Eight-stranded Β-barrel Research Articles

Molecular and immunological characterization of Pasteurella multocida serotype A:3 OmpA: evidence of its role in P. multocida interaction with extracellular matrix molecules

Pasteurella multocida OmpA-like gene (PmOmpA) was cloned and characterized. The mature protein had a molecular mass of 35,075 Da and significant similarity with Escherichia coli (E. coli) OmpA proteins. Membrane topology analyses predict that like E. coli OmpA, the N-terminal half of PmOmpA exists as an eight-stranded transmembrane antiparallel β-barrel that displays four variable hydrophilic and surface-exposed regions with predicted antigenic peaks that may be involved in serum resistance or adherence. In addition, the Ala-Pro repeat region between the N-terminal β-barrel and C-terminal periplasmic domains is completely missing in PmOmpA. PmOmpA was expressed in E. coli and immunoblots analysis revealed that the recombinant PmOmpA was immunogenic, and expressed in vivo.The binding of PmOmpA to biotinylated Madin Darby bovine kidney (MDBK) cells surface proteins, fibronectin and heparin was demonstrated. Furthermore, PmOmpA binds MDBK monolayers and pre-treatment of P. multocida whole cells with anti-PmOmpA significantly reduced adherence to fibronectin. Ligand blot analysis revealed that fibronectin binds to the native and heat modified forms of PmOmpA when heated at 37 and 100 °C, respectively. Collectively these data indicate that PmOmpA may be involved in P. multocida 232 adherence to host cells via heparin and/or fibronectin bridging.

Crystal structure of lipocalin-type prostaglandin D synthase

Lipocalin-type prostaglandin (PG) D synthase (L-PGDS) is responsible for the biosynthesis of PGD 2, a potent endogenous sleep-inducing substance found in the central nervous system. In this study, we crystallized recombinant mouse L-PGDS from a sodium citrate solution by the hanging drop vapor-diffusion method. The crystal structure of the selenomethionyl Cys 65Ala-substituted L-PGDS was determined at 2.5 Å resolution by using the multiwavelength anomalous diffraction method. The crystals belonged to the orthorhombic space group C222 1 with lattice constants a=45.5, b=66.8, c=104.5 Å. The overall architecture of L-PGDS had an eight-stranded β-barrel with a hydrophobic cavity, in which the Cys 65 residue, an active site for the catalysis, was identified.

Secondary and Tertiary Structure Formation of the β-Barrel Membrane Protein OmpA is Synchronized and Depends on Membrane Thickness

The mechanism of membrane insertion and folding of a β-barrel membrane protein has been studied using the outer membrane protein A (OmpA) as an example. OmpA forms an eight-stranded β-barrel that functions as a structural protein and perhaps as an ion channel in the outer membrane of Escherichia coli. OmpA folds spontaneously from a urea-denatured state into lipid bilayers of small unilamellar vesicles. We have used fluorescence spectroscopy, circular dichroism spectroscopy, and gel electrophoresis to investigate basic mechanistic principles of structure formation in OmpA. Folding kinetics followed a second-order rate law and is strongly depended on the hydrophobic thickness of the lipid bilayer. When OmpA was refolded into model membranes of dilaurylphosphatidylcholine, fluorescence kinetics were characterized by a rate constant that was about fivefold higher than the rate constants of formation of secondary and tertiary structure, which were determined by circular dichroism spectroscopy and gel electrophoresis, respectively. The formation of β-sheet secondary structure and closure of the β-barrel of OmpA were correlated with the same rate constant and coupled to the insertion of the protein into the lipid bilayer. OmpA, and presumably other β-barrel membrane proteins therefore do not follow a mechanism according to the two-stage model that has been proposed for the folding of α-helical bundle membrane proteins. These different folding mechanisms are likely a consequence of the very different intramolecular hydrogen bonding and hydrophobicity patterns in these two classes of membrane proteins.

Lipid-protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy.

Intermolecular nuclear Overhauser effects (NOEs) between the integral outer membrane protein OmpX from Escherichia coli and dihexanoylphosphatidylcholine (DHPC) provided a detailed description of protein-detergent interactions. The NOEs were measured in 3D (15)N- and (13)C-resolved [(1)H,(1)H]-NOESY spectra recorded with selectively methyl-protonated and otherwise uniformly (2)H,(13)C,(15)N-labeled OmpX in micelles of DHPC at natural isotope abundance. In these mixed micelles the NMR structure of OmpX consists of an eight-stranded antiparallel beta-barrel. The OmpX surface area covered with intermolecular NOEs to the DHPC hydrophobic tails forms a continuous cylinder jacket of approximately 28 A in height, which is centered about the middle of the long axis through the beta-barrel. In addition, some intermolecular NOEs with methyl groups of the DHPC polar head were identified along both boundaries of this cylinder jacket. The experimental data suggest that the hydrophobic surface areas of OmpX are covered with a monolayer of DHPC molecules, which appears to mimic quite faithfully the embedding of the beta-barrel in a double-layer lipid membrane.

Solution structure and dynamics of the outer membrane enzyme PagP by NMR.

The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response. The global fold of Escherichia coli PagP was determined in both dodecylphosphocholine and n-octyl-beta-d-glucoside detergent micelles using solution NMR spectroscopy. PagP consists of an eight-stranded anti-parallel beta-barrel preceded by an amphipathic alpha helix. The beta-barrel is well defined, whereas NMR relaxation measurements reveal considerable mobility in the loops connecting individual beta-strands. Three amino acid residues critical for enzymatic activity localize to extracellular loops near the membrane interface, positioning them optimally to interact with the polar headgroups of lipid A. Hence, the active site of PagP is situated on the outer surface of the outer membrane. Because the phospholipids that donate palmitate in the enzymatic reaction are normally found only in the inner leaflet of the outer membrane, PagP activity may depend on the aberrant migration of phospholipids into the outer leaflet. This finding is consistent with an emerging paradigm for outer membrane enzymes in providing an adaptive response toward disturbances in the outer membrane.

Intrinsic properties of allergens and environmental exposure as determinants of allergenicity.

Intrinsic properties of allergens and environmental exposure as determinants of allergenicity.

Direct detection of hydrogen bonds in monomeric superoxide dismutase: biological implications.

Hydrogen bonds were directly determined via NMR with different experimental approaches at 600 and 800 MHz for reduced monomeric superoxide dismutase (Q133M2SOD, 16 kDa). This protein contains a copper and a zinc ion and shows the classical superoxide dismutase (SOD) eight-stranded beta-barrel fold. The best results for this intermediate molecular mass protein were obtained using a TROSY version of the long-range HNCO experiment at high magnetic field (800 MHz) or with a cryoprobe at 600 MHz. The backbone hydrogen bond network that defines the secondary structure of the protein was detected. Thirty-five backbone hydrogen bonds were identified. The lower limit for their detection, their relation to the TROSY R(2) rates, and the correlation between hydrogen bond detectability and signal line width are discussed. Experiments were also optimized to detect hydrogen bonds involving key side chains, which lead to the observation of five hydrogen bonds. In particular, the hydrogen bonds involving the side chain of Asp 124 were observed, which show significant differences with respect to the bonds expected on the basis of the crystal structure. The relevance of this finding relies also on the fact that Asp 124 is a key residue in determining the affinity of the protein for zinc. It has now been determined that the gain of the toxic function of peroxynitrite formation in SOD mutants related to amyotrophic lateral sclerosis (ALS) is due to SOD species lacking the zinc ion, as a consequence of a reduced affinity for zinc. Therefore, this study provides structural hints for understanding the origin of the enzymatic behavior of the Zn-deficient SOD.

Nitrophorins: Lipocalin‐based heme proteins transporting nitric oxide

AbstractNitrophorins 1–4 (NPs; NP1 to NP4) are salivary heme proteins secreted from the blood‐sucking insect Rhodnius prolixus. NPs transfer nitric oxide (NO) to the victim, resulting in vasodilatation, sequester histamine, reducing host inflammation and immune response, and inhibit blood coagulation. The NP fold is based on an eight‐stranded antiparallel β‐barrel, typically observed in the lipocalin homology family, which hosts a heme group. Although NPs use the ferric heme to bind NO and histamine, they are unrelated to the six/eight α‐helix (non)vertebrate hemoglobins, which bind NO preferentially to the ferrous heme, but do not bind histamine. Therefore, NPs and hemoglobins can be considered as an evolutionary experiment, where the heme group has been adapted to structurally different protein families to achieve similar function(s).

The 1.2 Å structure of a novel quorum-sensing protein, Bacillus subtilis LuxS

In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. The autoinducer-2 production protein LuxS, is involved in a novel quorum-sensing system and is thought to catalyse the degradation of S-ribosylhomocysteine to homocysteine and the autoinducer molecule 4,5-dihydroxy-2,3-pentadione. The crystal structure of Bacillus subtilis LuxS has been determined at 1.2 Å resolution, together with the binary complexes of LuxS with S-ribosylhomocysteine and homocysteine to 2.2 and 2.3 Å resolution, respectively. These structures show that LuxS is a homodimer with an apparently novel fold based on an eight-stranded β-barrel, flanked by six α-helices. Each active site contains a zinc ion coordinated by the conserved residues His54, His58 and Cys126, and includes residues from both subunits. S-ribosylhomocysteine binds in a deep pocket with the ribose moiety adjacent to the enzyme-bound zinc ion. Access to the active site appears to be restricted and possibly requires conformational changes in the protein involving the movement of residues 125–129 and those at the N terminus. The structure contains an oxidised cysteine residue in the active site whose role in the biological process of LuxS has not been determined. The autoinducer-2 signalling pathway has been linked to aspects of bacterial virulence and pathogenicity. The structural data on LuxS will provide opportunities for targeting this enzyme for the rational design of new antibiotics.

Proposed lipocalin fold for apolipoprotein M based on bioinformatics and site-directed mutagenesis

Apolipoprotein M (apoM) is a novel apolipoprotein that is predominantly present in high-density lipoprotein. Sensitive sequence searches, threading and comparative model building experiments revealed apoM to be structurally related to the lipocalin protein family. In a 3D model, characterized by an eight-stranded anti-parallel β-barrel, a segment including Asn135 could adopt a closed or open conformation. Using site-directed mutagenesis, we demonstrated Asn135 in wild-type apoM to be glycosylated, suggesting that the segment is solvent exposed. ApoM displays two strong acidic patches of potential functional importance, one around the N-terminus and the other next to the opening of the β-barrel.

Ion channel formation by N-terminal domain: a common feature of OprFs of Pseudomonas and OmpA of Escherichia coli

The proteolytic fragments of OprFs of Pseudomonas aeruginosa and Pseudomonas fluorescens were identified, respectively, as the first 175 and 177 amino acids from the N-terminal domain. They induced ion channels after reincorporation into planar lipid bilayers (85 and 75 pS, respectively, in 1 M NaCl). A similar conductance value (72 pS) was found for the eight β-strand OmpA N-terminal domain (OmpA 171) of Escherichia coli. We conclude that the N-terminal domain of OprFs is sufficient to induce ion channels and the comparison with OmpA 171, provides strong evidence of the existence of an eight-stranded β-barrel in the N-terminal domain of OprFs.

The three-dimensional structure of a Plasmodium falciparum cyclophilin in complex with the potent anti-malarial cyclosporin A

Cyclosporin A (CsA) is a potent anti-malarial compound in vitro and in vivo in mice though better known for its immunosuppressive properties in humans. Crystal structures of wild-type and a double mutant Plasmodium falciparum cyclophilin (PfCyP19 and mPfCyP19) complexed with CsA have been determined using diffraction terms to a resolution of 2.1 Å (1 Å=0.1 nm). The wild-type has a single PfCyP19/CsA complex per asymmetric unit in space group P1 and refined to an R-work of 0.15 and R-free of 0.19. An altered cyclophilin, with two accidental mutations, Phe120 to Leu in the CsA binding pocket and Leu171 to Trp at the C terminus, presents two complexes per asymmetric unit in the orthorhombic space group P2 12 12. This refined to an R-work of 0.18 and R-free 0.21. The mutations were identified from the crystallographic analysis and the C-terminal alteration helps to explain the different crystal forms obtained. PfCyP19 shares approximately 61 % sequence identity with human cyclophilin A (hCyPA) and the structures are similar, consisting of an eight-stranded antiparallel β-barrel core capped by two α-helices. The fold creates a hydrophobic active-site, the floor of which is formed by side-chains of residues from four antiparallel β-strands and the walls from loops and turns. We identified C—H…O hydrogen bonds between the drug and protein that may be an important feature of cyclophilins and suggest a general mode of interaction between hydrophobic molecules. Comparisons with cyclophilin-dipeptide complexes suggests that a specific C—H…O hydrogen bonding interaction may contribute to ligand binding. Residues Ser106, His99 and Asp130, located close to the active site and conserved in most cyclophilins, are arranged in a manner reminiscent of a serine protease catalytic triad. A Ser106Ala mutant was engineered to test the hypothesis that this triad contributes to CyP function. Mutant and wild-type enzymes were found to have similar catalytic properties.

Structure and Mechanism of 3-Deoxy-d-manno-octulosonate 8-Phosphate Synthase

3-deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) with arabinose 5-phosphate (A5P) to form KDO8P and inorganic phosphate. KDO8P is the phosphorylated precursor of 3-deoxy-D-manno-octulosonate, an essential sugar of the lipopolysaccharide of Gram-negative bacteria. The crystal structure of the Escherichia coli KDO8P synthase has been determined by multiple wavelength anomalous diffraction and the model has been refined to 2.4 A (R-factor, 19.9%; R-free, 23.9%). KDO8P synthase is a homotetramer in which each monomer has the fold of a (beta/alpha)(8) barrel. On the basis of the features of the active site, PEP and A5P are predicted to bind with their phosphate moieties 13 A apart such that KDO8P synthesis would proceed via a linear intermediate. A reaction similar to KDO8P synthesis, the condensation of phosphoenolpyruvate, and erythrose 4-phosphate to form 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P), is catalyzed by DAH7P synthase. In the active site of DAH7P synthase the two substrates PEP and erythrose 4-phosphate appear to bind in a configuration similar to that proposed for PEP and A5P in the active site of KDO8P synthase. This observation suggests that KDO8P synthase and DAH7P synthase evolved from a common ancestor and that they adopt the same catalytic strategy.

The X-ray three-dimensional structure of avidin

Avidin is a basic, highly stable, homotetrameric protein, isolated from bird egg-white, binding up to four molecules of d-biotin with extremely high affinity ( K d∼10 −15 M). The protein has been the object of different crystallographic investigations. In all the crystal structures, the four avidin subunits display almost exact 222 symmetry. Each avidin chain (128 amino acids) is arranged in a eight-stranded antiparallel β-barrel, whose inner region defines the d-biotin binding site. The molecular bases of d-biotin affinity can be recognised in a fairly rigid binding site, which is sterically complementary to the shape and polarity of the incoming vitamin, and is readily accessible in the apoprotein structure. Avidin displays remarkable structural and functional relationships to the acidic protein sretpavidin, isolated from Streptomyces avidinii.

Characterization of the thyroxine-binding site of thyroxine-binding globulin by site-directed mutagenesis.

The principal transport protein for T4 in human blood, thyroxine-binding globulin (TBG), binds T4 with an exceptionally high affinity (Ka = 10(10) M(-1)). Its homology to the superfamily of the serpins has recently been used in the design of chimeric proteins, providing experimental evidence that an eight-stranded beta-barrel domain encompasses the ligand-binding site. We have now characterized the T4 binding site by site-directed mutagenesis. Sequence alignment of TBG from several species revealed a phylogenetically highly conserved stretch of amino acids comprising strands 2B and 3B of the beta-barrel motif. Mutations within this region (Val228Glu, Cys234Trp, Thr235Trp, Thr235Gln, Lys253Ala, and Lys253Asp), designed to impose steric hindrance or restriction of its mobility, had no significant influence on T4 binding. However, binding affinity was 20-fold reduced by introduction of an N-linked glycosylation site at the turn between strands 2B and 3B (Leu246Thr) without compromising the proper folding of this mutant as assessed by immunological methods. In most other serpins, this glycosylation site is highly conserved and has been shown to be crucial for cortisol binding of corticosteroid-binding globulin, the only other member of the serpins with a transport function. The ligand-binding site could thus be located to a highly aromatic environment deep within the beta-barrel. The importance of the binding site's aromatic character was investigated by exchanging phenylalanines with alanines. Indeed, these experiments revealed that substitution of Phe249 in the middle of strand 3B completely abolished T4 binding, while the substitution of several other phenylalanines had no effect.

The crystal structure of rubisco from Alcaligenes eutrophus reveals a novel central eight-stranded β-barrel formed by β-strands from four subunits

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is involved in photosynthesis where it catalyzes the initial step in the fixation of carbon dioxide. The enzyme also catalyzes a competing oxygenation reaction leading to loss of fixed carbon dioxide, thus reducing the net efficiency of photosynthesis significantly. Rubisco has therefore been studied extensively, and a challenging goal is the engineering of a more photosynthetically efficient enzyme. Hexadecameric rubiscos fall in two distinct groups, “green-like” and “red-like”. The ability to discriminate between CO2 and O2 as substrates varies significantly, and some algae have red-like rubisco with even higher specificity for CO2 than the plant enzyme. The structure of unactivated rubisco from Alcaligenes eutrophus has been determined to 2.7 Å resolution by molecular replacement and refined to R and Rfree values of 26.6 and 32.2%, respectively. The overall fold of the protein is very similar to the rubisco structures solved previously for green-like hexadecameric enzymes, except for the extended C-terminal domains of the small subunits which together form an eight-stranded β-barrel which sits as a plug in the entrance to the central solvent channel in the molecule. The present structure is the first which has been solved for a red-like rubisco and is likely to represent a fold which is common for this group. The small subunits in general are believed to have a stabilizing effect, and the new quaternary structure in the oligomer of the present structure is likely to contribute even more to this stabilization of the assembled rubisco protein.

The solution structure and dynamics of human neutrophil gelatinase-associated lipocalin

Human neutrophil gelatinase-associated lipocalin (HNGAL) is a member of the lipocalin family of extracellular proteins that function as transporters of small, hydrophobic molecules. HNGAL, a component of human blood granulocytes, binds bacterially derived formyl peptides that act as chemotactic agents and induce leukocyte granule discharge. HNGAL also forms a complex with the proenzyme form of matrix metalloproteinase-9 (pro-MMP-9, or progelatinase B) via an intermolecular disulphide bridge. This association allows the subsequent formation of ternary and quaternary metalloproteinase/inhibitor complexes that vary greatly in their metalloproteinase activities. The structure and dynamics of apo-HNGAL have been determined by NMR spectroscopy. Simulated annealing calculations yielded a set of 20 convergent structures with an average backbone RMSD from mean coordinate positions of 0.79(±0.13) Å over secondary structure elements. The overall rotational correlation time (13.3 ns) derived from 15N relaxation data is consistent with a monomeric protein of the size of HNGAL (179 residues) under the experimental conditions (1.4 mM protein, pH 6.0, 24.5 °C). The structure features an eight-stranded antiparallel β-barrel, typical of the lipocalin family. One end of the barrel is open, providing access to the binding site within the barrel cavity, while the other is closed by a short 310-helix. The free cysteine residue required for association with pro-MMP-9 lies in an inter-strand loop at the closed end of the barrel. The structure provides a detailed model of the ligand-binding site and has led to the proposal of a site for pro-MMP-9 association. Dynamic data correlate well with structural features, which has allowed us to investigate a mechanism by which a cell-surface receptor might distinguish between apo and holo-HNGAL through conformational changes at the open end of the barrel.

Membrane assembly of the Escherichia coli outer membrane protein OmpA: exploring sequence constraints on transmembrane β-strands

The eight-stranded antiparallel β-barrel domain of the OmpA protein from Escherichia coli serves as a paradigm for the study of membrane assembly of integral β-structured membrane proteins. Previous studies have shown that neither the periplasmic turns nor the surface-exposed loops contain topogenic information. Consequently, the question of whether any structural constraint is imposed onto individual transmembrane β-strands is now addressed. To this end, amino acid sequences of β-strands 4, 6 and 8 were randomized. In vivo membrane assembly of mutant proteins was assayed and 288 variants were sequenced. Three parameters were found to be important for efficient membrane assembly. (i) At least four of five randomized residues with side-chains pointing towards the lipid bilayer must be hydrophobic and none of the three central residues must be charged. (ii) Side-chains pointing into the β-barrel interior must not be enlarged too much, possibly because of packing constraints. (iii) Proline residues are, in general, hardly tolerated in the transmembrane β-strands.

Protein–water–ion interactions in a model of the pore domain of a potassium channel: a simulation study

A model of the selectivity filter of a voltage-gated K + (Kv) channel formed by an eight-stranded β-barrel is compared with physiological properties of the channel. Continuum electrostatic calculations suggest that only two of the eight Asp sidechains at the extracellular mouth of the pore will ionise. A ring of four Tyr sidechains forms the narrowest region of the pore. Molecular dynamic simulations of the potential energy of a K + ion as translated along the model pore indicate that the two ionised Asp sidechains and the hydroxyl groups of the Tyr sidechains stabilise the partially desolvated ion as it passes through the narrowest region.

The NMR solution conformation of unligated human cyclophilin A

The nuclear magnetic resonance (NMR) solution structure of free, unligated cyclophilin A (CypA), which is an 18 kDa protein from human T-lymphocytes that was expressed in Escherichia coli for the present study, was determined using multidimensional heteronuclear NMR techniques. Sequence-specific resonance assignments for 99.5% of all backbone amide protons and non-labile hydrogen atoms provided the basis for collection of an input of 4101 nuclear Overhauser enhancement (NOE) upper distance constraints and 371 dihedral angle constraints for distance geometry calculations and energy minimization with the programs DIANA and OPAL. The average RMSD values of the 20 best energy-refined NMR conformers relative to the mean coordinates are 0.49 Å for the backbone atoms and 0.88 Å for all heavy atoms of residues 2 to 165. The molecular architecture includes an eight-stranded antiparallel β-barrel that is closed by two amphipathic α-helices. Detailed comparisons with the crystal structure of free CypA revealed subtle but significant conformational differences that can in most cases be related to lattice contacts in the crystal structure. 15N spin relaxation times and NMR lineshape analyses for CypA in the free form and complexed with cyclosporin A (CsA) revealed transitions of polypeptide loops surrounding the ligand-binding site from locally flexible conformations in the free protein, some of which include well-defined conformational equilibria, to well-defined spatial arrangements in the CypA-CsA complex. Compared to the crystal structure of free CypA, where the ligand-binding area is extensively involved in lattice contacts, the NMR structure presents a highly relevant reference for studies of changes in structure and internal mobility of the binding pocket upon ligand binding, and possible consequences of this conformational variability for calcineurin recognition by the CypA-CsA complex.