Fluorescent probe of ribonuclease A conformation

Analysis of the redox regulation of protein tyrosine phosphatase superfamily members utilizing a cysteinyl-labeling assay

The catalytic activity of protein tyrosine phosphatase (PTP) superfamily members is regulated by the reversible oxidation of their invariant catalytic Cys residue in vivo. Transient and specific regulation of PTP activity by reactive oxygen species (ROS) attenuates dephosphorylation and, thereby, promotes phosphorylation, hence facilitating signal transduction. We have recently developed a modified cysteinyl-labeling assay [Boivin, B., Zhang, S., Arbiser, J. L., Zhang, Z. Y., and Tonks, N. K. (2008). Proc. Natl. Acad. Sci. USA105, 9959-9964.] that showed broad selectivity in detecting reversible oxidation of members from different PTP subclasses in platelet-derived growth factor (PDGF)-BB overexpressing cells. Herein, we applied this assay, which utilizes the unique chemistry of the invariant catalytic Cys residue to enrich and identify PTPs that are reversibly oxidized upon acute growth factor stimulation. Performing the cysteinyl-labeling assay with Rat-1 fibroblasts enabled us to capture both PTEN and SHP-2 as a consequence to acute PDGF-BB stimulation. Given the ability of this assay to detect reversible oxidation of a broad array of members of the PTP family, we anticipate that it should permit profiling of the entire ROS-regulated PTPome in a wide array of signaling paradigms.

Thiol-selective fluorogenic probes for labeling and release

Thiol alkylation is a powerful technique for the labeling of proteins. We report a new class of highly reactive, selective, and fluorogenic probes for thiols in aqueous solution at neutral pH, based on the 7-oxanorbornadiene (OND) framework. The maleate moiety in 7-oxabicyclo[2.2.1]hept-2,5-diene-2,3-dicarboxylic acid esters serves as both a tunable electrophile and an intramolecular quencher of an attached dansyl fluorophore. Thiols have been found to add with high rates (second-order rate constants of 40-200 M(-1) s(-1)) to give adducts that exhibit enhancements of fluorescence intensity up to 180-fold. The resulting adducts are also versatile with respect to cleavage (release) reactions by two mechanisms. First, retro-Diels-Alder fragmentation occurs with half-lives from days to weeks at room temperature, and an epoxide derivative is also reported that is incapable of cycloreversion cleavage. Second, monoamide OND derivatives undergo rapid closure to succinimides upon thiol addition, providing a thiol-triggered mechanism for immediate alcohol release. Peptides and proteins containing free thiol groups were labeled with OND electrophiles with high chemoselectivity. Since the system is so easily assembled from readily accessible modules, various functional groups can be added to OND linkers to allow the attachment of other molecules of interest.

Global methods to monitor the thiol-disulfide state of proteins in vivo

Cysteines play an important role in protein biochemistry. The unique chemical property and high reactivity of the free thiol group makes reduced cysteine a versatile component of catalytic centers and metal binding sites in many cytosolic proteins and oxidized cystine a stabilizing component in many secreted proteins. Moreover, cysteines readily react with reactive oxygen and nitrogen species to form reversible oxidative thiol modifications. As a result, these reversible thiol modifications have found a use as regulatory nano-switches in an increasing number of redox sensitive proteins. These redox-regulated proteins are able to adjust their activity quickly in response to changes in their redox environment. Over the past few years, a number of techniques have been developed that give insight into the global thiol-disulfide state of proteins in the cell. They have been successfully used to find substrates of thiol-disulfide oxidoreductases and to discover novel redoxregulated proteins. This review will provide an overview of the current techniques, focus on approaches to quantitatively describe the extent of thiol modification in vivo, and summarize their applications.

Protein adsorption orientation in the light of fluorescent probes: mapping of the interaction between site-directly labeled human carbonic anhydrase II and silica nanoparticles

Little is known about the direction and specificity of protein adsorption to solid surfaces, a knowledge that is of great importance in many biotechnological applications. To resolve the direction in which a protein with known structure and surface potentials binds to negatively charged silica nanoparticles, fluorescent probes were attached to different areas on the surface of the protein human carbonic anhydrase II. By this approach it was clearly demonstrated that the adsorption of the native protein is specific to limited regions at the surface of the N-terminal domain of the protein. Furthermore, the adsorption direction is strongly pH-dependent. At pH 6.3, a histidine-rich area around position 10 is the dominating adsorption region. At higher pH values, when the histidines in this area are deprotonated, the protein is also adsorbed by a region close to position 37, which contains several lysines and arginines. Clearly the adsorption is directed by positively charged areas on the protein surface toward the negatively charged silica surface at conditions when specific binding occurs.

Substrate and cofactor binding to fluorescently labeled cytoplasmic malate dehydrogenase

Cytoplasmic malate dehydrogenase (cMDH) is a key enzyme in several metabolic pathways. Though its activity has been examined extensively, there are lingering mechanistic uncertainties involving substrate and cofactor binding. To more completely understand this enzyme's interactions with cofactor and substrate ligands, a fluorescent reporter group was introduced into the enzyme's structure. This was accomplished by selective modification of Cys 110. The reaction placed an aminonaphthaline sulfonic acid group near the enzyme's active site. Substrate, inhibitor, and NAD binding activities were characterized using changes in this label's fluorescence. Results demonstrated that both substrate and cofactor molecules bound to the enzyme in the absence of their companion ligands. This is in contrast to strictly ordered cofactor then substrate binding as has been suggested by kinetic analyses of closely related enzymes. Binding results also indicated that the cofactor, NAD, bound to cMDH in a negatively cooperative manner, but substrates and the inhibitor, hydroxymalonate, bound non-cooperatively. Multiple substrate binding modes were identified and interactions between substrate and cofactor binding were found.

Quenching by acrylamide and temperature of a fluorescent probe attached to the active site of ribonuclease

The fluorescence properties of ribonuclease labelled at its active site with N-(iodoacetylamino)-ethyl-5-naphthylamine-1-sulfonic acid have been studied at different temperatures and in the presence of acrylamide. The rate constant for the quenching of the fluorescence of labelled ribonuclease by acrylamide is apparently not limited by the "accessibility" of the probe: similar values are obtained for the native and denatured states of the protein. Instead, acrylamide seems to be a rather inefficient quencher of this fluorescent group [acetamidoamino)ethyl-5-naphthylamine-1-sulfonic acid), as shown by non-linear Stern-Volmer representations, biphasic decay kinetics, and a low value of the rate constant. The fluorescence intensity of the native state of the labelled protein is highly sensitive to temperature and exhibits a 20% decrease for an increase of temperature of from 10 degrees C to 30 degrees C, independent of solvent viscosity. This thermal quenching is specific for the native conformation and disappears when the protein is unfolded. When the fluorescence lifetime of the label is shortened by addition of acrylamide, the effect of temperature becomes identical for native and unfolded structures. This suggests that the cause of the thermal quenching is the presence of conformational fluctuations within the native protein which apparently take place in the time range from 35 to 200 ns.

Sulfhydryl groups of rabbit liver arylsulfatase A

Rabbit liver arylsulfatase A (aryl-sulfate sulfhydrolase, EC 3.1.6.1) monomers of 130 kDa contain two free sulfhydryl groups as determined by spectrophotometric titration using 5,5'-dithiobis(2-nitrobenzoate) and by labeling with the fluorescent probe 5-(iodoacetamidoethyl)aminonaphthalene-1-sulfonic acid. Fluorescence quenching data indicate that the reactive sulfhydryl is present in proximity to one or more tryptophan residues. Chemical modification of the sulfhydryl groups does not alter the distinctive pH-dependent aggregation property of the arylsulfatase A. The free sulfhydryls of the enzyme react with numerous sulfhydryl reagents. Based on the reactions of iodoacetic acid, methyl methanethiosulfonate, 5,5'-dithiobis(2-nitrobenzoate) and 5-(iodoacetamidoethyl)aminonaphthalene-1-sulfonic acid with the sulfhydryl groups of arylsulfatase A, it is concluded that free sulfhydryls are not essential for the enzyme activity. In contrast, the observed inactivation of the enzyme by p-hydroxymercuribenzoate or p-hydroxymercuriphenylsulfonate is probably due to a modification of a histidine residue, consistent with previous reports that histidine is near the active site of arylsulfatase A. p-Hydroxymercuribenzoate and p-hydroxymercuriphenylsulfonate are able to react both with cysteine and with histidine residues of the protein molecule.