Determination of copper by isotopic dilution

Biological Trace Element Research - A rapid and selective method was used for the determination of copper by isotopic dilution employing substoichiometric extraction with dithizone in carbon...     

Comparison of mass-transfer and isotopic dilution methods for estimating milk intake in Antarctic fur seal pups

The efficacy of a new mass-transfer method for estimating milk intake was examined in Antarctic fur seals (Arctocephalus gazella) at Iles Kerguelen. Our method differed from previous mass-transfer approaches in that we estimated milk-mass transfer as the maternal mass lost (MML; kg) during an attendance bout, less the mass lost to metabolic maintenance (MML_E) over that time. MML was significantly related to pup mass-gain (PMG) and attendance bout duration (d days) as follows: MML=1.106PMG+1.002d (r²=0.998). Based on this and previous studies, we estimated that the MML_E was 0.0285 kg kg^–1 day^–1 for lactating females; and we developed the following milk-mass transfer equation: MML_M=1.106PMG+1.002d–0.0285MMd (where MM is maternal mass). Milk-mass intake was also estimated in an additional 21 pups, using the isotopic dilution method. These values were then compared with estimates based on the milk mass-transfer equation for the same individual pups. A pair-wise comparison indicated that milk-mass transfer estimated using tritium dilution methods were significantly lower than those based on mass-transfer (MML_M). Furthermore, the absolute PMG exceeded tritium dilution estimates of milk-mass transfer in 35% of cases. In contrast, all milk-mass transfer estimates using the mass transfer method were greater than PMG. Overestimation of metabolic water production (MWP), leading to a smaller proportion of the total water intake being attributed to milk ingestion, is believed to be the most likely cause for significant underestimation of milk-mass transfer using the tritium dilution method. Consumption of exogenous water by pups is the most likely reason for the overestimation of MWP, although errors in estimated milk water content may have also contributed to underestimates. We conclude that, in our study, the mass-transfer method provided a more reliable estimate of milk-mass transfer than the isotopic dilution method; and we argue that, under certain conditions, it provides a practical alternative method where the assumptions of isotopic dilution methodology (e.g., all exogenous water from maternal milk) and quantitative parameters (e.g., maternal milk water content) may either be violated or impractical to measure.     

Electron transfer dissociation of iTRAQ labeled peptide ions

Triply and doubly charged iTRAQ ( isobaric tagging for relative and absolute quantitation) labeled peptide cations from a tryptic peptide mixture of bovine carbonic anhydrase II were subjected to electron transfer ion/ion reactions to investigate the effect of charge bearing modifications associated with iTRAQ on the fragmentation pattern. It was noted that electron transfer dissociation (ETD) of triply charged or activated ETD (ETD and supplemental collisional activation of intact electron transfer species) of doubly charged iTRAQ tagged peptide ions yielded extensive sequence information, in analogy with ETD of unmodified peptide ions. That is, addition of the fixed charge iTRAQ tag showed relatively little deleterious effect on the ETD performance of the modified peptides. ETD of the triply charged iTRAQ labeled peptide ions followed by collision-induced dissociation (CID) of the product ion at m/ z 162 yielded the reporter ion at m/ z 116, which is the reporter ion used for quantitation via CID of the same precursor ions. The reporter ion formed via the two-step activation process is expected to provide quantitative information similar to that directly produced from CID. A 103 Da neutral loss species observed in the ETD spectra of all the triply and doubly charged iTRAQ labeled peptide ions is unique to the 116 Da iTRAQ reagent, which implies that this process also has potential for quantitation of peptides/proteins. Therefore, ETD with or without supplemental collisional activation, depending on the precursor ion charge state, has the potential to directly identify and quantify the peptides/proteins simultaneously using existing iTRAQ reagents.     

Distribution of unselectively bound ligands along DNA

Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight a(i). Each ligand covers L binding centers. For this model, expressions for binding averages are represented in a new simple form. This representation is convenient for the calculation of the fraction of inter-ligand distances of i binding centers f(d)(i) and the fraction of binding centers included in the distances of i binding centers f(bc)(i) for various types of interaction between bound ligands. It is shown that, for non-cooperative binding, contact cooperativity and long-range cooperativity, the fraction of the zero inter-ligand distance f(d)(0) is maximal at any relative concentration of bound ligands (r). Calculations demonstrate that, at low r, f(d)(0) approximately r . a(o), and f(d)(i) approximately r at 1 1/r-L, then f(d)(i) rapidly decreases with i at any r for all types of inter-ligand interaction. At high ligand concentration (r is close to r(max) = L(-1)), f(d)(0) is close to unity and f(d)(i) rapidly decreases with i for any type of inter-ligand interaction. For strong contact cooperativity, f(d)(0) is close to unity in a much lager r interval ((0.5-1) . r(max)), and f(d)(1) approximately a(o)(-1) at r approximately 0.5 . r(max). In the case of long-range interaction between bound ligands, the dependence f(d)(i) is more complex and has a maximum at i approximately (1/r-L)(1/2) for anti-cooperative binding. f(bc)(i) is maximal at i approximately 1/r-L for all types of binding except the contact cooperativity. A strong asymmetry in the influence of contact cooperativity and anticooperativity on the ligand distribution along DNA is demonstrated.     

Conformational diversity of ligands bound to proteins

The phenomenon of molecular recognition, which underpins almost all biological processes, is dynamic, complex and subtle. Establishing an interaction between a pair of molecules involves mutual structural rearrangements guided by a highly convoluted energy landscape, the accurate mapping of which continues to elude us. Increased understanding of the degree to which the conformational space of a ligand is restricted upon binding may have important implications for docking studies, structure refinement and for function prediction methods based on geometrical comparisons of ligands or their binding sites. Here, we present an analysis of the conformational variability exhibited by three of the most ubiquitous biological ligands in nature, ATP, NAD and FAD. First, we demonstrate qualitatively that these ligands bind to proteins in widely varying conformations, including several cases in which parts of the molecule assume energetically unfavourable orientations. Next, by comparing the distribution of bound ligand shapes with the set of all possible molecular conformations, we provide a quantitative assessment of previous observations that ligands tend to unfold when binding to proteins. We show that, while extended forms of ligands are indeed common in ligand-protein structures, instances of ligands in almost maximally compact arrangements can also be found. Thirdly, we compare the conformational variation in two sets of ligand molecules, those bound to homologous proteins, and those bound to unrelated proteins. Although most superfamilies bind ligands in a fairly conserved manner, we find several cases in which significant variation in ligand configuration is observed.     

Effect of ionic strength on the pKa of ligands bound to DNA

The pK_a of 3,8-diamino-6-phenyl-phenanthridine (DAPP), a nonquaternary analog of ethidium bromide, has been determined spectrophotometrically as a function of sodium ion concentration both free in solution and complexed to DNA. Unwinding angle determinations with this compound were determined with Col El DNA using ethidium bromide as a standard. The unwinding angle for DAPP was 24 ± 2° relative to 26° for ethidium, and this suggests that DAPP binds in a manner quite similar to ethidium and with no significant outside bound DAPP under these experimental conditions. Isobestic behavior was obtained on spectrophotometric pH titration above pH 5 as long as the ratio of DNA-phosphate to ligand was between 100 and 300 and the DNA phosphate concentration was approximately 0.01M or greater. The loss of isosbestic behavior which occurred below pH 5 is probably due to titration of the 8 amino group of the ligand complexed to DNA. To circumvent this problem, pK_a values and the extinction coefficient of the acidic species were both determined by a computer program using experimental data obtained above pH 5. The pK_a of the free compound has only a minor dependence on ionic strength, while the pK_a of the ligand bound to DNA in an intercalated complex depends strongly on the sodium ion concentration. The pK_a of the DAPP-DNA complex is a linear function of –log[Na⁺] as predicted by the ion-condensation theory of polyelectrolytes. It was determined that DAPP is essentially completely bound to DNA under the conditions of these experiments by (1) determination of apparent pK_a values as a function of total DNA concentration, (2) calculation of binding constants for the neutral species of DAPP, and (3) spectral analysis of the protonated and neutral species of DAPP bound to DNA relative to DAPP free in solution. These results support the ion-condensation theory; provide an independent method for measuring ψ*, the average number of counterions associated per phosphate of DNA in the intercalated conformation; and illustrate that there are no specific pH effects or absolute pK_a values for ligands bound to DNA, but only ionic-strength-dependent results.     

Ultrastructural evidence for the dissociation of free subunits from ferritin upon dilution

Previous biophysical and biochemical studies have not detected any free monomeric subunits when multimeric molecules of the metalloprotein, ferritin, were highly diluted with water. Electron microscope examination of diluted ferritin reveals many single objects much smaller than the whole molecules. These small objects are interpreted as being free apoferritin subunits. Since these small objects can be found in samples that originally contain only whole molecules, this result indicates that subunits indeed can dissociate from ferritin upon dilution. The available evidence suggests that the dissociation of subunits normally is balanced by a rapid reassociation into the polymeric state.     

Use of tritium labeled amino acid conjugates of prostaglandins and thromboxanes as labeled ligands in prostanoid radioimmunoassay

Conjugates of prostaglandins and thromboxanes with tritium labeled amino acids were prepared and employed as labeled ligands in porstaglandin and thromboxane radioimmunoassays. Assays for PGF_2α, 15-keto-13, 14-dihydro-PGF_2α, TXB₂ and 15-keto-13, 14-dihydro-TXB₂ were evaluated in comparative studies using either these heterologous ligands or the corresponding homologus tritiated eicosanoid as tracers. Binding properties for the respective antibodies were found to be similar using either tracer.Three biological studies were also conducted, viz. study of the release of TXB₂ during collagen induced platelet aggregation, of 15-keto-13, 14-dihydro-TXB₂ during guinea pig pulmonary anaphylaxis, and of PGF_2α (measured as 15-keto-13, 14-dihydro-PGF_2α in peripheral plasma) during bovine luteolysis. The analyses gave comparable results using either the heterologous or the homologous assay.Thus, this type of labeled prostanoid conjugates may serve as a convenient alternative to homologous tracers in radioimmunoassay. Heterologous tracers may even in certain cases provide the only simple solution to the problem of preparing a labeled ligand of high specific activity.     

Use of tritium labeled amino acid conjugates of prostaglandins and thromboxanes as labeled ligands in prostanoid radioimmunoassay

Conjugates of prostaglandins and thromboxanes with tritium labeled amino acids were prepared and employed as labeled ligands in prostaglandin and thromboxane radioimmunoassays. Assays for PGF2 alpha, 15-keto-13, 14-dihydro-PGF2 alpha, TXB2 and 15-keto-13,14-dihydro-TXB2 were evaluated in comparative studies using either these heterologous ligands or the corresponding homologous tritiated eicosanoid as tracers. Binding properties for the respective antibodies were found to be similar using either tracer. Three biological studies were also conducted, viz. study of the release of TXB2 during collagen induced platelet aggregation, of 15-keto-13,14-dihydro-TXB2 during guinea pig pulmonary anaphylaxis, and of PGF2 alpha (measured as 15-keto-13,14-dihydro-PGF2 alpha in peripheral plasma) during bovine luteolysis. The analyses gave comparable results using either the heterologous or the homologous assay. Thus, this type of labeled prostanoid conjugates may serve as a convenient alternative to homologous tracers in radioimmunoassay. Heterologous tracers may even in certain cases provide the only simple solution to the problem of preparing a labeled ligand of high specific activity.     

The movement of bound ligands over cell surfaces

The long range movements of membrane-bound ligands into surface caps and into the pseudopods of phagocytizing cells, the uropods of motile cells and the cleavage furrow of dividing cells appear to be analogous processes. A common mechanism to explain these movements must take into account several new and central observations: ligand-receptor complexes can migrate to regions of existing microfilament accumulation; laser photobleaching studies with fluorescent Con A indicate that ligand-receptor movement occurs unidirectionally; video computer analyses of Con A redistribution show that movement may exceed the maximum rates measured for protein diffusion in membranes. These observations are not consistent with models in which ligand-receptor movement occurs by diffusion or by direct interaction with contractile microfilaments. However, they can be satisfied by a new model that proposes the entrainment of selected membrane determinants on membrane waves directed towards regions such as caps, pseudopodia, uropods or cleavage furrow. These oriented waves are initiated by tension due to asymmetric microfilamentmembrane interaction.     

Substrate and dilution effects on the inhibition of acetylcholinesterase by carbamates

1. The kinetics of acetylcholinesterase (EC 3.1.1.7) activity and its inhibition by eserine or by Sevin (1-naphthyl N-methylcarbamate) have been studied over the substrate concentration range 5x10(-8) to 2.5x10(-2)m. 2. Equations are given for inhibition as a function of time, substrate and inhibitor concentrations, and the relevant parameters determined at 25 degrees and 37 degrees . 3. The observed and calculated effects of time, dilution, substrate addition and enzyme concentration were in good agreement and consistent with a steady-state carbamylation by eserine or by Sevin in the presence of excess of inhibitor. 4. The quantitative destruction of either inhibitor at high enzyme concentrations implied by the carbamylation hypothesis has been confirmed experimentally. 5. The importance and possibility of allowing quantitatively for dilution and substrate effects when estimating carbamate inhibition are demonstrated.     

Modeling the structure of bound peptide ligands to major histocompatibility complex

In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues near the ends of the binding groove are docked by using an efficient pseudo-Brownian rigid body docking procedure followed by (2) loop closure of the intervening backbone structure by satisfaction of spatial constraints, and subsequently, (3) the refinement of the entire backbone and ligand interacting side chains and receptor side chains experiencing atomic clash at the MHC receptor-peptide interface. The method was tested by remodeling of 40 nonredundant complexes of at least 3.00 A resolution for which three-dimensional structural information is available and independently for docking peptides derived from 15 nonredundant complexes into a single template structure. In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC-peptide complexes were modeled with a Calpha RMSD < 1.00 A.     

Kinetics of irreversible dissociation for proteins bound cooperatively to DNA

We consider the irreversible dissociation kinetics of proteins that bind cooperatively and nonspecifically to DNA. Our model consists of an infinitely long one-dimensional nucleic acid lattice on which are bound protein ligands. A set of adjacent bound proteins forms a cluster of length n. A protein molecule may dissociate from any site within the bound cluster, not only from the ends, as was assumed in a previous model of this process due to Lohman [(1983) Biopolymers 22 , 1697–1713]. By considering this additional pathway, we present a more general treatment of the dissociation kinetics of cooperatively bound ligands. We show that dissociation from the (n?2) internal positions of an n-cluster is an important pathway when the initial fractional saturation of the lattice is close to unity and the co operatively is low. When the fractional saturation is initially equal to 1 and the co operatively is low, our model does not give the zero-order dissociation kinetics predicted by the Lohman model.     

Fragmentation-tree density representation for crystallographic modelling of bound ligands

The identification and modelling of ligands into macromolecular models is important for understanding molecule's function and for designing inhibitors to modulate its activities. We describe new algorithms for the automated building of ligands into electron density maps in crystal structure determination. Location of the ligand-binding site is achieved by matching numerical shape features describing the ligand to those of density clusters using a "fragmentation-tree" density representation. The ligand molecule is built using two distinct algorithms exploiting free atoms with inter-atomic connectivity and Metropolis-based optimisation of the conformational state of the ligand, producing an ensemble of structures from which the final model is derived. The method was validated on several thousand entries from the Protein Data Bank. In the majority of cases, the ligand-binding site could be correctly located and the ligand model built with a coordinate accuracy of better than 1 ?. We anticipate that the method will be of routine use to anyone modelling ligands, lead compounds or even compound fragments as part of protein functional analyses or drug design efforts.     

Fluorescence spectral properties of labeled thiolated oligonucleotides bound to silver particles

We examined the fluorescent spectral properties of fluorescein-labeled DNA oligomers when directly bound to metallic silver particles via a terminal sulfhydryl group. We found a 12-fold increase in fluorescence intensity and 25-fold decrease in lifetime for a fluorescein residue positioned 23 nucleotides from the silver surface compared to labeled oligomers in free solution. Similar results were found for a 23-mer labeled with five fluorescein residues. The absence of long lifetime components in the intensity decays suggests that all labeled oligomers are bound to silver and affected similarly by the metallic surfaces. These results provide the basic knowledge needed to begin use of metal-enhanced fluorescence for the detection of target sequences in simple formats potentially without a washing separation step. The use of metal-enhanced fluorescence provides a generic approach to obtaining a hybridization-dependent increase in fluorescence with most, if not all, commonly used fluorophores.