Synthesis and Characterization of Stacked and Quenched Uridine Nucleotide Fluorophores

Abstract

Since the seminal work of Weber and Laurence (1) with 1-anilinonaphthalene-8-sulfonic acid, extrinsic fluorescent probes have been extensively used to monitor various aspects of protein-ligand or enzyme-substrate interactions. Among others, these probes have been used (i) to establish the degree of polarity or hydrophobicity of a particular region of a protein, (ii) to measure the distance between groups on protein surface, (iii) to measure the extent of flexibility of protein in solution, (iv) to measure the rate of very rapid conformational transitions, and (v) to measure kinetic constants of interaction between protein and ligand (2). To facilitate these studies, a variety of derivatized fluorescent ligands or substrate analogs have been synthesized over the years without any serious attention being given to their solution conformations or their transitions to new conformations on interaction with the target proteins. Such conformational transitions are often crucial steps in biological interactions as typically exemplified by NAD, the common cofactor for a very large number of dehydrogenases. The molecule exhibits reversible stacking between the adenine and pyridine moiety with both the open and the closed forms in rapid interconversionary equilibrium in aqueous solutions (3, 4). During catalysis, NAD takes a totally extended conformation on the enzyme surface; the conserved tertiary structure of the pyridine nucleotide binding site being a very characteristic feature of all these oxidoreductases (5).Etheno-ATP was originally synthesized as a fluorescent analog of ATP. It had a high quantum yield and a long fluorescence lifetime and could be used to follow ATP interactions primarily by polarization studies (6 -8). In contrast, as in case of NAD, significant population of etheno-NAD was in a folded conformation in aqueous solution as a result of aromatic interactions between the pyridine and the modified adenine moiety, leading to dynamic collisional quenching of fluorescence and short fluorescence life-time (9). This stacked and quenched fluorophore was brilliantly used to establish negative co-operativity for glyceraldehyde-3-phosphate dehydrogenase from rabbit muscle for the binding of the tetrameric apoenzyme to the coenzyme. The conformational transition of etheno-NAD from folded to stretched conformation as reflected by its enhanced fluorescence on interaction with the target protein was the monitoring parameter for this purpose (10). Although stacked fluorophore with quenched fluorescence can be of immense use in protein-ligand binding studies, as is exemplified by etheno-NAD, it is surprising to note that no deliberate effort has so far been made to design such compounds taking advantage of the potential aromatic interaction between the attached fluorophore and a suitable moiety of the desired biomolecule.The interaction between aromatic rings is of wide chemical and biological interest, because it plays important roles in vital biological processes, such as stabilization of protein and nucleic acid s...

An Arginine Residue Is Essential for Stretching and Binding of the Substrate on UDP-glucose-4-epimerase from Escherichia coli

“…In the previous paper we had shown that when a uridine nucleotide is derivatized with a suitable aromatic fluorophore such as AmNS via a phosphoramidate bond through the terminal phosphate, it takes a stacked conformation in aqueous solution that is in rapid equilibrium with its extended form (15). The dynamic collisional quenching of fluorescence in the stacked form should make such strongly quenched fluorophores eminently suitable as probes for protein or enzyme studies provided such designed molecules satisfy the following conditions.…”

“…Because the destacking energy was calculated to be 2.3 Kcal/mol for UDPAmNS (previous paper; Ref. 15), the binding energy for the UDP moiety of the substrate may be assumed to have a minimal value of that order.…”

“…Synthetic Fluorophores and Fluorescence Measurements-UDPAmNS and other AmNS derivatives were synthesized and purified according the methods described in our preceeding paper (15). Wherever necessary, excess ligands and reagents were removed from reaction mixtures by Sephadex G-50 spin column centrifugation as described by Maniatis et al (19).…”

“…2A shows the fluorescence spectra of UDPAmNS (9.3 M) as the concentration of epimerase was progressively increased in the cuvette. Quite evidently, the stacked and quenched fluorophore assumes a stretched conformation on interaction with the enzyme and hence is relieved of its quenching (15). Fig.…”

“…Quenching is fully released when complete destacking takes place (15). To explore the possibility of whether such designed fluorophores can be used to probe conformational transitions of a putative ligand as it interacts with its target protein, we used UDPAmNS as the probe and the E. coli epimerase as the model target enzyme for this purpose.…”