Changes In Fluorescence Polarization Research Articles

Effect of ionic strength on folding and aggregation of the hemolytic peptide melittin in solution

Melittin is a cationic, amphipathic, hemolytic peptide composed of 26 amino acid residues. It is intrinsically fluorescent due to the presence of a single tryptophan residue, which has been shown to be crucial for its hemolytic activity. It undergoes a structural transition from a random coil monomer to an alpha-helical tetramer at high ionic strength. Although the aggregation behavior of melittin in solution is well characterized, dynamic information associated with the aggregation of melittin is lacking. In this paper, we have monitored the effect of ionic strength on the dynamics and aggregation behavior of melittin in aqueous solution by utilizing sensitive fluorescence approaches, which include the red edge excitation shift (REES) approach. Importantly, we demonstrate that REES is sensitive to the self-association of melittin induced by ionic strength. The change in environment experienced by melittin tryptophan(s) is supported by changes in fluorescence emission maximum, polarization, and lifetime. In addition, the accessibility of the tryptophan residue was probed by fluorescence quenching experiments using acrylamide and trichloroethanol as soluble and hydrophobic quenchers, respectively. Circular dichroism studies confirm the ionic strength-induced change in the secondary structure of melittin. Taken together, these results constitute the first report showing that REES could be used as a sensitive tool to monitor the aggregation behavior of melittin in particular and other proteins and peptides in general.

Monitoring the organization and dynamics of bovine hippocampal membranes utilizing differentially localized fluorescent membrane probes

Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors such as the G-protein coupled serotonin1A receptor. In this paper, we have explored the organization and dynamics of bovine hippocampal membranes using environment-sensitive and differentially localized fluorescent probes NBD-PE and NBD-cholesterol, utilizing wavelength-selective and time-resolved fluorescence measurements. The NBD group in NBD-PE is localized at the membrane interface while in NBD-cholesterol it is localized deeper in the membrane. Our results show that native hippocampal membranes offer considerable motional restriction as evidenced from red edge excitation shift of NBD probes. However, this effect progressively decreases with increasing cholesterol depletion in the case of NBD-cholesterol, possibly indicating a reduction in membrane heterogeneity. In contrast, REES of NBD-PE in hippocampal membranes does not show any significant change upon cholesterol depletion indicating relative lack of sensitivity of the membrane interface to cholesterol depletion. These observations are supported by changes in fluorescence polarization with cholesterol depletion. Taken together, these results imply that the deeper hydrocarbon region of the hippocampal membrane is more sensitive to changes in membrane organization and dynamics due to cholesterol depletion than the interfacial region. The motional restriction in native membranes is maintained even in the absence of proteins. The fluorescence lifetimes of both the NBD probes show slight reduction upon cholesterol depletion indicating a change in micro-environmental polarity possibly due to water penetration. These results are relevant in understanding the complex organization of hippocampal membranes and could have possible functional implications.

Effect of Structural Transition of the Host Assembly on Dynamics of an Ion Channel Peptide: A Fluorescence Approach

Structural transition can be induced in charged micelles by increasing the ionic strength of the medium. We have monitored the organization and dynamics of the functionally important tryptophan residues of gramicidin in spherical and rod-shaped sodium dodecyl sulfate micelles utilizing a combination of wavelength-selective fluorescence and related fluorescence approaches. Our results show that tryptophans in gramicidin, present in the single-stranded β6.3 conformation, experience slow solvent relaxation giving rise to red edge excitation shift in spherical and rod-shaped micelles. In addition, changes in fluorescence polarization with increasing excitation or emission wavelength reinforce that the gramicidin tryptophans are localized in motionally restricted regions of these micelles. Fluorescence quenching experiments using acrylamide as a quencher of tryptophan fluorescence show that there is reduced water penetration in rod-shaped micelles. Taken together, we show that gramicidin conformation and dynamics is sensitive to the salt-induced structural transition in charged micelles. In addition, these results demonstrate that deformation of the host assembly could modulate protein conformation and dynamics.

CellScan technology for in vitro prediction of tumor response to chemotherapeutic agents

2125 Background: Tumor heterogeneity with respect to the response to chemotherapy is a major problem in the field of oncology. In this study we have used the CellScan, a novel static cytometer equipped with a unique cell carrier, for the purpose of monitoring changes in fluorescence intensity and polarization in cancer cells affected by anti neoplastic drugs and correlate it with in vivo clinical outcome. The novelty and advantage of the method presented here is its end-point, which is independent of tumor proliferation, avoiding the complication of tumor culturing and reducing significantly the duration of the assay. Methods: The CellScan assay for testing the drug sensitivity or refractoriness of cancer cells was developed by employing human breast cancer cell lines (T47D and T80) and common anti-cancer drugs. It is based on measuring changes in the degree of fluorescence intensity (FI) and polarization (FP) of various fluorescent probes that occur upon exposure of cancer cells to drugs on a patented CellCarrier. Using this technique, 88 surgically resected tumors were tested for in vitro response to drugs: 67 breast cancers (stages II, III and IV), 8 ovarian carcinomas, 12 digestive cancers and 1 malignant melanoma. Briefly, tumors were mechanically dissociated, exposed to the different drugs for 24 hours and stained with two different markers of apoptosis: FDA (fluorescein di acetate), and Rh123 (rhodamine Rh123). The cells were then scanned using the CellScan and changes in fluorescence intensity and polarization of the fluorescent dyes were measured and compared with untreated control cells. In parallel, the patients were treated with the standard protocol regimens and clinical outcome was followed. Results: In vitro results showed a wide variety of responses even among the same histopathological type or stage of disease. Whenever possible in cases of advanced disease, clinical outcome was compared with CellScan results showing good correlation. Different case reports will be presented. Conclusions: Tumors presented a strong individual sensitivity or resistance to drugs and CellScan test may be used to assist in the prediction of this response to anti-cancer agents. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Medis-El Medis-El

Effect of Graded Hydration on the Dynamics of an Ion Channel Peptide: A Fluorescence Approach

Water plays an important role in determining the folding, structure, dynamics, and, in turn, the function of proteins. We have utilized a combination of fluorescence approaches such as the wavelength-selective fluorescence approach to monitor the effect of varying degrees of hydration on the organization and dynamics of the functionally important tryptophan residues of gramicidin in reverse micelles formed by sodium bis(2-ethylhexyl) sulfosuccinate. Our results show that tryptophans in gramicidin, present in the single-stranded β6.3 conformation, experience slow solvent relaxation giving rise to red-edge excitation shift (REES). In addition, changes in fluorescence polarization with increasing excitation or emission wavelength reinforce that the gramicidin tryptophans are localized in motionally restricted regions of the reverse micelle. Interestingly, the extent of REES is found to be independent of the [water]/[surfactant] molar ratio (wo). We attribute this to heterogeneity in gramicidin tryptophan localization. Fluorescence intensity and mean fluorescence lifetime of the gramicidin tryptophans show significant reductions with increasing wo indicating sensitivity to increased polarity. Since the dynamics of hydration is related to folding, structure, and eventually function of proteins, we conclude that REES could prove to be a potentially sensitive tool to explore the dynamics of proteins under conditions of changing hydration.

Effects of Poly(ethylene glycol) (PEG) Concentration on the Permeability of PEG-Grafted Liposomes

Poly(ethylene glycol)-grafted liposomes (PEG-liposomes) were prepared from dipalmitoylphosphatidylcholine (DPPC) with various amounts of distearoyl-N-monomethoxy poly(ethylene glycol)-succinyl-phosphatidylethanolamines (DSPE-PEG) with PEG molecular weights of 1000, 2000, 3000 and 5000. The effects of DSPE-PEG concentration on the permeability of PEG-liposomes were investigated using carboxyfluorescein (CF). In the gel state, the CF leakage from PEG-liposomes was decreased with increasing mole fractions of DSPE-PEG for all PEG molecular weights. In the liquid-crystalline state, the CF leakage from PEG-liposomes containing DSPE-PEG1000 gradually increased with increasing mole fractions of DSPE-PEG, while that of PEG-liposomes whose molecular weight in PEG units was above 2000 rapidly decreased by the addition of DSPE-PEG. Furthermore, no effect of PEG molecular weight on CF leakage was observed. The relationship between the fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH) (or 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH)) and the mole fraction of DSPE-PEG for PEG-liposomes was also investigated. No significant changes in fluorescence polarization of DPH for liposomal bilayer membranes was observed in the gel and liquid-crystalline states due to the addition of DSPE-PEG, while that of TMA-DPH was decreased compared with that of liposomes without DSPE-PEG in both states.

Influence of Ester and Ether Linkage in Phospholipids on the Environment and Dynamics of the Membrane Interface: A Wavelength-Selective Fluorescence Approach

We have monitored the environment and dynamics of the membrane interface formed by the ester-linked phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and the ether-linked phospholipid 1,2-dihexadecyl-sn-glycero-3-phosphocholine (DHPC) utilizing the wavelength-selective fluorescence approach and using the fluorescent membrane probe 2-(9-anthroyloxy)stearic acid (2-AS). This interfacially localized probe offers a number of advantages over those which lack a fixed location in the membrane. When incorporated in membranes formed by DPPC and DHPC, 2-AS exhibits red edge excitation shift (REES) of 14 and 8 nm, respectively. This implies that the rate of solvent reorientation, as sensed by the interfacial anthroyloxy probe, in ester-linked DPPC membranes is slow compared to the rate of solvent reorientation in ether-linked DHPC membranes. In addition, the fluorescence polarization values of 2-AS are found to be higher in DHPC membranes than in DPPC membranes. This is further supported by wavelength-dependent changes in fluorescence polarization and lifetime. Taken together, these results are useful in understanding the role of interfacial chemistry on membrane physical properties.

The effect of merulinic acid on biomembranes

Merulinic acid (heptadecenylresorcinolic acid, resorcinolic acid) is one of the members of resorcinolic lipids, the natural amphiphilic long-chain homologues of orcinol (1,3-dihydroksy-5-methylbenzene). In the present study, membrane properties of merulinic acid were investigated. Merulinic acid exhibits strong haemolytic activity against sheep erythrocytes (EH 50 of 5±2 μM) regardless of the form of its application—direct injection into the erythrocyte suspension or injection as merulinic acid-enriched liposomes. The lysis of erythrocytes induced by merulinic acid was inhibited by the presence of divalent cations. The effectivity of the protection of erythrocytes was highest for Zn 2+ and weakest for Mn 2+. Merulinic acid at low concentrations also exhibits the ability for protection of cells against their lysis in hypoosmotic solutions. This protective effect is significant as, at 10 μM concentration of merulinic acid, the extent of osmotically induced cell lysis is reduced by approximately 40%. Merulinic acid induces increased permeability of liposomal vesicles. This effect was shown to be dependent on the composition of liposomal bilayer and it was stronger when lipid bilayer contained glycolipids (MGDG and DGDG) and sphingomyelin. Changes of TMA-DPH and NBD-PE fluorescence polarization show that the degree of merulinic acid incorporation into liposomal membrane is not very high. The polar “heads” of the molecules of investigated compounds are localized on the level of fatty acid's ester bonds in phospholipid molecules. Merulinic acid caused the increased fluorescence of the membrane potential fragile probe. This indicated an alteration of the surface charge and a decrease of the local pH at the membrane surface. This effect was visible in both low- and high-ionic strength environment. Merulinic acid causes also a decrease in activity of the membrane-bound enzyme acetylcholinesterase.

Identification of intermediates in the bile acid synthetic pathway as ligands for the farnesoid X receptor

Bile acid synthesis from cholesterol is tightly regulated via a feedback mechanism mediated by the farnesoid X receptor (FXR), a nuclear receptor activated by bile acids. Synthesis via the classic pathway is initiated by a series of cholesterol ring modifications and followed by the side chain cleavage. Several intermediates accumulate or are excreted as end products of the pathway in diseases involving defective bile acid biosynthesis. In this study, we investigated the ability of these intermediates to activate human FXR. In a cell-based reporter assay and coactivator recruitment assays in vitro, early intermediates possessing an intact cholesterol side chain were inactive, whereas 26- or 25-hydroxylated bile alcohols and C27 bile acids were highly efficacious ligands for FXR at a level comparable to that of the most potent physiological ligand, chenodeoxycholic acid. Treatment of HepG2 cells with these precursors repressed the rate-limiting cholesterol 7alpha-hydroxylase mRNA level and induced the small heterodimer partner and the bile salt export pump mRNA, indicating the ability to regulate bile acid synthesis and excretion. Because 26-hydroxylated bile alcohols and C27 bile acids are known to be evolutionary precursors of bile acids in mammals, our findings suggest that human FXR may have retained affinity to these precursors during evolution.

Cholesterol modulates ligand binding and G-protein coupling to serotonin1A receptors from bovine hippocampus

The serotonin 1A (5-HT 1A ) receptor is an important member of the superfamily of seven-transmembrane domain G-protein-coupled receptors. We have examined the modulatory role of cholesterol on the ligand binding activity and G-protein coupling of the bovine hippocampal 5-HT 1A receptor by depleting cholesterol from native membranes using methyl-β-cyclodextrin (MβCD). Removal of cholesterol from bovine hippocampal membranes using varying concentrations of MβCD results in a concentration-dependent reduction in specific binding of the agonist 8-OH-DPAT to 5-HT 1A receptors. This is accompanied by alterations in binding affinity and sites obtained from analysis of binding data. Importantly, cholesterol depletion affected G-protein-coupling of the receptor as monitored by the GTP-γ-S assay. The concomitant changes in membrane order were reported by changes in fluorescence polarization of membrane probes such as DPH and TMA-DPH, which are incorporated at different locations (depths) in the membrane. Replenishment of membranes with cholesterol led to recovery of ligand binding activity as well as membrane order to a considerable extent. Our results provide evidence, for the first time, that cholesterol is necessary for ligand binding and G-protein coupling of this important neurotransmitter receptor. These results could have significant implications in understanding the influence of the membrane lipid environment on the activity and signal transduction of other G-protein-coupled transmembrane receptors.

Cholesterol modulates ligand binding and G-protein coupling to serotonin 1A receptors from bovine hippocampus

The serotonin 1A (5-HT 1A) receptor is an important member of the superfamily of seven-transmembrane domain G-protein-coupled receptors. We have examined the modulatory role of cholesterol on the ligand binding activity and G-protein coupling of the bovine hippocampal 5-HT 1A receptor by depleting cholesterol from native membranes using methyl-β-cyclodextrin (MβCD). Removal of cholesterol from bovine hippocampal membranes using varying concentrations of MβCD results in a concentration-dependent reduction in specific binding of the agonist 8-OH-DPAT to 5-HT 1A receptors. This is accompanied by alterations in binding affinity and sites obtained from analysis of binding data. Importantly, cholesterol depletion affected G-protein-coupling of the receptor as monitored by the GTP-γ-S assay. The concomitant changes in membrane order were reported by changes in fluorescence polarization of membrane probes such as DPH and TMA-DPH, which are incorporated at different locations (depths) in the membrane. Replenishment of membranes with cholesterol led to recovery of ligand binding activity as well as membrane order to a considerable extent. Our results provide evidence, for the first time, that cholesterol is necessary for ligand binding and G-protein coupling of this important neurotransmitter receptor. These results could have significant implications in understanding the influence of the membrane lipid environment on the activity and signal transduction of other G-protein-coupled transmembrane receptors.

GP005 Identification of the Streptococcus pyogenes fas two-component signal transduction system-controlled regulon using differential proteome analysis

Physical properties of Escherichia coli membrane lipids in logarithmic- and stationary-phase cells were studied by measuring the fluorescence polarization change of cis- and trans-parinaric acid as a function of temperature. In aqueous dispersions of phospholipids extracted from cytoplasmic and outer membranes of cells of differing growth phase, a similar polarization increase was observed over the range from physiological temperature to below 0°C, and nearly the same transition ratios were obtained in all samples. The cytoplasmic membrane of both of the growth-phase cells showed a higher polarization ratio above the transition temperatures, compared to that in the aqueous dispersion of phospholipids. The polarization ratios below the transition temperatures of these specimens were lower than the value obtained with the lipids, especially in the stationary-phase specimens. The outer membrane specimens showed a similar polarization change but the transition temperature ranges were considerably higher both in the logarithmic- and the stationary-phase specimens, compared to those in the cytoplasmic membrane specimens. Freeze-thawing of logarithmic-phase cells showed the emergence of activity of certain enzymes which are known to be located in the membranes. The stationary-phase cells did not suffer from any such deleterious effect and maintained a high level of cell viability in a similar treatment. These results indicate that in the stationary-phase cell membranes lipids are in a highly ordered state, and the lipid state causes a membrane stability which results in the high resistance of the cell to freeze-thawing.

A tubulin-based fluorescent polarization assay for paclitaxel

This paper reports the development, characterization, and application of a separation-free, homogeneous, and simple to perform fluorescence polarization bioassay for paclitaxel. The bioassay is based on the binding interaction of paclitaxel to tubulin, the receptor protein on which this drug acts. The bioassay was carried out in a competitive format where the paclitaxel and a synthetic fluorescent-labeled paclitaxel (Rh-Tx) competed for tubulin binding, causing a change in fluorescence polarization, which was an inverse function of the paclitaxel concentration. The bioassay had a dynamic range from 0.03 to 0.35 μM, which falls in the therapeutic range (0.01–10 μM), and a limit of detection of 23 nM. The bioassay was selective against other naturally occurring taxanes such as baccatin III and 10-deacetylbaccatin III. However, there was interference from cephalomannine. The excellent sensitivity, accuracy, reproducibility, and simplicity make this analytical technique suitable for routine and high-throughput analyses and might be helpful in providing better care for patients. The bioassay was successfully applied to the determination of paclitaxel in human plasma.

Simultaneously monitoring DNA binding and helicase-catalyzed DNA unwinding by fluorescence polarization.

A new method for helicase-catalyzed DNA unwinding is described. This assay takes advantage of the substantial change in fluorescence polarization (FP) upon helicase binding and DNA unwinding. The low anisotropy value, due to the fast tumbling of the free oligonucleotide in solution, increases abruptly upon binding of helicase to the fluorescein-labeled oligonucleotide. The high anisotropy of the helicase- DNA complex decreases as the fluorescein-labeled oligonucleotide is released from the complex through helicase-catalyzed DNA unwinding. This FP signal can be measured in real time by fluorescent spectroscopy. This assay can simultaneously monitor DNA binding and helicase-catalyzed DNA unwinding. It can also be used to determine the polarity in DNA unwinding mediated by helicase. This FP assay should facilitate the study of the mechanism by which helicase unwinds duplex DNA, and also aid in screening for helicase inhibitors, which are of growing interest as potential anticancer agents.

Fluorescence Polarization Assay and SDS-PAGE Confirms Matrilysin Degrades Fibronectin and Collagen IV whereas Gelatinase: A Degrades Collagen IV but not Fibronectin

Matrilysin and gelatinase A are hypothesized to have significant roles in uterine and ovarian function. However, proteolytic activity assays for these enzymes are limited. We describe the development of simple and rapid assays for the proteolysis of fluorescein-labeled full-length substrates, collagen IV (Col-IV) and fibronectin (FN), and demonstrate the selectivity of matrilysin (MMP-7) compared to gelatinase A (MMP-2) for fibronectin. Changes in fluorescence intensity (FIU) and fluorescence polarization (mP) resulting from the protease activity of matrilysin and gelatinase A were measured. These studies show that the fluorescently labeled substrates, Col-IV and FN, are as reliable and amenable to rapid in vitro assay as peptide substrates. In addition, they are easier to use than previously described, non-fluorescent methods. The results demonstrate that assays using full-length, biological matrix proteins are more sensitive indicators of MMP-specific substrate activity than peptide based assays.

Regulation of ncd by the oligomeric state of tubulin

We have compared the interaction of ncd (non-claret disjunctional), a kinesin related protein, with microtubules and tubulin heterodimer. Ultracentrifugation experiments revealed that the ncd motor domain, residues 335–700 (ncd335), does not induce tubulin polymerization but stabilizes pre-formed microtubules with a maximum effect at a 1:1 ncd335:tubulin ratio. Ncd335 binding to tubulin or microtubules was estimated by following the change in fluorescence polarization of an exogenous dye attached to Cys670 of ncd335. Ncd335 binding to tubulin (containing GTP or GDP-bound) is characterized by a 2:1 stoichiometry, a higher affinity and an increased sensitivity towards salt, ADP, ATP and AMPPNP, as compared with ncd335 binding to microtubules. Maximum ATPases were 0.06–0.08 sec −1 and 1.8–2.0 sec −1 for the ncd335-tubulin and ncd335-microtubules complexes, respectively. Only the polymerized complex is fully functional, suggesting the presence of additional contacts between adjacent protofilaments. Moreover, the data reveal that the oligomeric state of microtubules is a potent regulator for the activity of kinesin related proteins.

Kinase Assay Based on Thiophosphorylation and Biotinylation

Protein kinases catalyze the transfer of the gamma-phosphate group from ATP to a serine, threonine or tyrosine residue of an acceptor protein. These enzymes play an important role in signal transduction. New inhibitors for these enzymes are actively being sought. In this article, we present a novel approach for detecting the activity of protein kinases, which could be useful for the high-throughput screening of chemical libraries. The method is based on the use of ATP gamma S instead of ATP in the phosphorylation reaction. This results in the transfer of a thiophosphate group onto a fluorescein-labeled acceptor peptide substrate. The mixture is then treated with a sulfur-reactive iodoacetyl derivative of biotin, which leads to the modification of the nucleophilic sulfur of the thiophosphate group and the generation of a fluorescently labeled, biotinylated molecule. Finally, streptavidin is added to the mixture and it binds to all biotinylated molecules present. The binding of streptavidin to the thiophosphorylated and biotinylated kinase substrate can be conveniently detected by measuring the change in fluorescence polarization of the fluorescent dye attached to the peptide. The detection of kinase inhibitors is demonstrated. The method is completely homogeneous and does not require any separation steps.

Fluorescence polarization studies on four biliproteins and a bilin model for phycoerythrin 545

Fluorescence (excitation) polarization spectroscopy in the wavelength region of the bilin chromophores was applied to phycoerythrocyanin (CV-phycocyanin), phycocyanins 645 and 612, and phycoerythrin 545. The cryptomonad biliproteins – phycoerythrin 545 and phycocyanins 612 and 645 – were studied as both protein dimers having an α 2β 2 polypeptide structure and as αβ monomers. The cyanobacterial phycoerythrocyanin (CV-phycocyanin) was a trimeric oligomer. The changes in polarization across the spectrum were attributed to transfers of energy between bilins. Cryptomonad biliproteins are isolated as dimers. The similarities between their steady-state fluorescence polarization spectra and those of the corresponding monomers suggested that the monomers’ conformations were analogous to the dimers. This supports the use of monomers in the study of dimer bilin organization. The unusual polarization spectrum of phycoerythrin 545 was explained using a model for the topography of its bilins. Obtaining the emission spectra of phycoerythrin 545 at several temperatures and a deconvolution of the dimer circular dichroism spectrum also successfully tested the bilin model. Circular dichroism spectroscopy was used to determine which polarization changes are formed by Förster resonance energy transfers and which may be produced by internal conversions between high- and low-energy states of pairs of exciton-coupled bilins. Attempts were made to assign energy transfer events to the corresponding changes in fluorescence polarization for each of the four biliproteins.

Dynamics of single dye molecules observed by confocal imaging and spectroscopy

The fluorescence emission of single rhodamine dye molecules (rhodamine 6G and rhodamine 630) at room temperature was analyzed by using scanning confocal laser microscopy in conjunction with polarization analysis, fluorescence spectroscopy, time-resolved detection (minutes to microseconds), and excitation saturation. Results are presented and discussed 1) for samples with dye molecules at the glass-air interface and 2) covered with an additional thin protective polymer film (polyvinylbutyral). Under the polymer layer, the single-molecule fluorescence was more stable than the glass-air interface. This result may be explained by fewer spontaneous variations of the fluorescence rate, polarization changes, spectral shifts, and longer photochemical lifetimes.

The constituent tryptophans and bisANS as fluorescent probes of the active site and of a secondary binding site of stromelysin-1 (MMP-3).

The active site of the catalytic domain of stromelysin-1 (matrix metalloproteinase-3, MMP-3) was probed by fluorescence quenching, lifetime, and polarization of its three intrinsic tryptophans and by the environmentally sensitive fluorescent reporter molecule bisANS. Wavelength-dependent acrylamide quenching identified three distinct emitting tryptophan species, only one of which changes its emission and fluorescence lifetime upon binding of the competitive inhibitor Batimastat. Significant changes in the tryptophan fluorescence polarization occur upon binding by any of the three hydroxamate inhibitors Batimastat, CAS108383-58-0, and Celltech CT1418, all of which bind in the P2'-P3' region of the active site. In contrast, the inhibitor CGS27023A, which is thought to bind in the P1-P1' region, does not induce any change in tryptophan fluorescence polarization. The use of the fluorescent probe bisANS revealed the existence of an auxiliary binding site extrinsic to the catalytic cleft. BisANS acts as a competitive inhibitor of stromelysin with a dissociation constant of Ki=22 microM. In addition to this binding to the active site, it also binds to the auxiliary site with a dissociation constant of 3.40+/-0.17 microM. The auxiliary site is open, hydrophobic, and near the fluorescing tryptophans. The binding of bisANS to the auxiliary site is greatly enhanced by Batimastat, but not by the other competitive inhibitors tested.