共查询到20条相似文献,搜索用时 15 毫秒
1.
Vinaya Kumar Golla Eulàlia Sans-Serramitjana Karunakar Reddy Pothula Lorraine Benier Jayesh Arun Bafna Mathias Winterhalter Ulrich Kleinekathöfer 《Biophysical journal》2019,116(2):258-269
Fosfomycin is a frequently prescribed drug in the treatment of acute urinary tract infections. It enters the bacterial cytoplasm and inhibits the biosynthesis of peptidoglycans by targeting the MurA enzyme. Despite extensive pharmacological studies and clinical use, the permeability of fosfomycin across the bacterial outer membrane is largely unexplored. Here, we investigate the fosfomycin permeability across the outer membrane of Gram-negative bacteria by electrophysiology experiments as well as by all-atom molecular dynamics simulations including free-energy and applied-field techniques. Notably, in an electrophysiological zero-current assay as well as in the molecular simulations, we found that fosfomycin can rapidly permeate the abundant Escherichia coli porin OmpF. Furthermore, two triple mutants in the constriction region of the porin have been investigated. The permeation rates through these mutants are slightly lower than that of the wild type but fosfomycin can still permeate. Altogether, this work unravels molecular details of fosfomycin permeation through the outer membrane porin OmpF of E. coli and moreover provides hints for understanding the translocation of phosphonic acid antibiotics through other outer membrane pores. 相似文献
2.
Balasundaresan Dhakshnamoorthy Suchismita Raychaudhury Lydia Blachowicz 《Journal of molecular biology》2010,396(2):293-2115
The OmpF porin from the Escherichia coli outer membrane folds into a trimer of β-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 β-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 β-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 P63 space group and two different data sets were obtained at 2.6 Å and 3.0 Å resolution with K+ and Rb+, respectively. The Rb+-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 Å 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. 相似文献
3.
E. V. Sidorin V. A. Khomenko N. Yu. Kim P. S. Dmitrenok A. M. Stenkova O. D. Novikova T. F. Solov’eva 《Biochemistry. Biokhimii?a》2017,82(11):1304-1313
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation. In aqueous solutions, rOmpF undergoes conformational changes, reversible self-association, and aggregation. When transferred from 8M urea into water, PBS (containing 0.15 M NaCl, pH 7.4), or buffer containing 0.8 M urea (pH 8.0), fully unfolded rOmpF forms relatively compact monomeric intermediates prone to self-association with formation of multimers. The oligomeric intermediates have high content of native protein-like secondary structure and pronounced tertiary structure. In acidic media (pH 5.0, close to the protein isoelectric point), rOmpF undergoes rapid irreversible aggregation. Therefore, we found that medium composition significantly affects both porin folding and processes of its self-association and aggregation. 相似文献
4.
OmpF from the outer membrane of Escherichia coli is a general porin considered to be the main pathway for beta-lactam antibiotics. The availability of a high-resolution crystal structure of OmpF and new experimental techniques at the single-molecule level have opened the way to the investigation of the microscopic mechanisms that allow the passage of antibiotics through bacterial pores. We applied molecular dynamics simulations to investigate the translocation process of ampicillin (Amp) through OmpF. Using a recent algorithm capable of accelerating molecular dynamics simulations we have been able to obtain a reaction path for the translocation of Amp through OmpF. The mechanism of passage depends both on the internal degrees of freedom of Amp and on interactions of Amp with OmpF. Understanding this mechanism would help us design more efficient antibiotics and shed light on nature's way of devising channels able to enhance the transport of molecules through membranes. 相似文献
5.
N. S. Buinovskaya L. A. Balabanova O. Yu. Portnyagina O. D. Novikova V. A. Rasskazov 《Russian Journal of Bioorganic Chemistry》2018,44(4):424-430
To improve the diagnostics of pseudotuberculosis by ELISA, a genetically engineered hybrid bifunctional protein (CmAP/OmpF) was obtained based on the pore-forming protein of the outer membrane of human pathogenic bacterium Yersinia pseudotuberculosis (OmpF) and the highly active alkaline phosphatase of marine bacterium Cobetia amphilecti KMM 296 (CmAP). The OmpF module in the fusion protein retains the properties of the diagnostic antigen of the pseudotuberculosis pathogen, and the CmAP module is an enzyme label for detecting porin complexes with specific antibodies. The CmAP/OmpF activity was successfully confirmed by the binding of antibodies to OmpF porin in murine antisera, as well as in the sera of patients with pseudotuberculosis. The use of hybrid complex CmAP/OmpF for the diagnostics of pseudotuberculosis will eliminate the use of enzyme-labeled secondary antibodies, usually necessary for detecting specific antibodies in the blood serum of patients, and thus simplify the procedure and shorten the analysis time. 相似文献
6.
Physicochemical Characterization of the Reassembled Dimer of an Integral Membrane Protein OmpF Porin
The in vitro reassembled species of OmpF porin, which was renatured from its denatured monomer using n-octyl-β-D-glucopyranoside, was characterized by low-angle laser light scattering photometry, circular dichroism spectroscopy and synchrotron radiation small-angle X-ray scattering measurements. The light scattering measurement reconfirmed that the reassembled species was the dimer of the protein. Circular dichroism spectra of the reassembled dimer showed a native-like β-structure. A small-angle X-ray scattering measurement indicated that the size of the reassembled dimer was nearly equal to that of the native trimer under the present experimental conditions. In a thermal denaturation experiment followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the reassembled dimer was less stable than the native trimer. 相似文献
7.
Tatiana K. Rostovtseva Ekaterina M. NestorovichSergey M. Bezrukov 《Biophysical journal》2002,82(1):160-169
To understand the physics of polymer equilibrium and dynamics in the confines of ion channel pores, we study partitioning of poly(ethylene glycol)s (PEGs) of different molecular weights into the bacterial porin, OmpF. Thermodynamic and kinetic parameters of partitioning are deduced from the effects of polymer addition on ion currents through single OmpF channels reconstituted into planar lipid bilayer membranes. The equilibrium partition coefficient is inferred from the average reduction of channel conductance in the presence of PEG; rates of polymer exchange between the pore and the bulk are estimated from PEG-induced conductance noise. Partition coefficient as a function of polymer weight is best fitted by a “compressed exponential” with the compression factor of 1.65. This finding demonstrates that PEG partitioning into the OmpF channel pore has sharper dependence on polymer molecular weight than predictions of hard-sphere, random-flight, or scaling models. A 1360-Da polymer separates regimes of partitioning and exclusion. Comparison of its characteristic size with the size of a 2200-Da polymer previously found to separate these regimes for the α-toxin shows good agreement with the x-ray structural data for these channels. The PEG-induced conductance noise is compatible with the polymer mobility reduced inside the OmpF pore by an order of magnitude relatively to its value in bulk solution. 相似文献
8.
9.
Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF
Soroosh Pezeshki 《Biophysical journal》2009,97(7):1898-1906
All-atom molecular dynamics simulations of the ion current through OmpF, the major porin in the outer membrane of Escherichia coli, were performed. Starting from the crystal structure, the all-atom modeling allows us to calculate a parameter-free ion conductance in semiquantitative agreement with experiment. Discrepancies between modeling and experiment occur, e.g., at salt concentrations above 1 M KCl or at high temperatures. At lower salt concentrations, the ions have separate pathways along the channel surface. The constriction zone in the channel contains, on one side, a series of positively charges (R42, R82, R132), and on the opposite side, two negatively charged residues (D113, E117). Mutations generated in the constriction zone by removing cationic residues enhance the otherwise small cation selectivity, whereas removing the anionic residues reverses the selectivity. Reduction of the negatively charged residues decreases the conductance by half, whereas cationic residues enhance the conductance. Experiments on mutants confirm the results of the molecular-level simulations. 相似文献
10.
MarieLouise R Francis Melissa N Webby Nicholas G Housden Renata Kaminska Emma Elliston Boonyaporn Chinthammit Natalya Lukoyanova Colin Kleanthous 《The EMBO journal》2021,40(21)
Bacteria deploy weapons to kill their neighbours during competition for resources and to aid survival within microbiomes. Colicins were the first such antibacterial system identified, yet how these bacteriocins cross the outer membrane (OM) of Escherichia coli is unknown. Here, by solving the structures of translocation intermediates via cryo‐EM and by imaging toxin import, we uncover the mechanism by which the Tol‐dependent nuclease colicin E9 (ColE9) crosses the bacterial OM. We show that threading of ColE9’s disordered N‐terminal domain through two pores of the trimeric porin OmpF causes the colicin to disengage from its primary receptor, BtuB, and reorganises the translocon either side of the membrane. Subsequent import of ColE9 through the lumen of a single OmpF subunit is driven by the proton‐motive force, which is delivered by the TolQ‐TolR‐TolA‐TolB assembly. Our study answers longstanding questions, such as why OmpF is a better translocator than OmpC, and reconciles the mechanisms by which both Tol‐ and Ton‐dependent bacteriocins cross the bacterial outer membrane. 相似文献
11.
Lishan Zhang Zujie Yao Huamei Tang Qingli Song Huanhuan Song Jindong Yao Zhen Li Xiaofang Xie Yuexu Lin Xiangmin Lin 《Molecular & cellular proteomics : MCP》2022,21(9):100248
Protein lysine acetylation (Kac) modification plays important roles in diverse physiological functions. However, there is little evidence on the role of Kac modification in bacterial antibiotic resistance. Here, we compared the differential expressions of whole-cell proteins and Kac peptides in oxytetracycline sensitive and oxytetracycline resistance (OXYR) strains of Aeromonas hydrophila using quantitative proteomics technologies. We observed a porin family protein Aha1 downregulated in the OXYR strain, which may have an important role in the OXY resistance. Interestingly, seven of eight Kac peptides of Aha1 decreased abundance in OXYR as well. Microbiologic assays showed that the K57R, K187R, and K197R Aha1 mutants significantly increased antibiotic resistance to OXY and reduced the intracellular OXY accumulation in OXY stress. Moreover, these Aha1 mutants displayed multidrug resistance features to tetracyclines and β-lactam antibiotics. The 3D model prediction showed that the Kac states of K57, K187, and K197 sites located at the extracellular pore vestibule of Aha1 may be involved in the uptake of specific types of antibiotics. Overall, our results indicate a novel antibiotic resistance mechanism mediated by Kac modification, which may provide a clue for the development of antibiotic therapy strategies. 相似文献
12.
Differential Expression of the OmpF and OmpC Porin Proteins in Escherichia coli K-12 Depends upon the Level of Active OmpR 总被引:6,自引:0,他引:6 下载免费PDF全文
We have generated a mutant form of the OmpR regulatory protein, OmpRD55E, that is active independent of the EnvZ kinase. Notably, the pattern of OmpF and OmpC expression can be altered simply by changing the level of this mutant protein in the cell. This result supports a key prediction of the current model of porin regulation, which states that the differential regulation of OmpF and OmpC is a direct consequence of the cellular level of the active form of OmpR. 相似文献
13.
Al Jamal JA 《The protein journal》2005,24(1):1-8
The proportion of hexokinase that is bound to the outer mitochondrial membrane is tissue specific and metabolically regulated. This study examined the role of the N,N-dicyclohexylcarbodiimide-binding domain of mitochondrial porin in binding to hexokinase I. Selective proteolytic cleavage of porin protein was performed and peptides were assayed for their, effect on hexokinase I binding to isolated mitochondria. Specificity of DCCD-reactive domain binding to hexokinase I was demonstrated by competition of the peptides for porin binding sites on hexokinase as well as by blockage hexokinase binding by N,N-dicyclohexylcarbodiimide. One of the peptides, designated as 5 kDa (the smallest of the porin peptides, which contains a DCCD-reactive site), totally blocked binding of the enzyme to the mitochondrial membrane, and significantly enhanced the release of the mitochondrially bound enzyme. These experiments demonstrate that there exists a direct and specific interaction between the DCCD-reactive domain of VDAC and hexokinase I. The peptides were further characterized with respect to their effects on certain functional properties of hexokinase I. None had any detectable effect on catalytic properties, including inhibition by glucose 6-phosphate. To evaluate further the outer mitochondrial membranes role in the hexokinase binding, insertion of VDAC was examined using isolated rat mitochondria. Pre-incubation of mitochondria with purified porin strongly increases hexokinase I binding to rat liver mitochondria. Collectively, the results imply that the high hexokinase-binding capability of porin-enriched mitochondria was due to a quantitative difference in binding sites. 相似文献
14.
Comparative Studies with Three Antibiotics Binding to Deoxyribonucleic Acid 总被引:1,自引:3,他引:1 下载免费PDF全文
The effects of the three antibiotics U-12,241, nogalamycin, and U-20,661 on (i) deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) synthesis in KB cell cultures and cell-free systems of bacterial and mammalian origin and on (ii) oxidative phosphorylation in rat liver mitochondria were compared. Nogalamycin and U-12,241 inhibited RNA synthesis more strongly than DNA synthesis in all test systems. Antibiotic U-20,661 inhibited DNA and RNA synthesis equally in whole mammalian cells and their corresponding cell-free systems. The RNA polymerase from Escherichia coli, however, was at least 100 times more sensitive to U-20,661 than was the DNA polymerase. U-12,241 caused significant uncoupling of oxidative phosphorylation in mitochondria. 相似文献
15.
16.
Diffusion, Exclusion, and Specific Binding in a Large Channel: A Study of OmpF Selectivity Inversion
We find that moderate cationic selectivity of the general bacterial porin OmpF in sodium and potassium chloride solutions is inversed to anionic selectivity in concentrated solutions of barium, calcium, nickel, and magnesium chlorides. To understand the origin of this phenomenon, we consider several factors, which include the binding of divalent cations, electrostatic and steric exclusion of differently charged and differently sized ions, size-dependent hydrodynamic hindrance, electrokinetic effects, and significant “anionic” diffusion potential for bulk solutions of chlorides of divalent cations. Though all these factors contribute to the measured selectivity of this large channel, the observed selectivity inversion is mostly due to the following two. First, binding divalent cations compensates, or even slightly overcompensates, for the negative charge of the OmpF protein, which is known to be the main cause of cationic selectivity in sodium and potassium chloride solutions. Second, the higher anionic (versus cationic) transport rate expected for bulk solutions of chloride salts of divalent cations is the leading cause of the measured anionic selectivity of the channel. Interestingly, at high concentrations the binding of cations does not show any pronounced specificity within the divalent series because the reversal potentials measured in the series correlate well with the corresponding bulk diffusion potentials. Thus our study shows that, in contrast to the highly selective channels of neurophysiology that employ mostly the exclusion mechanism, quite different factors account for the selectivity of large channels. The elucidation of these factors is essential for understanding large channel selectivity and its regulation in vivo. 相似文献
17.
Discrepancies were noted in the published conductance of the Escherichia coli porin OmpF. Results from various papers are hard to compare because of the use of different channel preparations, salt types and concentrations, and electrophysiological techniques (black lipid membrane (BLM) vs. patch clamp). To reconcile these data, we present a side-by-side comparison of OmpF activity studied with the two techniques on the same preparation of pure protein, and in the same low salt concentrations (150 mM KCl). The novel aspect of OmpF porin behavior revealed by this comparison is the ubiquitous existence of states of smaller conductance than the monomeric conductance (subconductance states), regardless of the techniques or experimental conditions used, and the drastic enhancement of subconductance gating by polyamines. Transitions to subconductance states have received little attention in previous publications, in particular when BLM electrophysiology was used. Monomeric closures are rare in recordings at clamped potentials, at least at voltages lower than ∼100-120 mV. Most closing activity is in the form of subconductance gating, which becomes more dominant in the presence of spermine, with a more frequent and prolonged occupation of these substates. A discussion of the molecular basis for this hallmark behavior of porin is presented. 相似文献
18.
Heterologous binding of rat brain hexokinase to wild type, porinless, and recombinant yeast mitochondria expressing human porin was assessed, partially characterized, and compared to that in the homologous system (rat liver mitochondria). With porin-containing yeast mitochondria it is shown that (i) a significant, saturatable association occurs; (ii) its extent and apparent affinity, correlated with the origin of porin, are enhanced in the presence of dextran; (iii) the binding requires Mg ions and apparently follows a complex cooperative mechanism. This heterologous association does not seem to differ fundamentally from that in the homologous system and represents a good basis for molecular studies in yeast. With porinless yeast mitochondria, binding occurs at much lower affinity, but to many more sites per mitochondrion. The results indicating a major but not exclusive role for porin in the binding are discussed in terms of (i) the mode and mechanism of binding, and (ii) the suitability of the rat hexokinase–yeast mitochondria couple for the study of heterogeneous catalysis in reconstituted cellular model systems. 相似文献
19.
Free-standing lipid bilayer membranes can be formed on small apertures (60 nm diameter) on highly ordered porous alumina substrates. The formation process of the membranes on a 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanol submonolayer was followed by impedance spectroscopy. After lipid bilayers had thinned, the reconstitution and ionic conducting properties of the outer membrane protein OmpF of E. coli were monitored using single-channel recordings. The characteristic conductance states of the three monomers, fast kinetics, and subconductance states were observed. Blockade of the ion flow as a result of interaction of the antibiotic ampicillin with the protein was verified, indicating the full functionality of the protein channel in nanometer-scale bilayer membranes. 相似文献
20.
Lígia S. Nobre Smilja Todorovic Ana Filipa N. Tavares Eric Oldfield Peter Hildebrandt Miguel Teixeira Lígia M. Saraiva 《Journal of bacteriology》2010,192(6):1527-1533
In this work, we report that flavohemoglobin contributes to the azole susceptibility of Staphylococcus aureus. We first observed that deletion of the flavohemoglobin gene leads to an increase in the viability of imidazole-treated S. aureus cells and that reversion to the wild-type phenotype occurs upon expression of flavohemoglobin from a multicopy plasmid. Further spectroscopic analyses showed that miconazole, the most efficient azole antibiotic against S. aureus, ligates to heme of both oxidized and reduced flavohemoglobin. The binding of miconazole to oxidized flavohemoglobin, with an association constant of 1.7 × 106 M−1, typical of a tight, specific binding equilibrium, results in augmentation of the superoxide production by the enzyme. These results are corroborated by in vivo studies showing that imidazole-treated S. aureus cells expressing flavohemoglobin contain a larger amount of reactive oxygen species. Moreover, it was observed that the survival of miconazole-treated S. aureus internalized by murine macrophages is higher for cells lacking flavohemoglobin. Altogether, the present data revealed that in S. aureus, flavohemoglobin enhances the antimicrobial activity of imidazoles via an increase of intracellular oxidative stress.Staphylococcus aureus is an opportunistic pathogen responsible for a large number of human infections that cause systemic diseases from a mild to life-threatening character. The increasing incidence of methicillin-resistant S. aureus (MRSA) strains observed in the past few years makes S. aureus infections a leading threat to public health, causing more deaths in the United States and Europe than human immunodeficiency virus (AIDS) (11). Like other Gram-positive bacteria, staphylococci are sensitive to imidazoles (27). Imidazoles (such as clotrimazole, miconazole, ketoconazole, and sulconazole) (Fig. (Fig.1)1) represent one of the major classes of azole antifungal that are useful in the treatment of infections, including cutaneous and vaginal candidiasis (8). The activity of these antifungal drugs derives primarily from inhibition of the biosynthesis of ergosterol, an essential component of the fungal plasma membrane, at the level of lanosterol 14-alpha demethylase. Furthermore, in fungi and yeast, azole treatment leads to an increase in the endogenous production of reactive oxygen species (ROS) (12, 25). For example, in Candida albicans and Saccharomyces cerevisiae, the miconazole inhibition of cytochrome c oxidase, peroxidase, and catalase has been reported to be responsible for a high level of ROS production (3, 4). It has also been reported that clotrimazole inhibition of Plasmodium falciparum hemoperoxidase leads to ROS accumulation in this protozoan pathogen (26). For S. cerevisiae, C. albicans, and Escherichia coli, the action of imidazoles was also correlated with the inhibition of the nitric oxide (NO) scavenger activity of flavohemoglobin (7).Open in a separate windowFIG. 1.Structures of the azole (imidazole; 1,2,4-triazole) antibiotics investigated.Flavohemoglobins (Hmp) are widespread among bacteria and yeast and contain three domains: C-terminal NAD- and flavin adenine dinucleotide (FAD)-binding domains, which together constitute a ferredoxin-NADP+ oxidoreductase-like domain, and an N-terminal globin domain, which harbors a single B-type heme. The high-spin heme contains one axial histidine and binds small molecules like NO, carbon monoxide (CO), and dioxygen (O2). The heme can also bind bulky aromatic bases, since it is inserted in a large hydrophobic pocket (7). We observed that the binding of imidazoles to S. aureus flavohemoglobin results in an increase in the amount of deleterious reactive oxygen species produced by flavohemoglobin that contributes to the bactericidal effect of azole antibiotics toward S. aureus. 相似文献