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The fluorescent nucleotide analogue 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine (5'-FSB epsilon A) reacts irreversibly with bovine liver glutamate dehydrogenase and modifies one of the natural inhibitory guanosine 5'-triphosphate (GTP) sites [Jacobson, M.A., & Colman, R.F. (1982) Biochemistry 21, 2177-2186]. Enzyme with 1.28 mol of 5'-(p-sulfonylbenzoyl)-1,N6-ethenoadenosine/mol of subunit incorporated and exhibiting maximum change in sensitivity to GTP inhibition is now shown by amino acid analysis to contain 0.95 mol of O-[(4-carboxyphenyl)sulfonyl]tyrosine (CBS-Tyr) and 0.33 mol of N epsilon-[(4-carboxyphenyl)sulfonyl]-lysine (CBS-Lys), quantitatively accounting for the total incorporation prior to acid hydrolysis. As a function of time of incubation with 5'-FSB epsilon A, the amount of CBS-Tyr formed was directly proportional to the change in GTP inhibition. In contrast, an initial formation of CBS-Lys was observed, followed by relatively little additional CBS-Lys although the percent change in GTP inhibition continued to increase. It was concluded that the tyrosine is an essential residue in the GTP binding site of glutamate dehydrogenase, while the lysine modified is not involved in the inhibitory action of GTP. The nucleotide analogue 2'(3')-O-(2,4,6-trinitrophenyl)adenosine 5'-diphosphate (TNP-ADP) was evaluated for its ability to occupy the adenosine 5'-diphosphate (ADP) activator site and to function as an energy acceptor conjointly with 5'-SB epsilon A covalently bound at the GTP site as the energy donor. TNP-ADP activates native enzyme 2-fold and competes kinetically with ADP. As determined by fluorometric titration, the maximum number of TNP-ADP binding sites on native enzyme was 0.5 mol/mol of subunit in the absence and 1 mol/mol of subunit in the presence of reduced coenzyme. The 5'-SB epsilon A-modified enzyme also binds TNP-ADP: 0.5 mol/mol of subunit in the absence or presence of reduced coenzyme. TNP-ADP competes for binding with ADP to native and 5'-SB epsilon A-modified enzyme, indicating that this nucleotide analogue is a satisfactory fluorescent probe of the ADP site of glutamate dehydrogenase. An energy-transfer efficiency of 0.77 was determined from the decrease in donor fluorescence upon addition of TNP-ADP in the absence of reduced coenzyme to modified enzyme containing 1.23 mol of 5'-SB epsilon A/mol of subunit. A value of 18 A was calculated as the average distance between the GTP and ADP regulatory sites. This result indicates that the inhibitory GTP and the activatory ADP sites are close but not identical.

The folding and organization of apolipoprotein A-I (apoA-I) in discoidal, high-density lipoprotein (HDL) complexes with phospholipids are not yet completely resolved. For about 20 years, it was generally accepted that the amphipathic helices of apoA-I lie parallel to the acyl chains of the phospholipids ("picket fence" model). However, based on the X-ray crystal structure of a large, lipid-free fragment of apoA-I, a "belt model" was recently proposed. In this model, the helices of two antiparallel apoA-I molecules are extended in a circular arrangement and lie perpendicular to the phospholipid acyl chains. To obtain conclusive information on the spatial organization of apoA-I in discoidal HDL, we engineered three separate cysteine mutants of apoA-I (D9C, A124C, A232C) for specific labeling with the fluorescence probes ALEXA-488 or ALEXA-546 (fluorescein and rhodamine derivatives). The labeled apoA-I was reconstituted into well-defined HDL complexes containing two molecules of protein and dipalmitoylphosphatidylcholine, and the complexes were used in three quantitative fluorescence resonance energy transfer (FRET) experiments to determine the distances between two specific sites in an HDL particle. Comparison of the distances measured by FRET (4.7-7.8 nm) with those predicted from the existing models indicated that neither the picket fence nor the belt model can account for the experimental results; rather, a hairpin folding of each apoA-I monomer with most helices perpendicular to the phospholipid acyl chains and a random head-to-tail and head-to-head arrangement of the two apoA-I molecules in the HDL particles are strongly suggested by the distance and lifetime data.

To obtain information about the interaction of tropomyosin (Tm) with actin associated with the regulatory states of the muscle thin filament, we used luminescence resonance energy transfer (LRET) between Tb(3+) as a donor and rhodamine as an acceptor. A novel Tb(3+) chelator, S-(2-nitro-5-thiobenzoate)cysteaminyl-DTPA-Cs124, was synthesized, which specifically labels Cys groups in proteins. With the Tb chelate as the donor and tetramethylrhodamine-5-maleimide as the acceptor, both bound to specific Cys groups of Tm, we obtained 67 A as the distance between Tm's across the actin filament, a much shorter value than that obtained from structural studies (72-86 A). The difference appears to be due to submillisecond motion associated with Tm flexibility, which brings the probes closer during the millisecond lifetime of the donor. Ca(2+) did not change the energy transfer with the reconstituted thin filament, but myosin subfragment 1 decreased the transfer, consistent with either a 5-6 A increase in distance or, more likely, a decrease in flexibility.

The location of several fluorescent chromophores in lipoproteins has been determined by using resonance energy transfer. The primary acceptor is 5-(N-hexadecanoylamino)fluorescein whose chromophore is shown to reside at the lipoprotein surface at pH 7.4. Polar donors include cis-parinaric acid (cis,trans,trans,cis-9,11,13,15-octadecatetraenoic acid), trans-parinaric acid (all-trans-9,11,13,15-octadecatetraenoic acid), and 16-(9-anthroyloxy)palmitic acid; nonpolar donors are parinaric acid methyl ester, parinaric acid cholesteryl ester, and 1,6-diphenyl-1,3,5-hexatriene. The polar donors transfer more efficiently than the nonpolar donors in several classes of lipoprotein particles. The data are analyzed by a simple mathematical model from which it is concluded that the polar donors are localized in the putative lipoprotein surface monolayer; the possibility that nonpolar donors are partitioned between the surface and core of lipoproteins is considered.

The distance from the protein surface to ferric or manganic ions in the two specific metal-binding sites of human serum transferrin has been estimated by measuring energy transfer from freely diffusing terbium chelaters in aqueous solution to transferrin-bound metal ions. In addition, both monoferric forms of the protein were studied, as well as the diferric complex formed by using oxalate instead of (bi)carbonate as the auxiliary anion in binding of iron(III) to transferrin. Second-order rate constants for energy transfer between electrically neutral terbium(III)--N-(2-hydroxy-ethyl)ethylenediaminetriacetate and the FeA, FeB, and Fe2 forms of transferrin were 0.9 X 10(5) M-1 S-1, 1.4 X 10(5) M-1 S-1, and 2.6 X 10(5) M-1 S-1, respectively (based on iron concentraton). For the Fe2 species, substitution of oxalate for (bi)carbonate has the effect of decreasing the accessibility of both electrically neutral and negatively charged terbium chelates to the protein-bound iron chromophores. Theoretical considerations of the effect of acceptor location in the protein on energy transfer suggest that the iron chromophores are not on the surface of the protein but are less than 1.7 nm below the surface. The use of diterbium transferrin as energy donor to a small cobalt chelate in solution or to diferric transferrin corroborates these results.

Nonradiative fluorescence energy transfer (FET) is thought to be a highly sensitive measure of distance, occurring through a dipole coupling (Forster) mechanism in which the efficiency of FET depends on the inverse sixth power of the distance between fluorophores. The current work assesses the utility of FET for measuring distances in duplex and branched DNA molecules. The apparent efficiencies of FET between donor (fluorescein) and acceptor (eosin) fluorophores attached to opposite ends of oligonucleotide duplexes of varying length were determined; the results suggest that FET is a useful qualitative indicator of distance in DNA molecules. However, the apparent FET efficiency values cannot be fit to the Forster equation without the specification of highly extended DNA-to-fluorophore tethers and motionally restricted fluorophores, conditions that are unlikely to coexist. Three other lines of evidence further suggest that factors in addition to Forster transfer contribute to apparent FET in DNA: (1) The efficiency of FET appears to depend on the base sequence in some instances. (2) Donor fluorescence changes with the extent of thermally induced DNA melting in a sequence-dependent fashion, indicating dye-DNA interactions. (3) The distances between the ends of various pairwise combinations of arms of a DNA four-way junction do not vary as much as expected from previous work. Thus, the occurrence of any nondipolar effects on energy transfer in oligonucleotide systems must be defined before distances in DNA molecules can be quantified by using FET.

Neutrophil elastase (NE), a mediator of inflammation, binds with high affinity numerous anionic molecules including suramin, a polysulfated naphthylurea, which inhibits it with a Ki of 0.2 microM and a 4:1 suramin:NE stoichiometry and thus constitutes a potential therapeutic agent. In an attempt to locate the suramin molecules on NE, we investigated the NE-suramin interaction using steady-state and time-resolved fluorescence spectroscopy. The time-resolved intensity decay of NE, a protein with three Trp residues, in positions 27, 141, and 237 (chymotrypsin numbering system) was best described by a three-exponential function with lifetimes ranging from 0.22 to 2.28 ns. Comparison of the accessibility of the three lifetime classes to the fluorescence quenchers acrylamide and iodide with the computed solvent accessibility of the three Trp residues in the crystal structure of NE indicates that the main, if not the sole, contribution to the 2.28 ns lifetime class is brought about by the fully buried Trp 141 residue. The addition of suramin to NE induces a sharp decrease in NE fluorescence and a corresponding increase in suramin fluorescence due to an efficient fluorescence resonance energy transfer (FRET) between the Trp residues of NE, acting as donors, and the naphthalene rings of suramin, behaving as acceptors. From the fate of the longest lifetime class in the presence of variable suramin concentrations, we deduce that two suramins are bound at less than 17 A from Trp 141, whereas the two others are located at least 29 A from Trp 141. Moreover, neither the binding of suramin to NE nor the FRET process was modified when NE was complexed with a peptide chloromethylketone inhibitor, suggesting that suramin does not directly interfere with the substrate binding site of NE. These data were used as constraints to model the NE-suramin complex.

We have used resonance energy transfer to read out the interactions of the alpha subunit of transducin (alpha T) with the transducin beta gamma subunit complex (beta gamma T) and to compare the rate of aluminum fluoride-induced alpha T activation, as reflected by the enhancement of the alpha T tryptophan fluorescence, with the rate for the dissociation of holotransducin into its component subunits. Specifically, a beta gamma T complex that was labeled with 5-(iodoacetamido)fluorescein (IAF-beta gamma T) served as a donor for resonance energy transfer and an alpha T-GDP species labeled with eosin 5-isothiocyanate (EITC-alpha TGDP) served as the acceptor. The quenching of IAF-beta gamma T fluorescence emission by the addition of the EITC-alpha TGDP species, due to resonance energy transfer between the IAF and EITC moieities, ranged from 10% to 15%. The association of the transducin subunits was rapid (i.e., within the time period of mixing) and dose-dependent, yielding an apparent Kd of approximately 150 nM for the alpha TGDP/beta gamma T interaction. Unexpectedly, we find that the dissociation of IAF-beta gamma T from an aluminum fluoride-activated alpha TGDP/IAF-beta gamma T complex occurs prior to the onset of the intrinsic fluorescence changes in alpha T that accompany activation of this subunit. Thus, there are at least two structural changes in alpha T that result from the occupation of the gamma-phosphate position in the nucleotide binding cleft of alpha T by aluminum fluoride.(ABSTRACT TRUNCATED AT 250 WORDS)

Resonance energy transfer was used to study the structure of cytochrome b5 and its nonpolar segment reconstituted into sonicated vesicles of dimyristoylphosphatidylcholine. The n-(9-anthroyloxy) (AO) fatty acid probes were added to these vesicles, and energy-transfer measurements were carried out between tryptophan and AO, tryptophan and the heme moiety of cytochrome b5, and AO and heme. Results of these measurements were analyzed by using the methods outlined in the previous paper [Kleinfeld, A. M. (1985) Biochemistry (preceding paper in this issue)]. We find, in agreement with Fleming et al. [Fleming, P. J., Koppel, D. E., Lau, A. L. Y., & Strittmatter, P. (1979) Biochemistry 18, 5458-5464], that the fluorescent tryptophan in both forms of the protein is buried about 20 A from the surface and that most of the fluorescence is associated with a single tryptophan. The results are consistent with the AO probe distance of closest approach to the protein, greater for whole b5 than for the nonpolar peptide. The tryptophan-heme and AO-heme measurements indicate that the heme moiety is about 15 A from the surface of the membrane. The agreement of our results with the previous studies supports the description of tryptophan-AO energy transfer outlined in the preceding paper.