Chemical modification of matrix porin from Escherichia coli: probing the pore topology of a transmembrane protein

Workflow for Validating Specific Amino Acid Footprinting Reagents for Protein Higher Order Structure Elucidation

Protein footprinting mass spectrometry probes protein higher order structure and dynamics by labeling amino acid side-chains or backbone amides as a function of solvent accessibility. One category of footprinting uses residue-specific, irreversible covalent modifications, affording flexibility of sample processing for bottom-up analysis. Although several specific amino acid footprinting technologies are becoming established in structural proteomics, there remains a need to assess fundamental properties of new reagents before their application. Often, footprinting reagents are applied to complex or novel protein systems soon after their discovery and sometimes without a thorough investigation of potential downsides of the reagent. In this work, we assemble and test a validation workflow that utilizes cyclic peptides and a model protein to characterize benzoyl fluoride, a recently published, next-generation nucleophile footprinter. The workflow includes the characterization of potential side-chain reactive groups, reaction "quench" efficacies, reagent considerations and caveats (e.g., buffer pH), residue-specific kinetics compared to those of established reagents, and protein-wide characterization of modification sites with considerations for proteolysis. The proposed workflow serves as a starting point for improved footprinting reagent discovery, validation, and introduction, the aspects of which we recommend before applying to unknown protein systems.

Chemical modification of the bacterial porin OmpF: gain of selectivity by volume reduction

OmpF is an essentially nonselective porin isolated from the outer membrane of Escherichia coli. Here we report on the manipulation of the ion selectivity of OmpF by chemical modification with MTS reagents (MTSET, MTSEA, and MTSES) and the (rather bulky) tripeptide glutathione, all cysteine specific. When recorded in a gradient of 0.1//1 M CaCl2 or 0.1//1 M NaCl, pH 7.4 solutions, measured reversal potentials of the most cation-selective modified mutants were (virtually) identical to the Nernst potential of Ca2+ or Na+. Compared to this full cation selectivity, the anion-selective modified mutants performed somewhat less but nevertheless showed high anion selectivity. We conclude that a low permanent charge in combination with a narrow pore can render the same selectivity as a highly charged but wider pore. These results favor the view that both the electrostatic potential arising form the fixed charge in the pore and the space available at the selectivity filter contribute to the charge selection (i.e., cation versus anion selectivity) of a biological ion channel.

Conformational epitope mapping of OmpC, a major cell surface antigen from Salmonella typhi

The outer membrane protein OmpC, a trimer made of 16 stranded beta-barrel monomers, is a major cell surface antigen from the human pathogen Salmonella typhi. The relative stability of the epitopes recognising a Salmonella specific MAb (referred as MPN5) and an Enterobacteria specific MAb (referred as P7D8) and the role of the trimeric organisation has been probed using gel electrophoresis and monoclonal antibodies. The assembly of the trimer and the stability of the beta-barrel are found to be important for epitope presentation. The Salmonella specific conformational epitope is found to be more stable than the Enterobacteria specific one. The important residues of the Salmonella specific (Asp 25 of loop 1, Asp 340 of loop 8, Lys 334 of loop 8, and Tyr 210 of loop 5) and the Enterobacteria specific (Asp 25 of loop 1, Tyr 210 of loop 5, and Lys 152 of loop 4) conformational epitope have been identified using monoclonal antibodies, chemical modification, and solid phase binding methods.

Characterization of the structure, function, and conformational stability of PorB class 3 protein from Neisseria meningitidis. A porin with unusual physicochemical properties

PorB proteins constitute the vast majority of channels in neisserial outer membranes and can be subdivided within meningococcal strains into two distinct and mutually exclusive families that are designated as class 2 and class 3 proteins. We recently characterized the functional activity and conformational stability of a PorB class 2 protein from Neisseria meningitidis (Minetti, C. A. S. A., Tai, J. Y., Blake, M. S., Pullen, J. K., Liang, S. M., and Remeta, D. P. (1997) J. Biol. Chem. 272, 10710-10720). To evaluate the structure-function relatedness among the PorB proteins, we have employed a combination of electrophoretic and spectroscopic techniques to assess the conformational stability of zwittergent-solubilized class 3 trimers. The functional, physicochemical, and structural properties of the meningococcal class 2 and class 3 proteins are comparable with the notable exception that the latter exhibits a significantly higher susceptibility to SDS. The SDS-induced dissociation and partial unfolding of PorB class 3 is characterized by a single two-state transition with a midpoint at 0.35% SDS. The native trimeric assembly dissociates reversibly, forming partially folded monomers that retain the characteristic beta-sheet content of the transmembrane domain with a concomitant increase in random coil structure arising from unfolding the rigid surface loops. These results provide new insight into the elucidation of porin folding pathways and the factors that govern the overall structural stability of meningococcal proteins.

Biophysics of the structure and function of porins

Gram-negative bacteria such asEscherichia coli(E. coli) andSalmonella typhimurium(S. typhimurium) have two layers of membranes in the cellular envelope – the cytoplasmic membrane and the outer membrane (Fig. I). Between these membranes is a periplasmic space in which there is a peptidoglycan layer that provides the cells with mechanical rigidity. In this periplasmic space, there are also a variety of hydrolases and binding proteins. The composition of the outer membrane is somewhat unusual. This membrane bilayer is asymmetric, having an inner (periplasmic) leaflet composed of phospholipids and an outer (extracellular) leaflet formed by lipopolysaccharide (LPS). Unlike phospholipids having two acyl chains, LPS has six or seven saturated fatty acid chains (see reviews, Lugtenberg & Van Alphen, 1983; Nikaido & Vaara, 1985; Nakae, 1986). The head groups of LPS have a strong affinity for divalent cations such as Ca2+, and given a sufficient concentration of these ions the outer membrane can form quite a formidable permeability barrier through this head group/salt bridge network (Nikaido & Vaara, 1985). The function of the outer membrane is to serve as a protective envelope against hostile environments such as those in the intestinal tract of animals where harmful and toxic substances - for example, bile salts and various enzymes - are often found. The outer membrane itself would be impermeable to most hydrophilic solutes were it not for the presence of membrane channels. The presence of a large number of pore-forming proteins provides both specific and nonspecific diffusion pathways across the outer membrane for solutes such as nutrients and waste products to diffuse into or out of the cell.

Immunological evidence for differences in the exposed regions of OmpF porins from Escherichia coli B and K-12

Nine monoclonal antibodies (MoF 0-8) directed against the native form (trimeric) of outer membrane protein OmpF of Escherichia coli B were obtained and characterized. All these antibodies bind to OmpF porin in intact E. coli B cells but not OmpF from E. coli K-12 cells which only differ at positions 66, 117 and 262 in the sequence. These antibodies exhibit a specificity to the native form, failing to recognize the denatured form in a liquid immunorecognition assay. Four tested antibodies are able to protect against colicin A, a bacteriotoxin using OmpF as receptor. One monoclonal antibody (MoF 0) is specific to the external topology of native porin in the outer membrane and three antibodies could recognize epitopes present in each conformation of subunits of trimer form. It is concluded that the region around the 66th and more probably around the 262nd amino acids are involved in cell-surface exposed epitopes. Moreover, these results support the assumption that the conformation of protruding regions of OmpF from E. coli B and K-12 are different.

Effect of lipid fluidity upon the activity and structure of the 39 kDa porin from Enterobacter cloacae 908S

The 39 kDa porin from Enterobacter cloacae 908S was isolated in a lipopolysaccharide-free form using the non-ionic detergent, octylpentaoxyethylene, and reconstituted into vesicles of dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC), respectively. Porin activity, measured by the rate of hydrolysis of the lipid-impermeant beta-lactam cephazoline by entrapped lactamase, could be demonstrated for porin-DMPC but not for porin-DOPC vesicles, and for the former was significantly lower in the gel than in the liquid-crystalline phase. The fluorescence changes are thought to arise from lipid phase-induced structural/dynamic changes of the porin structure.

Role of lysines in ion selectivity of bacterial outer membrane porins

The epsilon-amino groups of available lysine residues of the OmpC, OmpF and PhoE porin proteins of Escherichia coli and of the protein P porin of Pseudomonas aeruginosa, were modified by the bulky reagent trinitrobenzenesulphonic acid. Approximately 78% of the lysines of the anion-selective protein P and PhoE porins were modified whereas only 40-50% of the lysines of the cation selective OmpF and OmpC porins were altered. After modification, the three E. coli porins had very similar high selectivities for cations over anions, in contrast to the native porins which varied 86-fold in ion selectivity. Despite the large size of the trinitrophenyl group attached to modified lysines (i.e., a disc of approx. 0.86 nm diameter X 0.36 nm high) relative to the reported size of the constrictions of the E. coli porins (1.0-1.2 nm diameter), only the anion-selective PhoE porin was substantially blocked after trinitrophenylation. The protein P porin channel was relatively unaffected by trinitrophenylation, in contrast to previous data showing dramatic effects of acetylation of lysines on protein P conductance and selectivity. This favoured a model in which the critical lysines involved in anion binding by protein P were present in a constriction of the channel that was too small for trinitrobenzenesulphonic acid to enter. Overall, the data suggest that both the number and relative position of charged lysines are major determinants of ion selectivity.

Topographic labelling of pore-forming proteins from the outer membrane of Escherichia coli

The topography of three pore-forming proteins from the outer membrane of Escherichia coli has been explored by using two labelling techniques. Firstly, the distribution of nucleophilic residues has been investigated by selective chemical modification using arylglyoxals (for arginine residues), isothiocyanates (for lysine residues), carbodi-imides (for carboxy residues) and diazonium salts. Secondly, the membrane-embedded domains have been investigated by labelling with photoactivatable phospholipid analogues and a reagent that partitions into the membrane. Few nucleophilic groups are found to be freely accessible to pore-impermeant probes reacting in the aqueous medium. More groups are accessible to small, pore-permeant probes, suggesting that several groups of each sort are contained within the pore. In addition, there appear to be a number of arginine, lysine, carboxyl and many tyrosine residues that are rather inaccessible and that react only with small, hydrophobic probes, if at all. Amongst these more deeply buried residues there are four arginine residues and an as-yet-undetermined number of carboxy residues that appear to be essential to the structural integrity of the oligomeric molecule.

Native and chemically modified porin channels from Salmonella typhi Ty2 in planar lipid bilayers

Native porins, from Salmonella typhi Ty2 outer membrane, and porins alkylated with pyridoxal phosphate (Plp) were studied in planar lipid bilayers. The conductance of bilayers exposed to native or chemically modified porins increases in discrete jumps. Conductance histograms for native porins displayed two major peaks at 1.7 and 6.7 nS (in 0.5 M KCl). On the other hand, Plp-treated porins exhibited a single major peak at 1 nS. The relation between bilayer conductance and native porin concentration was linear. However, this relation became logarithmic in the presence of modified porins. The results support the notion that alkaline reduction of S. typhi Ty2 porins with Plp dissociates porin channel trimers in a reversible fashion.

Outer-membrane permeability of bacteria

Gram-negative bacteria evolved to survive under the conditions in which a number of hazardous compounds are abundant. The outer membrane which protects the cell interior acts as a barrier against such hazardous agents, yet the cells must incorporate the chemicals that are essential for the cellular activity. The devices that Gram-negative bacteria developed to incorporate such essence are the transmembrane pores. These pores could be subdivided into three categories: (1) pore made of porins has a weak solute selectivity; (2) pore made of lamB protein and tsx proteins hold intermediate solute specificity. and (3) pores for the diffusion of vitamin B12 and ferric ion-chelator complexes have a tight solute specificity. Porins are identified from a number of Gram-negatives and from the outer membrane of mitochondria of various sources. Studies on the diffusion properties of these outer-membrane proteins provided essential information to understand membrane transports.

The mechanism of ion selectivity of OmpF-porin pores of Escherichia coli

The OmpF porin from the outer membrane of Escherichia coli acts as a lightly cation-selective pore, allowing the diffusion of small cations and cationic molecules, whose Mr are a little larger than the threshold exclusion limit. To ascertain the mechanism of this cation selectivity, we have examined a possible influence of cationic solutes on the fluorescence emission and the circular dichroic spectrum of tryptophan residues of the porin trimer, searching for conformational change(s). The diffusion of cationic solutes was determined with the native and the amidated porins in the presence or the absence of the effector cations. The following results were obtained. (a) Cations, e.g. spermidine, caused fluorescence quenching in the native trimer, with a half-maximum fluorescence quenching at 11-18 microM. A change in the circular dichroic spectrum was also recorded at around 280 nm. (b) The dissociation constant of spermidine to the native trimer was calculated to be 16 microM as determined by the method of equilibrium dialysis. (c) The cation-caused fluorescence quenching was reversed when the carboxyl groups of the trimer were modified by the amidation reaction, though amidation of the trimer resulted in no significant change in the fluorescence intensity. (d) The diffusion rate of N-benzyloxycarbonyl-glycyl-L-prolyl-L-arginine p-nitroanilide through the native and the amidated porins was lowered in the presence and the absence, respectively, of cations. Both the extent of fluorescence quenching in the presence of cation and the rate of cation diffusion were inversely proportional to the number of amidated carboxyl residues. The relative fluorescence quenching of the porin trimer (the amidated versus the native) in the presence of cations was linearly related to the relative solute diffusion via the porin (the amidated versus the native). These results suggested that cations caused a conformational change in the trimer, resulting in an easier diffusion of the solutes. The results suggested further that a limited number of carboxyl groups in the pore interior are involved in the cation selectivity of OmpF-porin pores.

Demonstration of a bacteriophage receptor site on the Escherichia coli K12 outer-membrane protein OmpC by the use of a protease

The Escherichia coli K12 outer-membrane proteins OmpA, OmpC, OmpF, PhoE, and LamB (all of transmembrane nature) can serve as phage receptors. We have shown previously that one OmpA-specific phage, Ox2, can give rise to the host range mutants Ox2h10 and Ox2h12, with the latter being derived from the former [Morona, R. & Henning, U. (1984) J. Bacteriol. 159, 579-582]. Unlike Ox2, both host range phages can use the OmpA and OmpC proteins as receptors and Ox2h12 is better adapted to the OmpC protein than Ox2h10. In a search for the site(s) of OmpC protein involved in phage recognition, it was found that proteinase K is able to cleave all of the proteins mentioned above. OmpC protein (Mr = 38306) could be cleaved from outside the cell by proteinase K resulting in two fragments of Mr approximately equal to 21000 and Mr approximately equal to 17500. The use of OmpC-PhoE hybrid proteins allowed us to assign the approximately equal to 21000-Mr fragment to the CO2H-terminal moiety of the protein. Proteinase K treatment of intact cells abolished their activity to neutralize the OmpC-specific phage Tulb and reduced this ability towards phage Ox2h12. The OmpA, OmpF, PhoE and LamB proteins were cleaved by the protease not in intact cells but only when acting on cell envelopes. The sizes of the OmpC protein fragments and the results obtained with the hybrid proteins very strongly suggest that the protein is cleaved from outside the cell at a region involving amino acid residues 150-178 of the 346-residue protein, which shows homology to two regions of the OmpA protein which are involved in its phage receptor site (loc. cit.). These areas also exhibit some homology to a region of the LamB protein which is thought to be part of this protein's receptor site [Charbit et al. (1984) J. Mol. Biol. 175, 395-401]. This suggests that there is a common denominator for proteinaceous phage receptor site because the LamB-specific phage lambda and phage Tulb are of completely different nature. We conclude that the region of the OmpC protein in question is cell-surface-exposed and acts as a phage receptor site.

Lateral diffusion in nuclear membranes

Chemical modification of rat liver nuclei with citraconic anhydride selectively removed outer nuclear membrane. This conclusion was based on (a) transmission electron microscopy, (b) lipid analysis, (c) lamin B as an inner membrane-associated marker, and (d) the demonstration of phospholipid lateral mobility on outer membrane-depleted nuclei as a criteria for inner membrane integrity. Addition of urea or N-ethylmaleimide resulted in the additional disruption of inner membrane. Fluorescence photobleaching was used to determine the long range (greater than 4 microns) lateral transport of lectin receptors and a phospholipid analog in both membranes. The diffusion coefficient for wheat germ agglutinin on whole nuclei was 3.9 X 10(-10) cm2/s whereas the diffusion coefficient for wheat germ agglutinin in outer membrane-depleted nuclei was less than or equal to 10(-12) cm2/s. Phospholipid mobilities were the same in whole and outer membrane-depleted nuclei (3.8 X 10(-9) cm2/s). The protein diffusion differences observed between whole and outer membrane-depleted nuclei may be interpreted in the context of two functionally different membrane systems that compose the double bilayer of the nucleus.

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.

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.