Tris(2-carboxyethyl)phosphine stabilization of RNA: comparison with dithiothreitol for use with nucleic acid and thiophosphoryl chemistry

We assessed the utility of the sulfhydryl reductant Tris(2-carboxyethyl)phosphine (TCEP) for both nucleic acid and thiophosphate chemistry, including its effects on organomercurial gel electrophoresis, RNA catalysis, RNA backbone stability, and the intrinsic stability of TCEP. The sulfhydryls of dithiothreitol (DTT) compete with thiophosphates for binding to the mercury within [(N-acryloylamino)phenyl] mercuric chloride (APM) polyacrylamide gels, whereas millimolar concentrations of TCEP gave no difference in the fraction of thiophosphorylated RNA retained on the APM interface relative to samples containing no reductant. Ribozyme activity in TCEP, assessed by the self-thiophosphorylating Kin.46 ribozyme, was unaffected by the presence of DTT or TCEP or by the absence of reductant, as measured on APM gels and evaluated by Michaelis-Menten kinetics. Unexpectedly, TCEP more than doubled the half-life of full-length RNA at 50 and 70 degrees C, whether in 5 or 50mM MgCl(2), relative to DTT and the absence of reductant. Under these same conditions, the 5(')-thiophosphate showed negligible decay, and TCEP was more stable than DTT. TCEP thermostability was equivalent in the presence of 5 or 50mM MgCl(2) and 10mM adenosine or ATP.     

New water-soluble phosphines as reductants of peptide and protein disulfide bonds: reactivity and membrane permeability

Tris(2-carboxyethyl)phosphine (TCEP) is a widely used substitute for dithiothreitol (DTT) in the reduction of disulfide bonds in biochemical systems. Although TCEP has been recently shown to be a substrate of the flavin-dependent sulfhydryl oxidases, there is little quantitative information concerning the rate by which TCEP reduces other peptidic disulfide bonds. In this study, mono-, di-, and trimethyl ester analogues of TCEP were synthesized to evaluate the role of carboxylate anions in the reduction mechanism, and to expand the range of phosphine reductants. The effectiveness of all four phosphines relative to DTT has been determined using model disulfides, including a fluorescent disulfide-containing peptide (H(3)N(+)-VTWCGACKM-NH(2)), and with protein disulfide bonds in thioredoxin and sulfhydryl oxidase. Mono-, di-, and trimethyl esters exhibit phosphorus pK values of 6.8, 5.8, and 4.7, respectively, extending their reactivity with the model peptide to correspondingly lower pH values relative to that of TCEP (pK = 7.6). At pH 5.0, the order of reactivity is as follows: trimethyl- > dimethyl- > monomethyl- > TCEP > DTT; tmTCEP is 35-fold more reactive than TCEP, and DTT is essentially unreactive. Esterification also increases lipophilicity, allowing tmTCEP to penetrate phospholipid bilayers rapidly (>30-fold faster than DTT), whereas the parent TCEP is impermeant. Although more reactive than DTT toward small-molecule disulfides at pH 7.5, all phosphines are markedly less reactive toward protein disulfides at this pH. Molecular modeling suggests that the nucleophilic phosphorus of TCEP is more sterically crowded than the thiolate of DTT, contributing to the lower reactivity of the phosphine with protein disulfides. In sum, these data suggest that there is considerable scope for the synthesis of phosphine analogues tailored for specific applications in biological systems.     

Differences in the reduction kinetics of incorporated spin labels in undifferentiated and differentiated mouse neuroblastoma cells

Significant differences in the rate of reduction of two spin labels, 5-doxylstearic acid and TEMPOL, in the undifferentiated and differentiated NB-15 mouse neuroblastoma cells were demonstrated by using electron paramagnetic resonance (EPR) spectroscopy. The half-time (T1/2) values for decay of the EPR signal of 5-doxylstearic acid in the undifferentiated and differentiated neuroblastoma cells were 70 min and 290 min, respectively. The T1/2 values of TEMPOL in the undifferentiated and differentiated cells were 18 min and 34 min, respectively. The cellular reductant was characterized as non-protein-bound sulfhydryl groups. A corresponding difference in the cellular non-protein-bound sulfhydryl content, 19.30 nmol/mg protein for the undifferentiated cells and 6.78 nmol/mg protein for the differentiated cells, was observed. Comparison of the reduction rates of TEMPOL, 5-doxylstearic acid and 16-doxylstearic acid in the undifferentiated NB-15 cells suggested that the permeation of non-protein-bound sulfhydryl compounds from the cytosol to membrane may be responsible for the reduction of the lipid-soluble stearic acid spin labels.     

Selective spin-labeling of the ribosomal proteins of 70S ribosomes from Escherichia coli.

We have used a series of N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl) maleimide spin labels of different length to label, covalently and selectively, the most reactive sulfhydryl groups of 70S ribosomal proteins of Escherichia coli. Under short periods of labeling (1--2 min), less than two spin labels per ribosome are incorporated and were shown to be distributed mainly on five ribosomal proteins in the following order: S18 greater than S21, L27 greater than S17, and S12. With a long period of labeling (3 h) up to 13 spin labels are attached to the ribosome, and protein S1 is the most labeled. The shape of the electron paramagnetic resonance (epr) signal shows two components with a predominance for the strongly immobilized orientation, and the percentage of these components in each spectra has been evaluated. When the distance between the nitroxide group and the maleimide-attaching group exceeds 6 A (1 A = 0.1 nm) the strongly immobilized orientation disappears. The effect of magnesium ions on these selectively spinlabeled ribosomes shows that the dissociation into subunits does not affect the epr signal, but more spin labels are incorporated into the subunits if labeling is performed under conditions of dissociation.     

A spin-label study of the disposition of the Fe-S cluster with respect to the active center of aconitase

It has been reported by Johnson et al. ((1977) Biochem. Biophys. Res. Commun. 74, 384-389) that phenacyl bromide reacts with a single reactive sulfhydryl group of aconitase, abolishing enzyme activity. Substrate or analogs have a protective effect. This group is therefore at the catalytic site of the enzyme. Aconitase is also known to be an Fe-S protein, paramagnetic as obtained on purification (Ruzicka and Beinert (1978) J. Biol. Chem. 253, 2514-2517). We have attempted to obtain information on the location of the Fe-S cluster of aconitase with respect to the catalytically active site by attaching nitroxide-labelled sulfhydryl reagents of the bromoacyl and maleimide type to the sensitive sulfhydryl group. The EPR signals of those spin-labelled sulfhydryl reagents that abolish enzyme activity disappear during reaction with aconitase. EPR spectra at 13 K of the product obtained by reaction of three spin labels (two maleimides and one bromoacyl) with aconitase included a half-field transition at g approximately equal to 4.0 which is characteristic of spin-spin interaction. On the basis of calculations of the dependence of the intensity of the half-field transition on the distance between two interacting unpaired electrons (Eaton and Eaton, (1982) J. Am. Chem. Soc. 104, 5002-5003) the distances between the nitroxide N-O bond and the center of the Fe-S cluster for the three spin labels were calculated to be 10.5, 11 and 13 A. Combined distance and orientation data for the three spin labels indicate that the reactive sulfhydryl group is about 12 A from the center of the Fe-S cluster.     

Determination of ascorbic acid and dehydroascorbic acid in biological samples by high-performance liquid chromatography using subtraction methods: reliable reduction with tris[2-carboxyethyl]phosphine hydrochloride

Determination of dehydroascorbic acid in biological samples most commonly involves indirect measurement. The concentration is calculated by subtraction of the measured ascorbic acid concentration from that of total ascorbic acid analyzed after reduction of the dehydroascorbic acid present; a methodology also referred to as subtraction methods. Consequently, successful determination of dehydroascorbic acid is dependent on proper sample handling, quantitative reduction of the compound, and accurate quantification of both ascorbic acid and total ascorbic acid. In this paper, the recently introduced reductant tris[2-carboxyethyl]phosphine (TCEP) is evaluated as a reliable alternative to the commonly used reducing agent dithiothreitol (DTT). The results show that TCEP offers a more efficient reduction of dehydroascorbic acid at low pH compared to that of DTT. Moreover, while DTT maintains a reducing sample environment for less than 24 h, TCEP show complete protection from oxidation of ascorbic acid for at least 96 h following sample preparation. Removal of TCEP prior to analysis is unnecessary. A revised HPLC-EC method incorporating TCEP as reductant as well as the coanalysis of isoascorbic acid and uric acid is presented. The within- and between-day coefficients of variation for the complete assay are less than 1.5 and 3.5% for all analytes. As a whole, the method presented here is simpler and more reliable than existing methods.     

Electron spin resonance studies of the effects of lipids on the environment of proteins in mitochondrial membranes

The physical state of mitochondrial membranes has been investigated by means of stearic acid spin labels and of a maleimide spin label covalently bound to protein sulfhydryl groups. Stearic acid spin labels 5-NS and 16-NS show that n-butanol enhances the lipid fluidity of mitochondrial membranes in the whole temperature range between 4 and 37 degrees C; the effects in the hydrophobic membrane core, probed by 16-NS, are already apparent at 10 mM butanol. In liposomes formed of mitochondrial phospholipids, a fluidizing effect appears only at much higher concentration. Such results are compatible with the idea that butanol destabilizes lipid-protein interactions. On the other hand, the ratio between weakly and strongly immobilized SH groups probed by maleimide spin label is only slightly affected in the temperature range of 4-37 degrees C by addition of high concentrations of n-butanol, indicating that the environments probed are stable to agents inducing fluidity changes in the lipids. There are, however, indications that the environment probed by maleimide is affected by lipids, since the spin label, when bound to lipid-depleted mitochondria, becomes more immobilized, reconstitution of such lipid-depleted membranes with phospholipids restores the original spectra.     

On the location of the sulfhydryl group in bovine plasma albumin.

A series of spin labels has been empolyed to explore the environment of the sulfhydryl group in bovine plasma albumin. The spin labels consist of the nitroxide-free radical and a maleimide (or iodoacetamide)-attaching group separated by varying chain lenghths. Both sets of spin labels preferentially bind to the sulfhydryl group under appropriate conditions. From the change in the electron spin resonance spectra of these nitroxides as a function of chain length, we conclude that the sulfhydryl group is located in a crevice approx. 9.5 A in depth.     

Spin label studies of sulfhydryl environment in plasma fibronectin

The local environment of the free sulfhydryl groups in plasma fibronectin has been investigated by ESR techniques using a series of maleimide spin labels, varying in chain length between the maleimide and nitroxide free radical groups. Chemical modification with these analogs does not affect either the CD spectra or the cell adhesion activity of the protein molecule. The ESR results show that the free sulfhydryl group of plasma fibronectin is in a cleft about 10.5 A in length. The significance of this finding is discussed.     

Kinetic studies of a hepatoma alkaline phosphatase

To help interpret the electron spin resonance (esr) spectra of spin-labeled actin, the positions of attachment of the spin labels, N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl) maleimide and N-(1-oxyl-2,2,6,6-tetramethyl-4-piperidinyl) iodoacetamide to rabbit skeletal muscle actin have been determined. For this purpose spin-labeled peptides released by tryptic digestion of the spin-labeled actin were isolated by chromatography and identified from their positions of elution and amino acid composition.With purified F-actin that had not undergone structural changes both labels reacted exclusively with the sulfhydryl group of the C-terminal sequence. But if the actin was stored in the F-form in the absence of ATP it evidently underwent a structural alteration because reaction was then at another sulfhydryl group, in the N-terminal sequence, and the actin had an irregular appearance in the electron microscope. ADP and tripolyphosphate were as effective as ATP in preventing this alteration. A maximum of 1 equiv of spin label was bound, irrespective of the site of labeling, and the two sites appeared to be mutually exclusive, possibly because they are adjacent. With G-actin, and with actin denatured by guanidine hydrochloride, there was also reaction at other sites. The shapes of the esr spectra of F-actin that contained Mg²⁺, Ca²⁺, or Mn²⁺ did not depend on whether labeling was at the C- or N-terminal positions, although F-actin labeled in the latter position contained a small proportion of highly mobile label, possibly a result of denaturation. The reduction in the size of the esr signal of labeled G-actin on replacing Mg²⁺ with Mn²⁺ did not appear to be dependent on the position of labeling.     

Orientation of spin-labeled myosin heads in glycerinated muscle fibers.

We have used electron paramagnetic resonance (EPR) spectra to study spin labels selectively and rigidly attached to myosin heads in glycerinated rabbit psoas muscle fibers. Because the angle between the magnetic field and the principal axis of the probe determines the position of the EPR absorption line, spectra from labeled fibers oriented parallel to the magnetic field yielded directly the distribution of spin label orientations relative to the fiber axis. Two spin labels, having reactivities resembling iodoacetamide (IASL) and maleimide (MSL), were used. In rigor fibers with complete filament overlap, both labels displayed a narrow angular distribution, full width at half maximum approximately 15 degrees, centered at angles of 68 degrees (IASL) and 82 degrees (MSL). Myosin subfragments (heavy meromyosin and subfragment-1) were labeled and allowed to diffuse into fibers. The resulting spectra showed the same sharp angular distribution that was found for the labeled fibers. Thus is appears that virtually all myosin heads in a rigor fiber have the same orientation relative to the fiber axis, and this orientation is determined by the actomyosin bond. Experiments with stretched fibers indicated that the spin labels on the fraction of heads not interacting with actin filaments had a broad angular distribution. Addition of ATP to unstretched fibers under relaxing conditions produced orientational disorder, resulting in a spectrum almost indistinguishable from that of an isotropic distribution of probes. Addition of either an ATP analog (AMPPNP) or pyrophosphate produced partial disorder. That is a fraction of the probes remained sharply oriented as in rigor while a second fraction was in a disordered distribution similar to that of relaxed fibers.     

Succinate and phenylsuccinate as modifiers of sulfhydryl groups of inner mitochondrial membrane protein. Study by EPR

Paramagnetic labels specific for sulfhydryl (SH) groups have been used to study the conformational changes of the inner mitochondrial membrane. The EPR spectra of the SH-groups spin-labeled with maleimide or iodoacetamide show the existence of two populations of sulfhydryl groups, differing in their mobility (one weakly, the other strongly immobilized). The incubation with succinate or phenylsuccinate decreased the binding of these labels of the weakly immobilized sites while the number of total SH groups was the same before and after the incubation. These results suggest that succinate or phenylsuccinate induce a reversible change in protein conformation or in protein arrangement within the inner mitochondrial membrane. This change is concomitant to the protein movement between inner membrane and perimembranal space induced by either of these two molecules.     

Reappraisal of the electron spin resonance spectra of maleimide and iodoacetamide spin labels in erythrocyte ghosts.

The effects of sulfhydryl inhibitors (iodoacetamide and N-ethylmaleimide) on the electron spin resonance spectra of two maleimide and two iodoacetamide spin labels in erythrocyte ghosts were found to correlate with their relative “lipid”/water partition coefficients. But the spectral characteristics of the maleimide spin labels, and their ghost concentrations after iodoacetamide inhibition, are not consistent with the hypothesis that interprets their spectra solely on the basis of a heterogenous membrane distribution. An alternative hypothesis is suggested which is compatible with relative “lipid solubilities” and the iodoacetamide inhibition spectra.     

The environment of the sulfhydryl group in human plasma albumin as determined by spin labeling

A series of spin labels, varying in chain length between the maleimide attaching group and the nitroxide free radical, has been used to investigate the environment of the sulfhydryl group in human plasma albumin. From the electron spin resonance spectra, the degree of freedom of the nitroxide was determined and the location of the sulfhydryl was assessed. The effect of bound fatty acids on the sulfhydryl environment was also determined. The environment was found to be analogous to that in the bovine protein, that is, a crevice approximately 9.5 Å deep and not affected in the native state by fatty acids.     

Saturation fluorescence labeling of proteins for proteomic analyses

We present here an optimized and cost-effective approach to saturation fluorescence labeling of protein thiols for proteomic analysis. We investigated a number of conditions and reagent concentrations, including the disulfide reducing agent tris(2-carboxyethyl)phosphine (TCEP), pH, incubation time, linearity of labeling, and saturating dye/protein thiol ratio with protein standards to gauge specific and nonspecific labeling. Efficacy of labeling under these conditions was quantified using specific fluorescence estimation, defined as the ratio of fluorescence pixel intensities and Coomassie-stained pixel intensities of bands after digital imaging. Factors leading to specific versus nonspecific labeling in the presence of thiourea are also discussed. We found that reproducible saturation of available Cys residues of the proteins used as labeling standards (human carbonic anhydrase I, enolase, and α-lactalbumin) is achieved at 50- to 100-fold excess of the uncharged maleimide-functionalized BODIPY dyes over Cys. We confirmed our previous findings, and those of others, that the maleimide dyes are not affected by the presence of 2 M thiourea. Moreover, we established that 2 mM TCEP used as reductant is optimal. We also established that labeling is optimal at pH 7.5 and complete after 30 min. Low nonspecific labeling was gauged by the inclusion of non-Cys-containing proteins (horse myoglobin and bovine carbonic anhydrase) to the labeling mixture. We also showed that the dye exhibits little to no effect on the two-dimensional mobilities of labeled proteins derived from cells.     

Spin labeling of protein sulfhydryl groups by spin trapping a sulfur radical: application to bovine serum albumin and myosin

Reaction of sulfhydryl-containing compounds, RSH, with Ce4+ in the presence of the spin trap phenyl-N-t-butylnitrone results in the appearance of a nitroxide ESR spectrum, which is greatly diminished if the sulfhydryl group is blocked prior to reaction. The spectra have short lifetimes which can be increased two- to fivefold to half-lives of 5-60 min by prior flushing of the solutions with nitrogen. For small molecules, such as cysteine, N-acetylcysteine, glutathione, and 2-mercaptoethanol, the spectrum is that of a freely rotating nitroxide while for the proteins, bovine serum albumin and myosin, the spectrum is characteristic of a strongly immobilized nitroxide spin label rigidly attached to the protein. Since Ce4+ is reported to oxidize the sulfhydryl group via the thiyl radical, RS, the following reactions are proposed to account for the formation of the nitroxide: (formula; see text) These reactions permit the spin labeling of sulfhydryl proteins such that the nitroxide is much closer to the point of attachment than when using conventional spin-labeling methods.     

Toward the fourth dimension of membrane protein structure: insight into dynamics from spin-labeling EPR spectroscopy

Trapping membrane proteins in the confines of a crystal lattice obscures dynamic modes essential for interconversion between multiple conformations in the functional cycle. Moreover, lattice forces could conspire with detergent solubilization to stabilize a minor conformer in an ensemble thus confounding mechanistic interpretation. Spin labeling in conjunction with electron paramagnetic resonance (EPR) spectroscopy offers an exquisite window into membrane protein dynamics in the native-like environment of a lipid bilayer. Systematic application of spin labeling and EPR identifies sequence-specific secondary structures, defines their topology and their packing in the tertiary fold. Long range distance measurements (60 ?-80 ?) between pairs of spin labels enable quantitative analysis of equilibrium dynamics and triggered conformational changes. This review highlights the contribution of spin labeling to bridging structure and mechanism. Efforts to develop methods for determining structures from EPR restraints and to increase sensitivity and throughput promise to expand spin labeling applications in membrane protein structural biology.     

Spin-label studies of membrane-associated denatured hemoglobin in normal and sickle cells.

A maleimide spin label (N-(1-oxyl-2,2,5,5-tetramethylpyrrolidinyl)-maleimide) was reacted with oxyhemoglobin-free cell stromata of normal and sickle cells. The EPR spectrum of spin-labeled red cell membranes showed that the spin labels are attached to at least two different binding sites. There was a major signal, A, which characterized a strongly immobilized environment and a minor signal, B, which characterized a weakly immobilized environment. Quantitative EPR measurements using equal amounts of Hb AA and Hb SS red blood cells demonstrated that Hb SS red cell membranes had an approximately four times higher EPR signal intensity than Hb AA red cell membranes ((7.98 +/- 1.14 . 10(5) and (2.2 +/- 1.2) . 10(5) spin labels/cell, respectively). Moreover, the ratio of signal intensities A and B are different in these cells. Comparative spectrophotometric studies of membrane-associated denatured hemoglobins of Hb AA and Hb SS red cell membranes suggested that the EPR signal A is derived from spin labels attached to membrane-associated denatured hemoglobin, while signal B is mainly from spin labels attached to membranes. The combination of EPR spectrum of Hb AA membranes pretreated with N-ethylmaleimide and that of spin-labeled precipitated hemoglobin further strengthened this conclusion.