Trigonal crystals of porin from Escherichia coli

Deducing the symmetry of helical assemblies: Applications to membrane proteins

Helical reconstruction represents a convenient and powerful approach for structure determination of macromolecules that assemble into helical arrays. In the case of membrane proteins, formation of tubular crystals with helical symmetry represents an attractive alternative, especially when their small size precludes the use of single-particle analysis. An essential first step for helical reconstruction is to characterize the helical symmetry. This process is often daunting, due to the complexity of helical diffraction and to the low signal-to-noise ratio in images of individual assemblies. Furthermore, the large diameters of the tubular crystals produced by membrane proteins exacerbates the innate ambiguities that, if not resolved, will produce incorrect structures. In this report, we describe a set of tools that can be used to eliminate ambiguities and to validate the choice of symmetry. The first approach increases the signal-to-noise ratio along layer lines by incoherently summing data from multiple helical assemblies, thus producing several candidate indexing schemes. The second approach compares the layer lines from images with those from synthetic models built with the various candidate schemes. The third approach uses unit cell dimensions measured from collapsed tubes to distinguish between these candidate schemes. These approaches are illustrated with tubular crystals from a boron transporter from yeast, Bor1p, and a β-barrel channel from the outer membrane of E. coli, OmpF.

Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity

Electrophysiological characterization of large protein channels, usually displaying multi-ionic transport and weak ion selectivity, is commonly performed at physiological conditions (moderate gradients of KCl solutions at decimolar concentrations buffered at neutral pH). We extend here the characterization of the OmpF porin, a wide channel of the outer membrane of E. coli, by studying the effect of salts of divalent cations on the transport properties of the channel. The regulation of divalent cations concentration is essential in cell metabolism and understanding their effects is of key importance, not only in the channels specifically designed to control their passage but also in other multiionic channels. In particular, in porin channels like OmpF, divalent cations modulate the efficiency of molecules having antimicrobial activity. Taking advantage of the fact that the OmpF channel atomic structure has been resolved both in water and in MgCl₂ aqueous solutions, we analyze the single channel conductance and the channel selectivity inversion aiming to separate the role of the electrolyte itself, and the counterion accumulation induced by the protein channel charges and other factors (binding, steric effects, etc.) that being of minor importance in salts of monovalent cations become crucial in the case of divalent cations.

Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction

The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow "constriction zone". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets were obtained at 2.6 A and 3.0 A resolution with K(+) and Rb(+), respectively. The Rb(+)-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 A and cation positions were determined. A PEG molecule was observed in the pore region for both the K(+) and Rb(+)-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.

Three-dimensional crystallization of membrane proteins

Although the examination of the protein data bank reveals an important backlog in the number of three-dimensional structures of membrane proteins, several recent successes are serving as preludes to what will become a very prosperous decade in this field. Systematic investigations of various factors affecting the stability of membrane proteins, as well as their potential to crystallize three dimensionally, have paved the way for such achievements. The importance of the role of detergents both at the level of purification and crystallization is now well established. In addition, the recognition of the protein-detergent complex as the entity to crystallize, as well as the understanding of its physical-chemical properties and discovery of factors affecting these, have permitted the design of better crystallization strategies. As a consequence of the various efforts in the field, new crystallization methods for membrane proteins are being implemented. These have already been successful and are expected to contribute significantly to the future successes. This chapter will review some basic principles in membrane protein crystallization and give an overview of the current state of the art in the field. Some practical guidelines to help the novice approach the problem of membrane protein crystallization from the initial step of protein purification to crystallogenesis will also be given.

The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF

Several groups, including our own, have found molecular dynamics (MD) calculations to result in the size of the pore of an outer membrane bacterial porin, OmpF, to be reduced relative to its size in the x-ray crystal structure. At the narrowest portion of its pore, loop L3 was found to move toward the opposite face of the pore, resulting in decreasing the cross-section area by a factor of approximately 2. In an earlier work, we computed the protonation states of titratable residues for this system and obtained values different from those that had been used in previous MD simulations. Here, we show that MD simulations carried out with these recently computed protonation states accurately reproduce the cross-sectional area profile of the channel lumen in agreement with the x-ray structure. Our calculations include the investigation of the effect of assigning different protonation states to the one residue, D(127), whose protonation state could not be modeled in our earlier calculation. We found that both assumptions of charge states for D(127) reproduced the lumen size profile of the x-ray structure. We also found that the charged state of D(127) had a higher degree of hydration and it induced greater mobility of polar side chains in its vicinity, indicating that the apparent polarizability of the D(127) microenvironment is a function of the D(127) protonation state.

Direct proteolysis-based purification of an overexpressed hyperthermophile protein from Escherichia coli lysate: a novel exploitation of the link between structural stability and proteolytic resistance

The susceptibility of a peptide bond to cleavage by a protease is determined by: (a) the flexibility of the protein chain region in which it is located, (b) the extent to which the bond is exposed, and (c) the nature of the local interactions made by the sidechains of its flanking residues. Each of these parameters is known to be influenced by the overall structural stability of the protein; thus, proteins of higher structurally stability commonly show higher resistance to proteolysis. Extrapolating this relationship to 'ultrastable' proteins, our intention here was to investigate whether a hyperthermophile protein expressed and folded within Escherichia coli could prove to be so resistant to proteolysis as to allow direct purification from complex mixtures of E. coli cytoplasmic and/or membrane proteins, through proteolytic means. Thus, we cloned the gene encoding the triosephosphate isomerase enzyme of Pyrococcus furiosus (PfuTIM) and overexpressed it in E. coli in fusion with glutathione S-transferase (GST). The GST-PfuTIM fusion product partitioned mainly into the insoluble fraction of the whole cell lysate. Upon exposure of the E. coli cell lysate precipitate fractions to the non-specific protease, subtilisin, all polypeptides barring PfuTIM (including the GST affinity tag cloned in fusion with PfuTIM) were found to be degraded to undetectable levels. Trace residual amounts of an E. coli protein, OmpF, survived proteolytic digestion, together with an extremely pure population of PfuTIM. Either autonomously or in combination with the more conventional method of heating solutions to enrich heat-stable proteins through the thermal unfolding and aggregation of all other proteins, such proteolysis-based purification could prove to be useful.

The expression of outer membrane proteins for crystallization

The production of sufficient amounts of chemically and conformationally homogenous protein is a major requirement for successful crystallization and structure determination. With membrane proteins, this constitutes a particular problem because the membrane volume is limited and the organisms are usually very sensitive to changes in membrane properties brought about by massive protein insertion. Moreover, the extraction of membrane proteins from the membrane with detergents is generally a harsh treatment, which gives rise to conformational aberrations. A number of successful procedures for functional expression followed by purification are reviewed here together with nonfunctional expression into inclusion bodies and subsequent (re)folding to produce functional proteins. Most of the data are for prokaryotic outer membrane proteins, but the outer membrane proteins of eukaryotic organelles are also considered as they do show similar features.

Role of Charged Residues at the OmpF Porin Channel Constriction Probed by Mutagenesis and Simulation†,‡

The channel constriction of OmpF porin, a pore protein in the bacterial outer membrane, is highly charged due to the presence of three arginines (R42, R82, and R132) and two acidic residues (D113 and E117). The influence of these charges on ion conductance, ion selectivity, and voltage gating has been studied with mutants D113N/E117Q, R42A/R82A/R132A/D113N/E117Q, and V18K/G131K, which were designed to remove or add protein charge at the channel constriction. The crystal structures revealed no or only local changes compared to wild-type OmpF, thus allowing a comparative study. The single-channel conductance of the isosteric D113N/E117Q variant was found to be 2-fold reduced, and that of the pentuple mutant was 70% of the wild-type value, despite a considerably larger pore cross section. Ion selectivity was drastically altered by the mutations with cation/anion permeability ratios ranging from 1 to 12. Ion flow through these and eight other mutants, which have been characterized previously, was simulated by Brownian dynamics based on the detailed crystal structures. The calculated ion selectivity and relative channel conductance values agree well with the experimental data. This demonstrates that ion translocation through porin is mainly governed by pore geometry and charge, the two factors that are properly represented in the simulations.

Approaches to determining membrane protein structures to high resolution: do selections of subpopulations occur?

Three different methods are currently used for the study of high-resolution structures of membrane proteins: X-ray crystallography, electron crystallography, and nuclear magnetic resonance (NMR) spectroscopy. Thus far, all methods combined have yielded a rather modest number of crystal structures that have been solved at the atomic level. It is hypothesized here that different methods may select different populations of proteins on the basis of various properties. Thus, protein stability may be a significant factor in the formation of three-dimensional (3D) crystals from detergent solutions, since exposure of hydrophobic protein zones to water may cause structural perturbation or denaturation in conformationally labile proteins. This is different in the formation of two-dimensional (2D) crystals where a protein remains protected in its native membrane environment. A biological selection mechanism may therefore be operative in that highly ordered lattices may form only if strong protein-protein interactions are relevant in vivo, thereby limiting the number of proteins that are amenable to electron crystallography. Keeping a protein in a bilayer environment throughout 3D crystallization maintains the lateral pressure existing in native membranes. This can be accomplished by using lipidic cubic phases. Alternatively, the hydrophobic interface of a membrane protein may be spared from contact with water by crystallization from organic solvents where the polar caps are protected in reverse micelles by using appropriate detergents. Some of the criteria that are useful in optimizing the various approaches are given. While the usefulness of complementary methods seems obvious, the results presented may be particularly critical in recognizing key problems in other structural approaches.

Static light scattering studies of OmpF porin: implications for integral membrane protein crystallization

Integral membrane proteins carry out some of the most important functions of living cells, yet relatively few details are known about their structures. This is due, in large part, to the difficulties associated with preparing membrane protein crystals suitable for X-ray diffraction analysis. Mechanistic studies of membrane protein crystallization may provide insights that will aid in determining future membrane protein structures. Accordingly, the solution behavior of the bacterial outer membrane protein OmpF porin was studied by static light scattering under conditions favorable for crystal growth. The second osmotic virial coefficient (B22) was found to be a predictor of the crystallization behavior of porin, as has previously been found for soluble proteins. Both tetragonal and trigonal porin crystals were found to form only within a narrow window of B22 values located at approximately -0.5 to -2 X 10(-4) mol mL g(-2), which is similar to the "crystallization slot" observed for soluble proteins. The B22 behavior of protein-free detergent micelles proved very similar to that of porin-detergent complexes, suggesting that the detergent's contribution dominates the behavior of protein-detergent complexes under crystallizing conditions. This observation implies that, for any given detergent, it may be possible to construct membrane protein crystallization screens of general utility by manipulating the solution properties so as to drive detergent B22 values into the crystallization slot. Such screens would limit the screening effort to the detergent systems most likely to yield crystals, thereby minimizing protein requirements and improving productivity.

Stability of trimeric OmpF porin: the contributions of the latching loop L2

The channel-forming protein OmpF porin from Escherichia coli spans the bacterial outer membrane. Each of the three monomers comprises a hollow, 16-stranded beta-barrel. These are associated to homotrimers which are unusually stable, due mostly to hydrophobic interactions between the beta-barrels. In addition, a loop, L2 connects one subunit to its neighbor by latching into its channel. Residue E71 on loop 2 is integrated into an ionic network and forms salt bridges and hydrogen bonds with R100 and R132 on the channel wall in the adjacent subunit. To examine these contributions quantitatively, six single-site, two double, and one deletion mutant were constructed on the basis of the atomic coordinates of the protein. Differential scanning calorimetric analysis showed that the salt-bridge, E71-R100, contributes significantly to trimer stability: the substitution E71Q causes a decrease of the transition temperature from 72 to 48 degreesC, with DeltaHcal diminishing from 430 to 201 kcal mol-1. A nearby substitution in the loop, D74N, has lesser effects on thermal stability, while the deletion in L2 (Delta69-77) has an effect comparable to that of E71Q. X-ray structure analysis to 3.0 A resolution revealed only local structural differences in the mutants except for the substitution R100A, where another residue, R132, is found to fill the gap left by the truncated side chain of A100. Functional assays in planar lipid bilayers show significantly increased cation selectivities if the charge distribution was affected.

Hydrophobic free energy eigenfunctions of pore, channel, and transporter proteins contain beta-burst patterns

Hydropathy plots are often used in place of missing physical data to model transmembrane proteins that are difficult to crystallize. The sequential maxima of their graphs approximate the number and locations of transmembrane segments, but potentially useful additional information about sequential hydrophobic variation is lost in this smoothing procedure. To explore a broader range of hydrophobic variations without loss of the transmembrane segment-relevant sequential maxima, we utilize a sequence of linear decompositions and transformations of the n-length hydrophobic free energy sequences, Hi, i = 1...n, of proteins. Constructions of hydrophobic free energy eigenfunctions, psil, from M-lagged, M x M autocovariance matrices, CM, were followed by their all-poles, maximum entropy power spectral, Somega(psil), and Mexican Hat wavelet, Wa,b(psil), transformations. These procedures yielded graphs indicative of inverse frequencies, omega-1, and sequence locations of hydrophobic modes suggestive of secondary and supersecondary protein structures. The graphs of these computations discriminated between Greek Key, Jelly Role, and Up and Down categories of antiparallel beta-barrel proteins. With these methods, examples of porins, connexins, hexose transporters, nuclear membrane proteins, and potassium but not sodium channels appear to belong to the Up and Down antiparallel beta-barrel variety.

Mode matches in hydrophobic free energy eigenfunctions predict peptide-protein interactions

The dominant statistical hydrophobic free energy inverse frequencies amino acid wavelengths as hydrophobic modes, of neurotensin (NT), cholescystokinin (CCK), the human dopamine D2 receptor [(DA)D2], and the human dopamine transporter (DAT) were determined using orthogonal decomposition of the autocovariance matrices of their amino acid sequences as hydrophobic free energy equivalents in kcal/mol. The leading eigenvalues-associated eigenvectors were convolved with the original series to construct eigenfunctions. Eigenfunctions were further analyzed using discrete trigonometric wavelet and all poles, maximum entropy power spectral transformations. This yielded clean representations of the dominant hydrophobic free energy modes, most of which are otherwise lost in the smoothing of hydropathy plots or contaminated by end effects and multimodality in conventional Fourier transformations. Mode matches were found between NT and (DA)D2 and between CCK and DAT, but not the converse. These mode matches successfully predicted the nonlinear kinetic interactions of NT-(DA)D2 in contrast with CCK-(DA) D2 on 3H-spiperone binding to (DA) D2, and by CCK-DAT but not NT-DAT on [N-methyl-3H]-WIN 35,428 binding to DAT in (DA)D2 and DAT cDNA stably transfected cell lines without known NT or CCK receptors. Computation of the dominant modes of hydrophobic free energy eigenfunctions may help predict functionally relevant peptide-membrane protein interactions, even across neurotransmitter families.

Coupling site-directed mutagenesis with high-level expression: large scale production of mutant porins from E. coli

Combination of an origin repair mutagenesis system with a new mutS host strain increased the efficiency of mutagenesis from 46% to 75% mutant clones. Overexpression with the T7 expression system afforded large quantities of proteins from mutant strains. A series of E. coli BE host strains devoid of major outer membrane proteins was constructed, facilitating the purification of mutant porins to homogeneity. This allowed preparation of 149 porin mutants in E. coli used in detailed explorations of the structure and function of this membrane protein to high resolution.

Detergent binding in trigonal crystals of OmpF porin from Escherichia coli

The structure of the detergent, ocytyl hydroxyethylsufoxide (C8(HE)SO), bound to the OmpF porin from E coli (in the trigonal crystal form) has been determined by neutron crystallography. Due to a dynamic exchange of detergent molecules with their environment they are not ordered on an atomic scale. The structure reported here is therefore at a resolution of approximately 16 A. The X-ray crystallographically determined structure of the protein provides a starting point for the neutron analysis in which the detergent is visualized primarily thanks to its high contrast against D2O. The structure shows the detergent to be located mainly in two areas. It forms toroidal annuli around each OmpF trimer, these annuli fusing to form a detergent belt surrounding a solvent filled column traversing the crystal. Those areas of the protein to which the detergent binds are formed almost exclusively of hydrophobic residues and form a band about 30 A high around the trimer. Its upper and lower bounds are defined by two bands of aromatic residues, tyrosines pointing away from the detergent belt and interacting with the polar headgroups while phenylalanines point inwards. This strongly suggests that the same areas define, in vivo, the location at which protein interacts with lipid. The hydrophobic moiety of detergent is also found mediating the hydrophobic protein-protein interactions at the interface between two trimers on the crystallographic two-fold axis.

Voltage gating of Escherichia coli porin channels: role of the constriction loop

In the homotrimeric OmpF porin from Escherichia coli, each channel is constricted by a loop protruding into the beta-barrel of the monomer about halfway through the membrane. The water-filled channels exist in open or closed states, depending on the transmembrane potential. For the transition between these conformations, two fundamentally different mechanisms may be envisaged: a bulk movement of the constriction loop L3 or a redistribution of charges in the channel lumen. To distinguish between these hypotheses, nine mutant proteins were constructed on the basis of the high-resolution x-ray structure of the wild-type protein. Functional changes were monitored by measuring single-channel conductance and critical voltage of channel closing. Structural alterations were determined by x-ray analysis to resolutions between 3.1 and 2.1 A. Tethering the tip of L3 to the barrel wall by a disulfide bridge (E117C/A333C), mobilizing L3 by perturbing its interaction with the barrel wall (D312N, S272A, E296L), or deleting residues at the tip of the loop (Delta116-120) did not alter appreciably the sensitivity of the channels to an external potential. A physical occlusion, due to a gross movement of L3, which would cause the channels to assume a closed conformation, can therefore be excluded.

Secondary structure of the outer membrane proteins OmpA of Escherichia coli and OprF of Pseudomonas aeruginosa

When purified without the use of ionic detergents, both OmpA and OprF proteins contained nearly 20% alpha-helical structures, which disappeared completely upon the addition of sodium dodecyl sulfate. This result suggests that the proteins fold in a similar manner, with an N-terminal, membrane-spanning beta-barrel domain and a C-terminal, globular, periplasmic domain.

The structure of OmpF porin in a tetragonal crystal form

BACKGROUND

OmpF porin is a trimeric integral membrane protein responsible for the passive transport of small hydrophilic molecules, such as nutrients and waste products, across the outer membrane of Escherichia coli. Very few membrane proteins have been crystallized in three dimensions, yet this stable protein can be obtained in several crystal forms. Comparison of the structures of the same membrane protein in two different packing environments is of major interest, because it allows us to explore the integrity of the structure outside the natural membrane environment.

RESULTS

The structure of OmpF porin in a tetragonal crystal form with two trimers per asymmetric unit has been determined at 3.2 A resolution and compared with that obtained previously in a trigonal crystal form. The lattice contacts involve only polar atoms, whereas extensive hydrophobic protein-protein interactions were found in the trigonal lattice. The trimer structure is virtually identical in both.

CONCLUSIONS

Our comparison reveals that the overall structure of OmpF is not influenced by crystal lattice constraints and, thus, presumably bears close resemblance to the in vivo structure. The tetragonal crystal structure has provided the starting model for the phasing of neutron diffraction data obtained from this crystal form, as described in an accompanying article.

Crystallization and preliminary X-ray analysis of outer membrane phospholipase A from Escherichia coli

The outer membrane phospholipase A (OMPLA) of Escherichia coli is one of the few integral outer membrane proteins displaying enzymatic activity. It is encoded as a mature protein of 269 amino acids preceded by a signal sequence of 20 amino acids. There is no sequence homology with water-soluble lipases and phospholipases. Crystals of the mature enzyme were obtained at 22 degrees C from 24-28% (v/v) 2-methyl-2,4-pentanediol in Bis-Tris buffer, pH 5.9-6.0, with 1 mM calcium chloride and 1.5% (w/v) beta-octylglucoside. They have the symmetry of the trigonal spacegroup P3(1)21 (or P3(2)21) with cell dimensions of a = b = 79.6 A and c = 102.8 A (alpha = beta = 90 degrees, gamma = 120 degrees). Native crystals diffract to a resolution of 2.6 A.

Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli

A strain of Escherichia coli, selected on the basis of its resistance to colicin N, reveals distinct structural and functional alterations in unspecific OmpF porin. A single mutation [Gly-119-->Asp (G119D)] was identified in the internal loop L3 that contributes critically to the formation of the construction inside the lumen of the pore. X-ray structure analysis to a resolution of 3.0 A reveals a locally altered peptide backbone, with the side chain of residue Asp-119 protruding into the channel, causing the area of the constriction (7 x 11 A in the wild type) to be subdivided into two intercommunicating subcompartments of 3-4 A in diameter. The functional consequences of this structural modification consist of a reduction of the channel conductance by about one-third, of altered ion selectivity and voltage gating, and of a decrease of permeation rates of various sugars by factors of 2-12. The structural modification of the mutant protein affects neither the beta-barrel structure nor those regions of the molecule that are exposed at the cell surface. Considering the colicin resistance of the mutant, it is inferred that in vivo, colicin N traverses the outer membrane through the porin channel or that the dynamics of the exposed loops are affected in the mutant such that these may impede the binding of the toxin.

Bacterial porins: structure and function

Within the class of integral membrane proteins, the bacterial porins display a remarkable resistance to denaturants and proteases. This stability is probably crucial for the formation of highly ordered, three-dimensional crystals. Structural analysis of these crystals has been possible in atomic detail. This analysis has revealed interesting features, such as the aromatic girdles, and has helped to explain several observations, including the porins' ability to discriminate between polar and non-polar solutes. Recent research has thus improved our understanding of the porins in a qualitative fashion.

A novel purification of ferric citrate receptor (FecA) from Escherichia coli UT5600 and further characterization of its binding activity

In our earlier paper, it was demonstrated that the FecA receptor protein from Escherichia coli UT5600/pBB2 (leu-, proC-, trpE-, entA-, rpsl-, delta (ompT-fepA)-/Ampr, fepA) binds with ferric enterobactin. In order to explore this further the outer membrane receptor protein, FecA, has been isolated from UT5600 (fepA-) and purified to homogeneity by DE-52-cellulose anion exchange chromatography followed by MonoPFPLC chromatofocusing. Partially purified FecA and homogeneous FecA show binding activity to [55Fe]ferric enterobactin and the binding is specific. Binding activity of FecA can be enhanced by ferric citrate. Lipopolysaccharide-free FecA as ascertained by silver staining and the endotoxin test still retains the same activity. In vivo uptake studies using different strains of E. coli suggest that FecA in E. coli plays an important role in ferrienterobactin transport.

Crystal structures explain functional properties of two E. coli porins

Porins form aqueous channels that aid the diffusion of small hydrophilic molecules across the outer membrane of Gram-negative bacteria. The crystal structures of matrix porin and phosphoporin both reveal trimers of identical subunits, each subunit consisting of a 16-stranded anti-parallel beta-barrel containing a pore. A long loop inside the barrel contributes to a constriction of the channel where the charge distribution affects ion selectivity. The structures explain at the molecular level functional characteristics and their alterations by known mutations.

Crystallization and preliminary X-ray analysis of phosphoporin from the outer membrane of Escherichia coli

Phosphoporin is a pore-forming transmembrane protein that spans the outer membrane of Escherichia coli and facilitates the diffusion of phosphates and phosphorylated compounds. Phosphoporin has been crystallized in several different crystal forms, although only one appears to be suitable for X-ray analysis. These crystals, which are hexagonal plates, diffract X-rays to 3 A resolution and belong to the space-group P6(3)22, with unit cell dimensions a = b = 121 A and c = 111 A.

Molecular architecture and electrostatic properties of a bacterial porin

The integral membrane protein porin from Rhodobacter capsulatus consists of three tightly associated 16-stranded beta barrels that give rise to three distinct diffusion channels for small solutes through the outer membrane. The x-ray structure of this porin has revealed details of its shape, the residue distributions within the pore and at the membrane-facing surface, and the location of calcium sites. The electrostatic potential has been calculated and related to function. Moreover, potential calculations were found to predict the Ca2+ sites.

A common channel-forming motif in evolutionarily distant porins

Four new crystal packings of Escherichia coli porins are presented (phosphoporin, maltoporin, and two crystal forms of matrix porin). These were determined by molecular replacement methods using a polyalanine trial model acquired from the refined coordinates of porin from Rhodobacter capsulatus. The successful molecular replacement shows that the dominant motif found in R. capsulatus porin (a 16-stranded antiparallel beta-barrel) also applies to the E. coli porins, despite the lack of significant amino acid sequence homology. A 30 degrees-40 degrees tilt of the beta-strands with respect to the membrane normal was derived from the intensity distributions in the X-ray diffraction patterns for each porin studied, stressing their similarity. In view of the evolutionary distance between enteric and photosynthetic bacteria, the antiparallel beta-barrel may have significance as a basic structural motif for the formation of bacterial membrane channel structures.