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PubMed1995

alpha-Fluoro acid and alpha-fluoro amide analogs of acetyl-CoA as inhibitors of citrate synthase: effect of pKa matching on binding affinity and hydrogen bond length.

An alpha-fluoro acid analog and an alpha-fluoro amide analog of acetyl-CoA have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.7 A resolution. The structures are similar to those reported for the corresponding non-fluorinated analogs (Usher et al., 1994), with all forming unusually short hydrogen bonds to Asp 375. The alpha-fluoro amide analog binds with an affinity 1.5-fold lower than that of a previously described amide analog lacking the alpha-fluoro group. The alpha-fluoro acid analog binds with a 50-fold decreased affinity relative to the corresponding unfluorinated analog. The binding affinities are consistent with increased strengths of hydrogen bonds to Asp 375 with closer matching of pKa values between hydrogen bond donors and acceptors. The results do not support any direct correlation between hydrogen bond strength and hydrogen bond length in enzyme-inhibitor complexes.

Acetyl Coenzyme A↗
PubMed1975

Steroidal 21-diazo ketones: photogenerated corticosteroid receptor labels.

The 21-diazo derivatives of 9 alpha-fluoro- and 9 alpha-bromo-21 deoxycorticosterone, 21-deoxycorticosterone, and progesterone were synthesized for use as photoaffinity labels for corticosteroid receptors. In the isolated toad bladder system, 9 alpha-bromo-21-diazo-21-deoxycorticosterone was as active as d-aldosterone and more active than 9 alpha-fluoro-cortisol in augmenting active Na+ transport. The activities of 21-diazoprogesterone and progesterone were equal; both were much less potent than d-aldosterone, however. These results indicate that the 21-diazo derivatives had significant functional activity in the toad bladder system. The rat kidney slice system was used to estimate the relative affinities of the diazo steroids for aldosterone receptor sites by competition experiments. At 100-fold excess of competitor to [3-H]aldosterone, the order of affinities was 9 alpha-fluoro-21-diazo-21-deoxycorticosterone greater than 9 alpha-bromo-21-diazo-21-deoxycorticosterone greater than 21-diazoprogesterone. Moreover, 9 alpha-bromo-21-diazo-21-deoxycorticosterone reduced binding of [3-H]aldosterone to cytoplasmic and nuclear forms of the receptor proportionately. On the basis of competition for [3-H]corticosterone binding, presumably to corticosteroid-binding globulin (CBG), the order of affinities was 21-diazo-21-deoxycorticosterone greater than 21-diazoprogesterone greater than 9 alpha-bromo-21-diazo-21-deoxycorticosterone. These findings indicate that 21-diazo steroids may be suitable as photogenerated affinity labels for mineralocorticoid receptors. The tritiated derivative, [1,2-3-H]-9 alpha-bromo-21-diazo-21-deoxycorticosterone (specific activity 25 Ci/mol) was synthesized and used in model experiments on photogenerated covalent binding to rat plasma proteins. Irradiation with uv light resulted in binding of [1,2-3-H]-9 alpha-bromo-21-diazo-21-deoxycorticosterone to plasma proteins, that was resistant to extraction with methylene dichloride and did not exchange with unlabeled corticosterone. The diazocorticosteroids, therefore, may have the requisite functional and selectivity properties for photoaffinity labeling of corticosteroid-binding proteins. Further studies are needed, however, to assure that photogenerated labeling with these steroids was site specific.

Animals↗
PubMed1996

A low-barrier hydrogen bond in subtilisin: 1H and 15N NMR studies with peptidyl trifluoromethyl ketones.

The N delta 1 proton of His 64 forms a hydrogen bond with Asp 32, as part of the catalytic triad in serine proteases of the subtilisin family. His 64 in subtilisin has been studied by 1H and 15N NMR spectroscopy in the presence and absence of peptidyl trifluoromethyl ketones (TFMKs) that are transition state analog inhibitors. For subtilisin Carlsberg, the downfield resonance of the imidazolium N delta 1 proton is approximately 18.3 ppm and the D/H fractionation factor is 0.55 +/- 0.04 at pH 5.5 (11 degrees C), and 0.63 +/- 0.04 (5 degrees C) and 0.68 +/- 0.04 at pH 6 (11 degrees C). In the complex between subtilisin Carlsberg and Z-L-leucyl-L-leucyl-L-phenylalanyltrifluoromethyl ketone (Z-LLF-CF3) at pH values between 6.5 and 10.6, His 64 remains positively charged, and the D/H fractionation factor of its N delta 1 proton is 0.85 +/- 0.05. In the complex between a subtilisin variant from Bacillus lentus and Z-LLF-CF3, the proton resonance at 18.8 ppm is correlated with a 15N resonance at 197.6 ppm downfield from liquid NH3 with a 1JNH of 81 Hz. The chemical shifts of subtilisin complexes with peptidyl TFMKs are among the most downfield shifts reported for any protein. At pH 9.5, His 64 is neutral and the D/H fractionation factor increases to 1.2 with a chemical shift of 15.0. His 64 is positively charged in the free enzyme at low pH, the inhibitor hemiketal complex at neutral pH, and the transition state for amide bond hydrolysis. These data thus provide indirect evidence for the presence of a low-barrier hydrogen bond in the catalytic mechanism of subtilisin proteases.

Bacterial Proteins↗
PubMed2001

Accumulation of trifluoroacetate in seasonal wetlands in California.

Trifluoroacetate (TFA, CF3COO-) is a stable and mildly phytotoxic breakdown product of several fluorinated organic compounds including the hydro(chloro)fluorocarbons (HFC/HCFCs) that have largely replaced the stratospheric ozone-depleting chlorofluorocarbons (CFCs). TFA enters aquatic ecosystems primarily through precipitation and has the potential to accumulate in water bodies with little or no outflow to the point where toxic concentrations could be achieved. This study demonstrated that seasonal wetlands lacking outflow concentrated TFA as they evaporated during the dry season. In addition, the TFA within the pools was retained between years, which may result in long-term TFA accumulation. Since plants acquire TFA from their growing media, the plants exposed to high aqueous concentrations of TFA within the pools had elevated TFA concentrations with a median concentration of 279 ng/g dry weight in their tissues as compared to 33 ng/g for species growing outside the pools. The highest TFA concentrations in water, which occurred just prior to the pools drying up, were in the 2-10 micrograms/L range. These concentrations are approximately 190 or less than reported toxic concentrations for the most sensitive species tested, but our evidence suggests that these concentrations will increase with continued TFA deposition into the pools.

Environmental Monitoring↗
PubMed2002

Monitoring perfluorinated surfactants in biota and surface water samples following an accidental release of fire-fighting foam into Etobicoke Creek.

Perfluorinated surfactants have emerged as priority environmental contaminants due to recent reports of their detection in environmental and biological matrices as well as concerns regarding their persistence and toxicity. In June 2000, 22000 L of fire retardant foam containing perfluorinated surfactants was accidentally released at L. B. Pearson International Airport, Toronto, ON, and subsequently entered into Etobicoke Creek, a tributary to Lake Ontario. A suite of analytical tools that include liquid chromatography/tandem mass spectrometry (LC/MS/MS) and 19F NMR were employed to characterize fish (common shiner, Notropus cornutus) and surface water samples collected following the discharge of the perfluorinated material. Total perfluoroalkanesulfonate (4, 6, and 8 carbons) concentrations in fish liver samples ranged from 2.00 to 72.9 microg/g, and total perfluorocarboxylate (5-14 carbons) concentrations ranged from 0.07 to 1.02 microg/g. In addition to fish samples, total perfluoroalkanesulfonate (6 and 8 carbons) concentrations were detected in creek water samples by LC/MS/MS over a 153 day sampling period with concentrations ranging from <0.017 to 2260 microg/L; perfluorooctanoate concentrations (<0.009-11.3 microg/L) were lower than those observed for the perfluoroalkane-sulfonates. By 19F NMR, the total perfluorinated surfactant concentrations in surface water samples ranged from < 10 to 17000 microg/L. A bioaccumulation factor range of 6300-125000 was calculated for perfluorooctanesulfonate, based on concentrations in fish liver and surface water. The residence time of perfluorooctanesulfonate in Etobicoke Creek as well as the high bioaccumulation in fish liver suggests that perfluorinated surfactants will persist and bioaccumulate following release into the aquatic environment.

Animals↗
PubMed2004

Vapor pressures of the fluorinated telomer alcohols--limitations of estimation methods.

The influence of the unique, physical properties of poly- and perfluorinated chemicals on vapor pressure was investigated. Vapor pressures of a suite of fluorinated telomer alcohols (FTOHs) (CF3(CF2)nCH2CH2OH, where n = 3, 5, 7, or 9) were measured using the boiling point method and ranged from 144 to 992 Pa. Comparison of experimental and literature values indicate that perfluorocarbons (CF3(CF2)nCF3, where n = 0-6) and fluorinated telomer alcohols have vapor pressures equal to or greater than that of their hydrogen analogues. These chemically counterintuitive results can be explained by the unique geometry of poly- and perfluorinated chemicals--in particular the stiff, helical perfluorinated chain and the significant intramolecular hydrogen bonding of the FTOHs. The majority of models investigated for the estimation of vapor pressure did not compensate for this unique geometry and consistently underpredicted the vapor pressures of the FTOHs. Calculation of partitioning constants using both experimental and estimated vapor pressures indicate that both the Antoine and Modified Grain models, and to a lesser degree the Mackay model, are insufficiently accurate for estimating the vapor pressures of the FTOHs, particularly the longer chain FTOHs. Future models should consider parameters such as geometry, strength, and location of intramolecular hydrogen bonds and otherfunction groups in the molecule in order to improve vapor pressure estimation accuracy. It appears likely that the unique molecular geometry of the FTOHs influences not only their vapor pressure but also other physical properties and hence environmental fate and dissemination.

Alcohols↗
PubMed2006

Perfluorochemicals in pooled serum samples from United States residents in 2001 and 2002.

Manufacturers have used perfluorochemicals (PFCs) since the 1950s in many industrial and consumer products, including protective coatings for fabrics and carpet, paper coatings, insecticide formulations, and surfactants. Some PFCs are persistent ubiquitous contaminants in the environment and in humans. Exposures to PFCs result in potential developmental and other adverse effects in animals. The sources of human exposure to PFCs and the potential health risks associated with exposure are still unclear, and differences in patterns of human exposure may vary. We measured the serum concentrations of perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA; C8), perfluorohexane sulfonic acid (PFHxS), and 8 other PFCs in 54 pooled serum samples collected from 1832 participants of the 2001-2002 National Health and Nutrition Examination Survey. Participants were 12 years of age and older. The pools represented three major racial groups/ethnicities (non-Hispanic blacks, non-Hispanic whites, and Mexican Americans), four age categories (12-19 years, 20-39 years, 40-59 years, and 60 years and older), and both genders. PFCs were extracted from 100 microL of serum using on-line solid-phase extraction coupled to isotope dilution-high performance liquid chromatography-tandem mass spectrometry. The limits of detection ranged from 0.05 ng/mL to 0.2 ng/mL. The concentrations of most PFCs were similar among the four age groups. For PFOS, the estimated least-squares mean (LSM) concentrations among non-Hispanic white males (40.19 ng/mL) and females (23.97 ng/mL) were greater than among non-Hispanic black males (18.27 ng/mL) and females (17.93 ng/mL) or Mexican American males (13.71 ng/mL) and females (10.40 ng/ mL). Similarly, for PFOA, the LSM concentrations among non-Hispanic white males (6.98 ng/mL) and females (3.97 ng/ mL) were greater than among non-Hispanic black males (3.62 ng/mL) and females (2.85 ng/mL) or Mexican American males (2.89 ng/mL) and females (2.08 ng/mL). Non-Hispanic whites had also greater LSM concentrations of PFHxS than non-Hispanic blacks and Mexican Americans. These findings indicate different patterns of human exposure to PFCs among the population groups examined and stress the importance of conducting research to identify the environmental sources and pathways of human exposure to PFCs.

Chromatography, High Pressure Liquid↗
PubMed2001

Hydroxo-bridged Cubane-type tetrairon(II) clusters supported by sterically-hindered carboxylate ligands.

A series of hydroxo-bridged cubane-type tetrairon(II) clusters, [Fe(4)(mu-OH)(4)(mu-O(2)CAr(4)(-)t(BuPh))(2)(mu-OTf)(2)L(4)] (L = C(5)H(5)N (1), 4-(t)BuC(5)H(4)N (2), 3-FC(5)H(4)N (3)), were synthesized by using a sterically hindered carboxylate ligand, 2,6-di(4-tert-butylphenyl)benzoate (Ar(4)(-)t(BuPh)CO(2)(-)). Three different bridging units that mediate weak antiferromagnetic coupling interactions between the metal centers support the unprecedented cubane-type [Fe(4)(mu-OH)(4)](4+) cores in 1-3. The solution structures of 1 and 3 probed by FT-IR and (19)F NMR spectroscopy are consistent with the solid-state geometry determined by X-ray crystallography. Zero-field Mössbauer spectra of 1-3 at 4.2 K are characteristic of high-spin iron(II) centers in nearly identical coordination environments. Compound 1 undergoes two irreversible oxidation processes at ca -10 and +880 mV (vs Fc/Fc(+)), the former approaching quasi-reversible behavior with increased scan rates and a narrow potential sweep range. Comparisons are made with analogous known [Fe(4)X(4)](n)()(+) (X = O, S) units, and the structural integrity of tetrairon fragments upon a change in oxidation state is discussed together with some possible biological implications.

Algorithms↗
PubMed2000

Low-valent gallium, indium, and tin compounds that contain a highly fluorinated tris(pyrazolyl)borate ligand: syntheses and characterization of.

Syntheses and characterization of gallium(I), indium(I), and tin(II) complexes of the [HB(3,5-(CF3)2Pz)3]- ligand (where [HB(3,5-(CF3)2Pz)3]- = hydrotris(3,5-bis(trifluoromethyl)pyrazolyl)borate)) are reported. X-ray crystal structures of [HB(3,5-(CF3)2Pz)3]In and [HB(3,5-(CF3)2Pz)3]Sn(CF3SO3) show monomeric structures in the solid state. The In-N and Sn-N bond distances are longer than the corresponding bond distances of nonfluorinated analogues. NMR data of the gallium(I) adduct [HB(3,5-(CF3)2Pz)3]Ga are very similar to those of the indium(I) analogue suggesting similar solution structures.

Journal Article↗
PubMed2002

Product binding to the diiron(III) and mixed-valence diiron centers of methane monooxygenase hydroxylase studied by (1,2)H and (19)F ENDOR spectroscopy.

The binding of ethanol and 1,1,1-trifluoroethanol (TFE) to both the H(mv) and H(ox) forms of soluble methane monooxygenase (sMMO) in solution has been studied by Q-band (35 GHz) CW and pulsed ENDOR spectroscopy of (1)H, (2)H and (19)F nuclei of exogenous ligands. As part of this investigation we introduce (19)F, in this case from bound TFE, as a new probe for the binding of small molecules to a metalloenzyme active site. The H(mv) form was prepared in solution by chemical reduction of H(ox). For study of H(ox) itself, frozen solutions were subjected to gamma-irradiation in the frozen solution state at 77 K, which affords an EPR-visible mixed-valent diiron center, denoted (H(ox))(mv), held in the geometry of the diiron(III) state. The (19)F and (2)H ENDOR spectra of bound TFE together with (1,2)H ENDOR spectra of bound ethanol indicate that the alcohols bind close to the Fe(II) ion of the mixed-valence cluster in H(mv) and in a bridging or semi-bridging fashion to H(ox). DMSO does not affect the binding of either of the ethanols or of methanol to H(ox), nor of ethanol or methanol to H(mv). It does, however, displace TFE from the diiron site in H(mv). These results provide the first evidence that crystal structures of sMMO hydroxylase into which product alcohols were introduced by diffusion represent the structures in solution.

Binding Sites↗
PubMed2004

Design of a functional protein for molecular recognition: specificity of ligand binding in a metal-assembled protein cavity probed by 19f NMR.

A metal-assembled homotrimeric coiled coil based on the GCN4-p1 sequence has been designed that noncovalently binds hexafluorobenzene and other similar ligands in a hydrophobic cavity, created by making the core substitution Asn16Ala ([Fe(bpyGCN4-N16A)3]2+). The KD of binding of hexafluorobenzene with [Fe(bpyGCN4-N16A)3]2+ was observed to be 1.1(9) x 10(-4) M by diffusion NMR experiments. A control coiled coil with the core substitution Asn16Val ([Fe(bpyGCN4-N16V)3]2+) exhibited a significantly weaker association with hexafluorobenzene, providing evidence that even in the absence of structural data, benzene-like ligands bind in the cavity created by the Asn16Ala substitution. 19F NMR was employed to observe hexafluorobenzene binding and to monitor titrations with competing hydrophobic and polar ligands similar in size and shape to hexafluorobenzene. All hydrophobic ligands bound with greater affinity than the polar ligands in the hydrophobic core, although the cavity seems to be somewhat flexible in terms of the sizes of molecules it can accommodate. Thus 19F NMR has proved to be a useful spectral tool to probe molecular recognition in a hydrophobic cavity of a metal-assembled coiled coil.

Amino Acid Sequence↗