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Biomedical subjects

D J Winzor

Publications and source records attributed to D J Winzor.

At least 37 records · Page 2Linked to original sources
PubMed1999

Purification and characterization of Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase and comparison with the human enzyme.

The human malaria parasite Plasmodium falciparum is auxotrophic for purines and relies on the purine salvage pathway for the synthesis of its purine nucleotides. Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) is a key purine salvage enzyme in P. falciparum, making it a potential target for chemotherapy. Previous attempts to purify this enzyme have been unsuccessful because of the difficulty in obtaining cultured parasite material and because of the inherent instability of the enzyme during purification and storage. Other groups have tried to express recombinant P. falciparum HGXPRT but only small amounts of activity were obtained. The successful expression of recombinant P. falciparum HGXPRT in Escherichia coli has now been achieved and the enzyme purified to homogeneity in mg quantities. The measured molecular mass of 26 229+/-2 Da is in excellent agreement with the calculated value of 26232 Da. A method to stabilise the activity and to reactivate inactive samples has been developed. The subunit structure of P. Jilciparum HGXPRT has been determined by ultracentrifugation in the absence (tetramer) and presence (dimer) of KC1. Kinetic constants were determined for 5-phospho-alpha-D-ribosyl-1-pyrophosphate, for the three naturally-occurring 6-oxopurine bases guanine, hypoxanthine, and xanthine and for the base analogue, allopurinol. Differences in specificity between the purified P. falciparum HGXPRT and human hypoxanthine guanine phosphoribosyltransferase enzymes were detected which may be able to be exploited in rational drug design.

Animals↗
PubMed1999

COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules.

An interactive program is described for calculating the second virial coefficient contribution to the thermodynamic nonideality of solutions of rigid macromolecules based on their triaxial dimensions. The FORTRAN-77 program, available in precompiled form for the PC, is based on theory for the covolume of triaxial ellipsoid particles [Rallison, J. M., and S.E Harding. (1985). J. Colloid Interface Sci. 103:284-289]. This covolume has the potential to provide a magnitude for the second virial coefficient of macromolecules bearing no net charge. Allowance for a charge-charge contribution is made via an expression based on Debye-Hückel theory and uniform distribution of the net charge over the surface of a sphere with dimensions governed by the Stokes radius of the macromolecule. Ovalbumin, ribonuclease A, and hemoglobin are used as model systems to illustrate application of the COVOL routine.

Animals↗
PubMed1998

Evidence for multiple enzyme site involvement in the modulation of thrombin activity by products of prothrombin proteolysis.

Kinetic evidence is presented for the interaction of prothrombin with several distinctive topological regions of the thrombin molecule. Modulations of thrombin catalytic activity on the protein substrates prothrombin and prethrombin 1 are demonstrated that involve the fragment 1 and fragment 2 portions. The inhibitory effects are demonstrably non-competitive. In addition to exhibiting non-competitive inhibition, fragment 2 is capable of enhancing proteolysis by thrombin; and therefore to react with a second region of the enzyme. On the basis of the crystallographic studies of the complex between fragment 2 and thrombin (Arni et al., Biochemistry 32 (1992) 4727), this activating site is proposed to be associated with exosite II. The allosteric switch between procoagulant and anticoagulant activities identified from studies by Di Cera (Dang et al., Proc. Natl. Acad. Sci USA 92 (1995) 5977) could be 'thrown' by a macromolecular effector that is generated during thrombin formation--a plausible mechanism for switching that deserves further investigation.

Allosteric Site↗
PubMed1998

Second-order kinetic analysis of IAsys biosensor data: its use and applicability.

The kinetic analysis of IAsys biosensor association data usually relies upon the assumption of constant ligate concentration. In certain circumstances this assumption may no longer be valid. In a similar vein, the analysis of the dissociation phase assumes the concentration of ligate to be negligible in the liquid phase-an assumption that may not be sustainable for high-affinity interactions. In this paper we derive analytical solutions of the second-order differential kinetic equations for the association and dissociation phases, together with a binding isotherm that also allows for changes in concentration of both the ligand and the ligate. Using these equations it is possible to determine the conditions under which the pseudo-first-order assumption ceases to be valid. It is found that the effect of ligate depletion on the association rate constant becomes significant only when binding low ligate concentrations to ligand on surfaces with high binding capacities or high affinities. Similarly, the rebinding in the dissociation phase is dependent upon the affinity and the ligand capacity together with the starting dissociation response compared to the capacity. Finally, depletion also affects the form of the binding isotherm, particularly in situations involving high matrix capacities for ligate and high-affinity interactions.

Biosensing Techniques↗
PubMed1998

Potential of biosensor technology for the characterization of interactions by quantitative affinity chromatography.

This review places the characterization of interactions by biosensor technology in the broader context of their study by quantitative affinity chromatography. The general reluctance to consider biosensor-based characterization as a form of quantitative affinity chromatography on the grounds of a difference in aims of the two techniques reflects a mistaken belief that BIAcore and IAsys studies characterize the kinetics of the chemical reaction responsible for biospecific adsorption of a soluble reactant to an immobilized form of its affinity partner. It now transpires that the association and dissociation rate constants thereby determined refer to thermodynamic characterization of biospecific adsorption in terms of a single-phase model in which affinity sites are distributed uniformly throughout the liquid-phase volume accessible to the partitioning reactant--the model used for characterization of biospecific adsorption by quantitative affinity chromatography. In that light the most important attribute of biosensor technology is its potential for thermodynamic characterization of biospecific adsorption by virtue of its ability to monitor complex formation directly; and hence its potential for the characterization of interactions with affinities that are too strong for study by forms of quantitative affinity chromatography that monitor complex formation on the basis of reactant depletion from the liquid phase. Kinetic as well as thermodynamic analyses of biosensor data are described for attainment of that potential.

Biosensing Techniques↗
PubMed1998

Folding, calcium binding, and structural characterization of a concatemer of the first and second ligand-binding modules of the low-density lipoprotein receptor.

The ligand-binding domain of the low-density lipoprotein (LDL) receptor is comprised of seven tandemly repeated ligand-binding modules, each being approximately 40 amino acids long and containing six conserved cysteine residues. We have expressed and characterized a concatemer of the first two modules (LB1 and LB2) of the human LDL receptor. Oxidative folding of the recombinant concatemer (rLB1-2), in the presence of calcium ions, gave a single dominant isomer with six disulfide bonds. Peptic cleavage of the short linker region that connects the last cysteine residue of LB1 and the first cysteine residue of LB2 yielded two discrete fragments, thus excluding the presence of intermodule disulfide bonds. The N-terminal module, LB1, reacted with a conformation-specific monoclonal antibody (IgG-C7) made to LB1 in the native LDL receptor. From this, we concluded that the first module was correctly folded, with the same set of disulfide bonds as LB1 of the LDL receptor. The disulfide bond connections of LB2 were identified from mass spectral analysis of fragments formed by digestion of the C-terminal peptic fragment with elastase. These data showed that the disulfide bonds of LB2 connected Cys(I) and Cys(III), Cys(II) and Cys(V), and Cys(IV) and Cys(VI). This pattern is identical to that found for recombinant LB1 and LB2. The concatemer has two high-affinity calcium-binding sites, one per module. An analysis of the secondary chemical shifts of Calpha protons shows that the conformations of LB1 and LB2 in the concatemer are very similar to those of the individual modules, with no evidence for strong interactions between the two modules.

Amino Acid Sequence↗
PubMed1998

On the need to consider kinetic as well as thermodynamic consequences of the parking problem in quantitative studies of nonspecific binding between proteins and linear polymer chains.

Attention is drawn to a need for caution in the thermodynamic characterization of nonspecific binding of a large ligand to a linear acceptor such as a polynucleotide or a polysaccharide-because of the potential for misidentification of a transient (pseudoequilibrium) state as true equilibrium. The time course of equilibrium attainment during the binding of a large ligand to nonspecific three-residue sequences of a linear acceptor lattice has been simulated, either by numerical integration of the system of ordinary differential equations or by a Monte Carlo procedure, to identify the circumstances under which the kinetics of elimination of suboptimal ligand attachment (called the parking problem) create such difficulties. These simulations have demonstrated that the potential for the existence of a transient plateau in the time course of equilibrium attainment increases greatly (i) with increasing extent of acceptor saturation (i.e., with increasing ligand concentration), (ii) with increasing magnitude of the binding constant, and (iii) with increasing length of the acceptor lattice. Because the capacity of the polymer lattice for ligand is most readily determined under conditions conducive to essentially stoichiometric interaction, the parameter so obtained is thus likely to reflect the transient (irreversible) rather than equilibrium binding capacity. A procedure is described for evaluating the equilibrium capacity from that irreversible parameter; and illustrated by application to published results [M. Nesheim, M.N. Blackburn, C.M. Lawler, K.G. Mann, J. Biol. Chem. 261 (1986) 3214-3221] for the stoichiometric titration of heparin with thrombin.

Journal Article↗
PubMed1998

Direct analysis of sedimentation equilibrium distributions reflecting complex formation between dissimilar reactants.

Procedures are developed for the characterization of thermodynamically ideal complex formation between dissimilar macromolecular reactants by direct analysis of sedimentation equilibrium distributions. Studies of an electrostatic interaction between ovalbumin and cytochrome c are used to illustrate the application of analyses pertaining to (i) the situation in which separate sedimentation equilibrium distributions for the two macromolecular constituents are available, (ii) that in which the experimental record reflects the distribution of only one constituent, and (iii) the situation in which a composite distribution for both constituents is the sole experimental record. An association constant of 63 000 (+/- 2000) M-1 is obtained for the 1:1 interaction between ovalbumin and cytochrome c under the conditions examined (pH 6.3, I 0.03). Because of their inherent simplicity, these direct analytical procedures offer potential for accommodating the effects of thermodynamic nonideality in dissimilar reactant systems.

Animals↗
PubMed1997

Theoretical and experimental considerations of the pseudo-first-order approximation in conventional kinetic analysis of IAsys biosensor data.

The validity of the conventional interpretation of IAsys biosensor profiles in terms of pseudo-first-order kinetic behavior is subjected to closer scrutiny by its application to simulated data for low- and high-affinity interactions between ligate and immobilized ligand. As might reasonably have been expected, analysis of the simulated data for the low-affinity system (association equilibrium constant of 10(5) M-1) in such terms returned the input association and dissociation rate constants (10(3) M-1 s-1 and 10(-2) s-1, respectively)-a consequence of essential compliance with the assumed constancy of ligate concentration in the liquid phase. For the high-affinity interaction (ka = 10(5) M-1 s-1, kd = 10(-2) s-1, KAX = 10(7) M-1) the ligate concentration was depleted by up to 35%, and hence its assumed constancy was clearly an untenable approximation. Whereas no symptomatic evidence of such violation (apart from the return of incorrect estimates of ka and kd) was evident from pseudo-first-order kinetic analysis of the adsorption profiles, the corresponding analysis of desorption profiles was more informative in that the data deviated demonstrably from pseudo-first-order kinetic behavior. A second-order kinetic analysis was therefore developed and shown to be applicable to adsorption and desorption profiles, irrespective of the validity or otherwise of the pseudo-first-order kinetic approximation. Experimental results obtained for the interaction of histidine-rich glycoprotein with immobilized IgG were then used to illustrate various features of the pseudo-first-order and second-order kinetic analyses, and to determine from the second-order analysis an association equilibrium constant of 2 x 10(8) M-1, which is 20-fold greater than the value obtained by interpretation of the profiles in terms of pseudo-first-order kinetic behavior.

Adsorption↗
PubMed1997

An ultracentrifugal approach to quantitative characterization of the molecular assembly of a physiological electron-transfer complex: the interaction of electron-transferring flavoprotein with trimethylamine dehydrogenase.

The interaction between two physiological redox partners, trimethylamine dehydrogenase and electron-transferring flavoprotein, has been characterized quantitatively by analytical ultracentrifugation at 4 degrees C. Analysis of sedimentation-equilibrium distributions obtained at 15 000 rpm for mixtures in 10 mM potassium phosphate, pH 7.5, by means of the psi function [Wills, P. R., Jacobsen, M. P. & Winzor, D. J. (1996) Biopolymers 38, 119-130] has yielded an intrinsic dissociation constant of 3-7 microM for the interaction of electron-transferring flavoprotein with two equivalent and independent sites on the homodimeric enzyme. This investigation indicates the potential of sedimentation equilibrium for the quantitative characterization of interactions between dissimilar macromolecules.

Bacteria↗
PubMed1997

Use of a resonant mirror biosensor to characterize the interaction of carboxypeptidase A with an elicited monoclonal antibody.

The binding of apocarboxypeptidase A to an immobilized form of its elicited monoclonal antibody has been used to explore the potential of a biosensor instrument (IAsys) based on resonant mirror technology for the quantitative characterization of antibody-antigen interactions. Advantage has been taken of the stirred cuvette design of the IAsys instrument to develop a stepwise titration procedure for thermodynamic characterization of the interaction, an association equilibrium constant of 3.3 (+/-0.9) x 10(7) M-1 having been obtained under the conditions studied (0.1 M Tris/HCl-0.5 M NaCl, pH 7.5, 21 degrees C). In a test of the feasibility of subjecting the time course of biosensor response to conventional pseudo-first-order kinetic analysis, nonconformity of results with such description was encountered at high and low concentrations of apocarboxypeptidase A. Whereas the deviations from Langmuirian kinetic behavior at high antigen concentrations undoubtedly stem from the same sources as those already encountered in studies with the BIA-core biosensor instrument, the deviations at the other concentration extreme occur in a range in which the assumed constancy of free antigen concentration in the liquid phase is becoming a poor approximation. An alternative approach in such circumstances has been tested in which prior thermodynamic characterization is a prerequisite for rate constant evaluation by means of a second-order kinetic analysis. Finally, the effect of soluble anticarboxypeptidase A on the pseudo-first-order kinetics of the biosensor response has been used to illustrate a simple kinetic procedure for evaluating the affinity constant for the antibody-antigen interaction in solution, a value of 1.9 (+/-0.2) x 10(8) M-1 being obtained by such means.

Antibodies, Monoclonal↗
PubMed1997

Studies of protein interactions by biosensor technology: an alternative approach to the analysis of sensorgrams deviating from pseudo-first-order kinetic behavior.

A procedure for evaluating the thermodynamic equilibrium constant by kinetic analysis of sensorgrams which deviate from the pseudo-first-order kinetic behavior predicted for 1:1 interactions between ligate and affinity sites on the sensor surface is described. This analysis employs quantitative expressions that are used in conventional kinetic characterization of protein interactions by biosensor technology, but with the equilibrium sensorgram response fixed at a predetermined magnitude. Simulated sensorgrams for situations in which the aberrant kinetic behavior reflects (i) heterogeneity of affinity sites and (ii) isomerization of the complex between ligate and affinity sites are used to explore the feasibility of the approach. Its application is then illustrated with BIAcore studies of the interaction between the Fab fragment of an anti-paraquat monoclonal antibody and immobilized antigen in the form of a paraquat analog attached covalently to the sensor surface. Studies with an extremely high degree of antigen substitution on the sensor surface yielded sensorgrams that deviated markedly from pseudo-first-order kinetic behavior. However, they yielded the same binding constant (3 x 10(6) M-1) as the value deduced by conventional analysis of sensorgrams that conformed with pseudo-first-order kinetics because of a much lower concentration of immobilized antigen on the sensor surface. Such identity of binding constants eliminates heterogeneity of immobilized paraquat sites as the likely source of the aberrant kinetic behavior.

Antibodies, Monoclonal↗
PubMed1997

Effects of molecular crowding on the interaction between DNA and the Escherichia coli regulatory protein TyrR.

Fluorescence quenching has been used to measure quantitatively the effects of sucrose and triethylene glycol on the interaction between the Escherichia coli regulatory protein TyrR and a 30-basepair oligonucleotide containing the strong TyrR box of the TyrR operon. It was observed that the apparent binding constant increased in the presence of co-solutes, the dependence of the logarithm of the apparent binding constant on molar concentration being indistinguishable and essentially linear for both co-solutes. This activation of the TyrR-oligonucleotide interaction is attributed to thermodynamic nonideality arising from molecular crowding, an interpretation which is supported by the reasonable agreement observed between the experimental extent of reaction enhancement and that predicted on the statistical-mechanical basis of excluded volume.

Base Sequence↗
PubMed1996

Evaluation of affinity constants by competitive binding assays: removal of empiricism from the Müller method.

A method is described for the quantitative screening of antigen analogs by competitive radioimmunoassay. This analytical procedure is based on an experimental design developed for the comparison of binding affinities by means of an empirical quantitative expression (Müller, R. (1980) J. Immunol. Methods 92, 589-601). The present analysis, which allows retention of the same general approach without sacrifice of thermodynamic rigor, is illustrated by application to literature results obtained by radioimmunoassay screening of the interactions between antigen analogs and antibodies elicited in response to (i) a scorpion toxin and (ii) 8-hydroxy-2-deoxyguanosine.

Antigen-Antibody Reactions↗
PubMed1996

Thermodynamic analysis of the effects of small inert cosolutes in the ultracentrifugation of noninteracting proteins.

Considerations of the effect of a small cosolute on the sedimentation equilibrium distribution for a noninteracting protein have led to the development of a simple procedure for evaluating both the molecular weight of the protein and the second virial coefficient describing the excluded volume interaction between protein and cosolute. Its application is illustrated by analysis of sedimentation equilibrium distributions for bovine thyroglobulin and horse liver alcohol dehydrogenase in the presence of a range of sucrose concentrations, and also of those for aldolase in the presence of urea to obtain the subunit molecular weight of this tetrameric enzyme. The effects of sucrose concentration on the sedimentation coefficients of thyroglobulin, catalase, and horse liver alcohol dehydrogenase are also examined to demonstrate that the second virial coefficients for protein-cosolute excluded volume interaction may be determined, albeit with less precision, from the cosolute concentration required to render the sedimentation coefficient zero by virtue of its effect on the buoyancy term. These findings serve to reinforce the fact that the effects of small cosolutes usually ascribed to changes in "protein solvation" are envisaged more realistically in terms of excluded volume.

Alcohol Dehydrogenase↗
PubMed1996

Further observations on the measurement of fatty acid incorporation by erythrocyte ghosts to quantify unbound palmitate concentration in albumin-palmitate mixtures.

Advantage has been taken of the extensive and reversible incorporation of long-chain fatty acids by erythrocyte ghosts to characterize the interaction of tritium-labeled palmitic acid with human serum albumin (pH 7.4, 37 degrees C). A stoichiometric binding constant for 1:1 complex formation (K1) of 4.6 (+/-0.3) x 10(8) M-1 was obtained from experiments in which erythrocyte ghosts were the source of fatty acid. An essentially identical estimate of 4.1 (+/-0.7) x 10(8) M-1 was obtained from a second series of experiments in which the [3H]palmitate was included with the albumin in the aqueous phase. The magnitude of the present K1 estimate, which is three- to fivefold larger than most recently reported values, reflects binding measurements restricted to a very limited range of unbound palmitate concentration (-0.2 nM) to ensure that the ligand is essentially monomeric. This use of erythrocyte ghosts to quantify the palmitate-albumin interaction has reinforced the basic tenets of a published procedure [I. N. Bojesen, and E. Bojesen (1992) J. Lipid Res. 33, 1327-1334], the major virtue of which is its ability to provide a direct measure of the equilibrium concentration of unbound fatty acid in albumin-palmitate mixtures.

Binding Sites↗