii) those modified by either small or large sugars, the latter including pore-impermeant sugars such as stachyose. The results suggest that the three classes of amino groups correspond, respectively, to groups buried in the trimeric molecule, those in the interior of the pore and those exposed on the surface of porin. In addition modification experiments performed on whole cells suggested that all the reactive groups modified by the pore-impermeant sugars (class iii) are located on the surface of porin exposed on the outside of the outer membrane.