Identification of inhibitors of the E. coli chaperone SurA using in silico and in vitro techniques

SurA is a gram-negative, periplasmic chaperone protein involved in the proper folding of outer membrane porins (OMPs), which protect bacteria against toxins in the extracellular environment by selectively regulating the passage of nutrients into the cell. Previous studies demonstrated that deletion of SurA renders bacteria more sensitive to toxins that compromise the integrity of the outer membrane. Inhibitors of SurA will perturb the folding of OMPs, leading to disruption of the outer membrane barrier and making the cell more vulnerable to toxic insults. The discovery of novel SurA inhibitors is therefore of great importance for developing alternative strategies to overcome antibiotic resistance. Our laboratory has screened over 10,000,000 compounds in silico by computationally docking these compounds onto the crystal structure of SurA. Through this screen and a screen of fragment compounds (molecular weight?less than?250?g/mol), we found twelve commercially readily available candidate compounds that bind to the putative client binding site of SurA. We confirmed binding to SurA by developing and employing a competitive fluorescence anisotropy-based binding assay. Our results show that one of these compounds, Fmoc-β-(2-quinolyl)-d-alanine, binds the client binding site with high micromolar affinity. Using this compound as a lead, we also discovered that Fmoc-l-tryptophan and Fmoc-l-phenylalanine, but not Fmoc-l-tyrosine, bind SurA with similar micromolar affinity. To our knowledge, this is the first report of a competitive fluorescence anisotropy assay developed for the identification of inhibitors of the chaperone SurA, and the identification of three small molecules that bind SurA at its client binding site.     

In-situ fluorescence monitoring of cyanobacteria: Laboratory-based quantification of species-specific measurement accuracy

In recent years, in-situ fluorometers have been extensively deployed to monitor cyanobacteria in near real-time. Acceptable accuracy can be achieved between measured pigments and cyanobacteria biovolume provided the cyanobacteria species are known. However, cellular photosynthetic pigment content and measurement interferences are site and species specific and can dramatically affect sensor reliability. We quantified the accuracy of an in-situ fluorometer compared with traditional methods using mono- and mixed cultures of four different cyanobacterial species. We found: (1) lower pigment content in cultures in stationary phase, (2) higher precision with the sensor compared to traditional pigment quantification methods of measuring phycocyanin and chlorophyll a, (3) species-specific relationships between sensor readings and measurements related to biovolume, (4) overestimation of pigments in mixed compared with mono cultures, (5) dissolved organic matter causing a loss in signal proportional to its degree of aromaticity, and (6) potential to quantify the degree of cell lysis with a fluorescent dissolved organic matter sensor. This study has provided important new information on the strengths and limitations of fluorescence sensors. The sensor readings can provide accurate biovolume quantification and species determination for a number of bloom-forming species when sensors are properly compensated and calibrated.     

Mapping of the detergent-exposed surface of membrane proteins and peptides by 1H solution NMR in detergent: Application to the gramicidin A ion channel

The present work evaluates the use of intermolecular polypeptide–detergent 1H through-space connectivities to determine the bilayer exposed-surface and the bilayer topography of membrane polypeptides solubilized in non- deuterated detergents. For this purpose, the membrane peptide gramicidin A, solubilized in non-deuterated sodium dodecylsulfate as its dimeric 6,3 helix channel conformation was used. For this peptide, a high-resolution 3D structure, as well as reasonable assumptions concerning its membrane arrangement, exist. Band-selective 2D NOESY, ROESY and 3D NOESY-NOESY experiments were used to detect detergent–polypeptide through-space correlations in the presence of an excess of the non-deuterated detergent. The observed intermolecular NOEs appear to be strongly temperature- dependent. Based on the known 3D structure of the gramicidin channel, the detergent–polypeptide through-space correlations appear to be selective for 1H located on the hydrophobic surface of gramicidin A with very few contributions from interior 1H or water-exposed 1H. It is suggested that this method can be of general use to evaluate the bilayer-exposed surface and topography of membrane peptides and small proteins.     

Mechanosensitive Calcium Entry and Mobilization in Renal A6 Cells

Using spectrofluorescence imaging of fura-2 loaded renal A6 cells, we have investigated the generation of the cytosolic Ca²⁺ signal in response to osmotic shock and localized membrane stretch. Upon hypotonic exposure, the cells began to swell prior to a transient increase in [Ca²⁺] _i and the cells remained swollen after [Ca²⁺] _i had returned towards basal levels. Exposure to 2/3rd strength Ringer produced a cell volume increase within 3 min, followed by a slow regulatory volume decrease (RVD). The hypotonic challenge also produced a transient increase in [Ca²⁺] after a delay of 22 sec. Both the RVD and [Ca²⁺] _i response to hypotonicity were inhibited in a Ca²⁺-free bathing solution and by gadolinium (10 μm), an inhibitor of stretch-activated channels. Stretching the membrane by application of subatmospheric pressure (-2 kPa) inside a cell-attached patch-pipette induced a similar global increase in [Ca²⁺] _i as occurred after hypotonic shock. A stretch-sensitive [Ca²⁺] _i increase was also observed in a Ca²⁺-free bathing solution, provided the patch-pipette contained Ca²⁺. The mechanosensitive [Ca²⁺] _i response was by gadolinium (10 μm) or Ca²⁺-free pipette solutions, even when Ca²⁺ (2 mm) was present in the bath. Long-term (>10 min) pretreatment of the cells with thapsigargin inhibited the [Ca²⁺] _i response to hypotonicity. These results provide evidence that cell swelling or mechanical stimulation can activate a powerful amplification system linked to intracellular Ca²⁺ release mechanisms. Received: 3 August 1998/Revised: 19 November 1998     

Thermodynamic features of the chemical and thermal denaturations of human serum albumin

The unfolding process of human serum albumin between pH 5.4 and 9.9 was studied by chemical and thermal denaturations. The experimental results showed that there is no correlation between the stability of albumin at different pH values determined by both methods. The free energy change of unfolding versus concentration of guanidine showed a close dependence on the pH, suggesting that the variation of the electrical charge of albumin influences the final state of the unfolded form of the protein. Spectroscopic techniques, such as native fluorescence of the protein and circular dichroism, demonstrated that the unfolded state of the protein obtained from both methods possesses a different helical content. The solvophobic effect and the entropy of the chains have no influence on the final unfolding state when the protein is unfolded by thermal treatment, while, when the protein is unfolded by chemical denaturants, both effects depend on the medium pH. The results indicate that guanidine and urea interact with albumin by electrostatic forces, yielding a randomly coiled conformation in its unfolded state, while thermal denaturation produces a molten globule state and the aggregation of the protein; therefore, both methods yield different structurally unfolded states of the albumin.     

Synergism in the Oviposition Behavior of Plutella xylostella: Sinigrin and Wax Compounds

Diamondback moth, Plutella xylostella, host examining and oviposition behaviors were measured in response to sinigrin dosages (10 ^–3 , 10 ^–4 , and 10 ^–5 M) and controls with and without the addition of n-alkanes. Individual females were presented with a treatment and videotaped while an observer documented specific behaviors during 5-min observation periods. Behavior in response to sinigrin alone was not significantly different from that in response to controls. Alkane alone significantly reduced movement rate during treatment contact, but did not significantly affect other behaviors. Sinigrin concentrations combined with alkane significantly slowed the rate of insect movement, increased turning, and led to significantly longer treatment encounter durations. Behavior changes in response to sinigrin + alkane increased insect exposure to the sinigrin concentrations and led to greater oviposition compared to that in response to sinigrin treatments alone. The synergistic effect that mixing sinigrin and alkane has on P. xylostella behavior arises because the additional time females spend in contact with the treatment increases the rate at which they experience the available stimuli. Involvement of the antennae during examining of a treatment, referred to as swabbing, was usually associated with oviposition on alkane-coated sinigrin treatments. The presence of alkane may alter the way sinigrin is perceived. Oviposition in response to the treatment combinations was also tested in overnight bioassays. The pattern of oviposition in response to treatments during bioassays differed from that established during observations. The value of direct observations and the mechanistic interpretations they allow are emphasized.     

Halide fluxes in epithelial cells measured with an automated cell plate reader

A method is introduced to measure chloride permeability in cultured epithelial cells using 6-methoxy-N-(3-sulfopropyl)quinolinium (SPQ) and 6-methoxy-N-ethylquinolinium iodide quinolinium (MEQ) as fluorescent chloride-sensitive probes. The method involves growing cells in multiwell plates, incubating cells with SPQ or MEQ, and then exchanging intracellular or extracellular halide ions with nitrate. The resulting time course of SPQ or MEQ fluorescence is followed by repetitive readings with a multiwell fluorescence plate reader. Exchange times are extracted by fitting the time course with a single exponential function of time. The method was validated by measuring the effect of chloride channel activators and blockers in A6 and MDCK cells. The baseline iodide/nitrate exchange time was 200-300 s. Isoproterenol (a modulator of cAMP-activated chloride channels) increased the exchange rate by a factor of 1.4+/-0.1; A23187 (a modulator of calcium-activated chloride channels) increased the rate by 3.4+/-0.4; bradykinin (also a modulator of calcium-activated chloride channels) increased the rate by 2.0+/-0.4; forskolin (a direct stimulator of adenylate cyclase) increased the rate by 2.7+/-0.3. Diphenylamine-2-carboxylate (a chloride channel blocker) decreased the rate by 0.12+/-0.03. These results indicate that our method is a valid indicator of halide-nitrate exchange in cultured epithelial cells.     

Preparation and characterization of Alexa Fluor 594-labeled epidermal growth factor for fluorescence resonance energy transfer studies: application to the epidermal growth factor receptor

We have prepared and characterized a new fluorescent derivative of murine epidermal growth factor (EGF), Alexa Fluor 594-labeled EGF (A-EGF), for fluorescence studies of EGF-EGF receptor interactions. We describe the synthesis of this derivative and its physical and biological characterization. The significant overlap between the excitation and the emission spectra of A-EGF makes this probe well suited to fluorescence resonance energy homo-transfer. Using time-resolved fluorescence to examine the oligomeric state of the EGF receptor, we have observed resonance energy homo-transfer of A-EGF bound to EGF receptors in cells, but not of A-EGF bound to EGF receptors in membrane vesicles. Our results, interpreted in the context of recent crystallographic studies of the ligand-binding domains of EGF receptors, suggest that observed fluorescence resonance energy transfer does not result from transfer within receptor dimers, but rather results from transfer within higher-order oligomers. Furthermore, our results support a structural model for oligomerization of EGF receptors in which dimers are positioned head-to-head with respect to the ligand-binding site, consistent with the head-to-head interactions observed between adjacent receptor dimers by X-ray crystallography.