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PubMed2003

Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi.

The enzyme ornithine carbamoyltransferase (OTCase) of Moritella abyssi (OTCase(Mab)), a new, strictly psychrophilic and piezophilic bacterial species, was purified. OTCase(Mab) displays maximal activity at rather low temperatures (23 to 25 degrees C) compared to other cold-active enzymes and is much less thermoresistant than its homologues from Escherichia coli or thermophilic procaryotes. In vitro the enzyme is in equilibrium between a trimeric state and a dodecameric, more stable state. The melting point and denaturation enthalpy changes for the two forms are considerably lower than the corresponding values for the dodecameric Pyrococcus furiosus OTCase and for a thermolabile trimeric mutant thereof. OTCase(Mab) displays higher K(m) values for ornithine and carbamoyl phosphate than mesophilic and thermophilic OTCases and is only weakly inhibited by the bisubstrate analogue delta-N-phosphonoacetyl-L-ornithine (PALO). OTCase(Mab) differs from other, nonpsychrophilic OTCases by substitutions in the most conserved motifs, which probably contribute to the comparatively high K(m) values and the lower sensitivity to PALO. The K(m) for ornithine, however, is substantially lower at low temperatures. A survey of the catalytic efficiencies (k(cat)/K(m)) of OTCases adapted to different temperatures showed that OTCase(Mab) activity remains suboptimal at low temperature despite the 4.5-fold decrease in the K(m) value for ornithine observed when the temperature is brought from 20 to 5 degrees C. OTCase(Mab) adaptation to cold indicates a trade-off between affinity and catalytic velocity, suggesting that optimization of key metabolic enzymes at low temperatures may be constrained by natural limits.

Adaptation, Biological↗
PubMed2005

Genomic organization and effects of ivermectin selection on Onchocerca volvulus P-glycoprotein.

Ivermectin (IVM) was first developed for use with livestock. It is now the only drug used for mass treatment of onchocerciasis. It is difficult to prove whether reports of sub-optimal responses to IVM in some Onchocerca volvulus infected patients are a result of drug resistance, as procedures typically used to examine IVM efficacy in livestock can not be performed on humans. To determine the effects of IVM on O. volvulus, one approach is to examine allele frequencies before and after treatment. Allele(s) linked to resistance may increase in frequency after repeated treatment. Mass treatment of large human populations to reduce transmission of O. volvulus will impose selection pressure for resistance. P-glycoprotein has been implicated as a candidate IVM resistance gene in nematodes. In this study, the intron-exon structure of O. volvulus P-glycoprotein (OvPGP) has been defined. The gene spans 10.6 kb, is AT-rich, contains 24 exons and a high proportion of class 0 introns. The genetic diversity of 28 loci spanning the entire OvPGP gene was examined in four O. volvulus populations from the Volta Region of Ghana. Worms collected in 1999 and 2002 from IVM treated patients showed reduced genetic polymorphism and an increase in the number of loci not in Hardy-Weinberg equilibrium. Changes in allelic patterns and a reduction in diversity at many loci in P-glycoprotein in the parasites from IVM treated patients in 1999 and 2002 suggest that IVM is imposing selection on this gene, consistent with a possible development of IVM resistance.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2003

Polyamines and novel polyamine conjugates interact with DNA in ways that can be exploited in non-viral gene therapy.

As a part of our continuing studies on 'Polyamines and their role in human disease' we are investigating how polyamines, and especially how novel polyamine conjugates, interact with DNA. We are studying how these conjugates interact with circular plasmids in order to produce nanometre-sized particles suitable for transfecting cells. Our considerations of structure--activity relationships (SAR) within naturally occurring and synthetic polyamines have shown the significance of the inter-atomic distances between the basic nitrogen atoms. As these atoms are typically fully protonated under physiological conditions, they exist in equilibrium as polyammonium ions. The covalent addition of a lipid moiety, typically one or two alkyl or alkenyl chains, or a steroid, allows much greater efficiency in DNA condensation and in the cellular transfection achieved. Thus efficient DNA condensation and subsequently drug delivery (i.e. with DNA as the drug) can be brought about using novel polyamine conjugates. Taking further advantage of the functionalization of specific steroids (e.g. cholesterol and certain bile acids), we have designed and prepared novel fluorescent molecular probes as tools to throw light on the problematic steps in non-viral gene delivery which still impede efficient gene therapy. Thus, the current aims of our research are to understand, design and prepare small-molecule lipopolyamines for non-viral gene therapy (NVGT). The rational design and practical preparation of non-symmetrical polyamine carbamates and amides, based on steroid templates of cholesterol and the bile acid lithocholic acid as the lipid moiety, provides fluorescent molecular probes that condense DNA. These novel lipopolyamine conjugates mimic the positive charge distribution found in the triamine spermidine and the tetra-amine spermine alkaloids. After optimizing their SAR, these fluorescent probes will be useful in monitoring gene delivery in NVGT.

DNA↗
PubMed2003

[Principle of least action, physiology of vision, and conditioned reflexes theory].

The variation principles such as principle of least action by Maupertuis (1740) and Fermat principle (1660) are fundamental for physics. They permit to establish a property by which the actual state is differing from all possible states of the system. The variation approach permits to establish equation of motion and equilibrium of a material system on the basis of one common rule which reduces to the search of the function extremes, describes this property of the system. So for the optical systems, crucial is the time and not the length of the way. According to Fermat principles, the light "choosen" from all possible ways connects two dots in the way which needs the least time. Generality of the variation principles guarantees success of their use in brain function investigations. Between different attempts to apply the variation principles to psychology and linguistics, the Zipf principle of least effort must be distinguished. Zipf (1949) demonstrated that languages and some artificial codes satisfied the least principle. For the brain physiology, classical conditioned reflex theory is the ideal area of variation principles application. According to this approach, conditioning leads to finding the extreme during fixation of the temporal link. In vision, physiological investigations are difficult because the signal has many dimensions. For example, during perception of spatial properties of surrounding world, in vision is realized minimization (reduction) of spatial-frequency spectrum of the scene. The receptive fields provide optimal accumulation of the signal. In ontogenesis, signal--noise ratio becomes optimal as receptive fields minimized the internal noise spectrum. According to the theory of match filtration, in the visual system recognition is carryied out by minimal differences between the image description in the visual system and storage in the human memory template of that image. The variation principles help to discover the physical property of phenomenon. The law discovered for mechanical system may be translated to quantum level. In physiology, variation principles permit us to connect information approach with concrete physiological mechanisms of pattern recognition and conditioned reflex.

Conditioning, Classical↗
PubMed1977

Energy-linked protonation of quinacrine in beef heart submitochondrial membranes.

1. The absorption spectrum of quinacrine in aqueous solution, in the visible region, changes with the pH of the medium in the pH range from 6.0 to 9.0 with an isosbestic point at 353 nm. This indicates that the monoprotonated (quinacrine - H+) and the diprotonated (quinacrine - 2H+) forms of quinacrine at equilibrium in this pH range have a 1 to 1 stoichiometry. 2. The monoprotonated and the dipronated forms to quinacrine exhibit similar fluorescence emission spectra, but distinctive fluorescence excitation spectra. 3. The relative fluorescence quantum yields of quinacrine in aqueous media of various pH values are estimated. The relative fluorescence quantum yield of quinacrine at pH 9.0 is more than 3 fold of that at pH 6.0. 4. The fluorescence excitation and emission spectra, as well as the relative fluorescence quantum yield of quinacrine associated with non-energized submitochondrial membranes, are similar to those of quinacrine alone. 5. Analyses of the absorption spectra, the fluorescence excitation spectra and the relative fluorescence quantum yield indicate that the energy-linked fluorescence decrease of quinacrine associated with the energized submitochondrial membranes results from the protonation of quinacrine - H+ to form quinacrine - 2H+. 6. Quantitative data are provided indicating that the maximal efficiency of protonation of quinacrine - H+ to form quinacrine - 2H+ depends on the concentration of H+ in the membranes generated through energy coupling, and the concentration of quinacrine - H+ initially present in the reaction medium. Under optimal conditions virtually complete conversion of quinacrine - H+ into quinacrine - 2H+ is observed. 7. The fluorescence intensity of quinacrine, either alone or associated with non-energized submitochondrial membranes, decreases with increasing temperature. When quinacrine is associated with the energized membranes, however, its fluorescence intensity increases slightly with increasing temperature. This unusual fluorescence behavior towards temperature, together with the fact that under optimal conditions virtually all the quinacrine molecules associated with the energized membranes are in the diprotonated form, further substantiate our earlier conclusion that the diprotonated quinacrine molecules are tightly bound to the energized membranes in a fashion which does not permit ready equilibration with the external medium.

Animals↗
PubMed2004

Evolution of cannibalism: referring to costs of cannibalism.

A rational explanation for cannibalism is that it would be favored under conditions of crowding of conspecific individuals and/or low availability of alternative prey with the fear of starvation, so as to maximize individual fitness. Cannibalism has, however, not evolved and is not maintained by a simple individual optimization, while it has evolved and is maintained as a game among population members. We analysed the attainable state of an evolutionary cannibalism game within a framework that reflects the minimum essence of cause-effect in the cannibalism phenomenon. Cannibalism is predator-prey interaction among conspecifics. Immediate direct payoffs (survival in the interaction among conspecifics) and indirect payoffs (growth results in potential productivity and survival against the threat of starvation) would be included. No morphological specialization and no size priority of cannibalism individuals are assumed as conservative situations in which we analyse the possibility of cannibalism. Cannibalism would be possible under the conservative condition, if initially the wild population's cannibalism rate is not sufficiently lower than a threshold value. Crowding and/or low availability of alternative prey with the fear of starvation facilitates cannibalism evolution. Energy gain from conspecific prey would be attenuated by costs of counterattacks by conspecific victims and by challenge cost of its own. Discounting net intake energy required in the arms race for cannibalism challenge result in a relative disadvantage of having a high cannibalism rate and makes an evolutionary equilibrium of low cannibalism rate, even when potential profitability of conspecific prey is high.

Animals↗
PubMed1994

Biochemical characteristics of a calmodulin-phosphodiesterase activator increased in spontaneously hypertensive mice and rats.

The biochemical characteristics of calmodulin-phosphodiesterase (CaM-PDE) are described. It is a cytosolic, hydrophobic, and heat-, acid-, and base-stable compound sensitive to proteases. It is optimally extracted from neutral supernatants by CHCl3/MeOH (2:1 or 1:1). It partitions into the organic fraction of CHCl3/MeOH extracts, whereas the aqueous fraction contains a component that potentiates the activator's capacity to stimulate CaM-PDE. The activator interacts with PDE by increasing its apparent affinity for CaM. Size partition chromatography of CHCl3/MeOH extracts from spontaneously hypertensive rats produces two activity peaks, one eluting at void volume with the second eluting at a position corresponding to a 4-kDa peptide. The compound at void volume can be converted to the 4-kDa entity by sonication. The CaM-PDE activator behaves as a lipopeptide that shares several characteristics with parathyroid hypertensive factor.

Acid-Base Equilibrium↗
PubMed2005

Energetics of DNA end binding by E.coli RecBC and RecBCD helicases indicate loop formation in the 3'-single-stranded DNA tail.

We examined the equilibrium binding of Escherichia coli RecBC and RecBCD helicases to duplex DNA ends possessing pre-existing single-stranded (ss) DNA ((dT)(n)) tails varying in length (n=0 to 20 nucleotides) in order to determine the contributions of both the 3' and 5' single strands to the energetics of complex formation. Protein binding was monitored by the fluorescence enhancement of a reference DNA labeled at its end with a Cy3 fluorophore. Binding to unlabeled DNA was examined by competition titrations with the Cy3-labeled reference DNA. The affinities of both RecBC and RecBCD increase as the 3'-(dT)(n) tail length increases from zero to six nucleotides, but then decrease dramatically as the 3'-(dT)(n) tail length increases from six to 20 nucleotides. Isothermal titration calorimetry experiments with RecBC show that the binding enthalpy is negative and increases in magnitude with increasing 3'-(dT)(n) tail length up to n=6 nucleotides, but remains constant for n > or =6. Hence, the decrease in binding affinity for 3'-(dT)(n) tail lengths with n > or =6 is due to an unfavorable entropic contribution. RecBC binds optimally to duplex DNA with (dT)6 tails on both the 3' and 5'-ends while RecBCD prefers duplex DNA with 3'-(dT)6 and 5'-(dT)10 tails. These data suggest that both RecBC and RecBCD helicases can destabilize or "melt out" six base-pairs upon binding to a blunt DNA duplex end in the absence of ATP. These results also provide the first evidence that a loop in the 3'-ssDNA tail can form upon binding of RecBC or RecBCD with DNA duplexes containing a pre-formed 3'-ssDNA tail with n > or =6 nucleotides. Such loops may be representative of those hypothesized to form upon interaction of a Chi site contained within the unwound 3' ss-DNA tail with the RecC subunit during DNA unwinding.

Base Sequence↗
PubMed2006

Positron emission tomography displacement sensitivity: predicting binding potential change for positron emission tomography tracers based on their kinetic characteristics.

There is great interest in positron emission tomography (PET) as a noninvasive assay of fluctuations in synaptic neurotransmitter levels, but questions remain regarding the optimal choice of tracer for such a task. A mathematical method is proposed for predicting the utility of any PET tracer as a detector of changes in the concentration of an endogenous competitor via displacement of the tracer (a.k.a., its 'vulnerability' to competition). The method is based on earlier theoretical work by Endres and Carson and by the authors. A tracer-specific predictor, the PET Displacement Sensitivity (PDS), is calculated from compartmental model simulations of the uptake and retention of dopaminergic radiotracers in the presence of transient elevations of dopamine (DA). The PDS predicts the change in binding potential (DeltaBP) for a given change in receptor occupancy because of binding by the endogenous competitor. Simulations were performed using estimates of tracer kinetic parameters derived from the literature. For D(2)/D(3) tracers, the calculated PDS indices suggest a rank order for sensitivity to displacement by DA as follows: raclopride (highest sensitivity), followed by fallypride, FESP, FLB, NMSP, and epidepride (lowest). Although the PDS takes into account the affinity constant for the tracer at the binding site, its predictive value cannot be matched by either a single equilibrium constant, or by any one rate constant of the model. Values for DeltaBP have been derived from published studies that employed comparable displacement paradigms with amphetamine and a D(2)/D(3) tracer. The values are in good agreement with the PDS-predicted rank order of sensitivity to displacement.

Binding, Competitive↗
PubMed1996

A comparative study of histone deacetylases of plant, fungal and vertebrate cells.

The enzymatic equilibrium of reversible core histone acetylation is maintained by two enzyme activities, histone acetyltransferase and histone deacetylase (HD). These enzyme activities exist as multiple enzyme forms. The present report describes methods to extract different HD-forms from three organisms, germinating maize embryos, the myxomycete Physarum polycephalum, and chicken red blood cells; it provides data on the chromatographic separation and partial purification of HD-forms. In germinating maize embryos three HDs (HD1-A, HD1-B, HD2) can be discriminated; HD1-A, HD1-B, and HD2 were characterized in terms of their dependence on pH, temperature and various ions, as well as kinetic parameters (Km for core histones) and inhibition by various compounds. The same parameters were investigated for the corresponding enzymes of Physarum polycephalum, and mature and immature chicken erythrocytes. Based on these results, optimum assay conditions were established for the different enzyme forms. The kinetic data revealed that the maize histone deacetylase HD1-B peak after partial purification by Q-Sepharose chromatography was heterogeneous and consisted of two histone binding sites that differed significantly in their affinity for purified core histones. Optimized affinity chromatography on poly-Lysine Agarose indeed showed that the former defined deacetylase HD1-B can be separated clearly into two individual HD enzyme forms. The high multiplicity of histone deacetylases underlines the importance of these enzymes for the complex regulation of core histone acetylation.

Acetylation↗
PubMed2005

Solution structure of the complex between CR2 SCR 1-2 and C3d of human complement: an X-ray scattering and sedimentation modelling study.

Complement receptor type 2 (CR2, CD21) forms a tight complex with C3d, a fragment of C3, the major complement component. Previous crystal structures of the C3d-CR2 SCR 1-2 complex and free CR2 SCR 1-2 showed that the two SCR domains of CR2 form contact with each other in a closed V-shaped structure. SCR 1 and SCR 2 are connected by an unusually long eight-residue linker peptide. Medium-resolution solution structures for CR2 SCR 1-2, C3d, and their complex were determined by X-ray scattering and analytical ultracentrifugation. CR2 SCR 1-2 is monomeric. For CR2 SCR 1-2, its radius of gyration R(G) of 2.12(+/-0.05) nm, its maximum length of 10nm and its sedimentation coefficient s20,w(o) of 1.40(+/-0.03) S do not agree with those calculated from the crystal structures, and instead suggest an open structure. Computer modelling of the CR2 SCR1-2 solution structure was based on the structural randomisation of the eight-residue linker peptide joining SCR 1 and SCR 2 to give 9950 trial models. Comparisons with the X-ray scattering curve indicated that the most favoured arrangements for the two SCR domains corresponded to an open V-shaped structure with no contacts between the SCR domains. For C3d, X-ray scattering and sedimentation velocity experiments showed that it exists as a monomer-dimer equilibrium with a dissociation constant of 40 microM. The X-ray scattering curve for monomeric C3d gave an R(G) value of 1.95 nm, and this together with its s20,w(o) value of 3.17 S gave good agreement with the monomeric C3d crystal structure. Modelling of the C3d dimer gave good agreements with its scattering and ultracentrifugation parameters. For the complex, scattering and ultracentrifugation experiments showed that there was no dimerisation, indicating that the C3d dimerisation site was located close to the CR2 SCR 1-2 binding site. The R(G) value of 2.44(+/-0.1) nm, its length of 9 nm and its s20,w(o) value of 3.45(+/-0.01) S showed that its structure was not much more elongated than that of C3d. Calculations with 9950 models of CR2 SCR 1-2 bound to C3d through SCR 2 showed that SCR 1 formed an open V-shaped structure with SCR 2 and was capable of interacting with the surface of C3d. We conclude that the open V-shaped structures formed by CR2 SCR 1-2, both when free and when bound to C3d, are optimal for the formation of a tight two-domain interaction with its ligand C3d.

Complement C3d↗
PubMed1993

Analysis of the functions of the first epidermal growth factor-like domain of factor X.

Upon activation, factor X participates in the prothrombin activation complex. Similar to 4-carboxyglutamic acid (Gla)-domainless protein C, the Gla-domainless factor X (GDFX) contains a high affinity Ca(2+)-binding site critical for the function of these molecules. In the case of protein C, we recently demonstrated that the high affinity Ca(2+)-binding site critical for activation is outside the first epidermal growth factor (EGF) homology domain. To examine if this is also true for factor X, we have expressed in human 293 cells a deletion mutant of factor X (E2FX) which lacks the entire Gla region as well as the NH2-terminal EGF homology region of factor X. Direct binding studies by equilibrium dialysis indicate that E2FX contains a single Ca(2+)-binding site with a dissociation constant (Kd) of 154 +/- 48 microM. The functional properties of E2FX are equivalent or improved over those of GDFX. For instance, the factor X coagulant protein of Russell's viper venom activates E2FX three times faster than recombinant GDFX. Kinetic analysis of prothrombin activation in the absence of membranes indicates that activated GDFX and E2FX bind to factor Va with equal affinity (Kd = 4.1 microM). The Ca2+ concentration required for half-maximal prothrombin activation rates in the above activation system shifted from 721 +/- 113 microM for activated GDFX to 193 +/- 64 microM for activated E2FX. GDFX and E2FX activation rates with the soluble tissue factor-factor VIIa complex were identical as was the Ca2+ dependence of the reaction. We conclude that E2FX retains a high affinity Ca(2+)-binding site and that the first EGF homology domain does not appear to have a positive functional role in the GDFX molecule. However, Ca2+ occupancy of the Ca(2+)-binding site in the first EGF domain of intact factor X may be essential for optimal prothrombin activation.

Animals↗
PubMed1980

Purification and properties of acyl-CoA oxidase from rat liver.

Acyl-CoA oxidase, the initial enzyme of the peroxisomal beta-oxidation system, was purified from rat liver. The final preparation was judged to be nearly homogeneous from the results of sedimentation analysis. Ultrogel AcA-34 column chromatography, and phosphocellulose column chromatography. The molecular weight of the enzyme was determined to be 139,000 by the sedimentation equilibrium method and Ultrogel AcA-34 column chromatography. The S020,W of the enzyme was 7.85S. Three protein components, A, B, and C, were found in the enzyme preparation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (molecular weights, 75,500, 50,100, and 19,000) and high-pressure liquid chromatrography in the presence of 6 M guanidine . HCl (molecular weights, 71,900, 51,700, and 20,500). It was concluded that components B and C were formed from component A, probably by proteolytic cleavage, based on the result of amino acid analysis of each component. The pI of the enzyme was 9.2. The enzyme contained FAD as a prosthetic group, and exhibited absorption maxima at 278, 378, and 450 nm. The FAD content was 1.22 mol/mol of enzyme. When palmitoyl-CoA was added to the enzyme solution under anaerobic conditions, the bound FAD was reduced. The Km values were lower for C14 to C18 acyl-CoA's than for others tested, whereas Vmax values were roughly the same for C8 to C18 acyl-CoA's. The Km value for O2 was 5 microM. The optimal pH was 8. 3-Ketohexadecanoyl-CoA inhibited the enzyme (Ki=0.47 microM), forming a charge-transfer complex with the enzyme.

Acyl Coenzyme A↗
PubMed1988

Radionuclide ventriculography (equilibrium gated blood pool scanning)--its present clinical position and recent developments.

Myocardial scanning (MS) and radionuclide ventriculography (RNV) are the foundation of nuclear cardiology. These procedures aim in two completely different directions: RNV tries to image heart motion, that is, mechanical (pump) function, and therefore belongs to the group of first-order functional imaging (FI, imaging mechanical function), whereas MS is based on myocardial metabolism, and therefore can be attributed to third-order functional imaging (metabolism). This statement is relevant for the assessment of the clinical position of RNV: Third-order (metabolism) functional imaging is the domain of nuclear medicine (NM), whereas first-order FI has to face the competition of alternative noninvasive procedures such as ultrasound (US), digital subtraction angiography (DSA), computer tomography (CT), and nuclear magnetic resonance (NMR). The domain of RNV includes stages two (acute infarction) and three (postinfarction period) of coronary arterial disease (CAD). The advantageous combination of quantitative data on global, left ventricular (LV) function and imaging of regional motion ensures the superiority of RNV over US. However, RNV is inferior to MS in physical examinations in the preinfarction stage of CAD, whereas US is clearly inferior to both NM procedures. Recent progress could be attained by gated SPECT (GASPECT). A proposal is presented for simplification of this time-consuming procedure. Technetium-labeled isonitriles offer the chance for the combination of "perfusion-motion" imaging of the myocardium. However, even standard RNV offers new possibilities. The multitude of parameters produced by quantitation has not yet been exploited completely. This can be done by discriminant analysis. The computer finds out an optimal subset from the whole set of parameters for the solution of a significant clinical problem. The software "learns" to find the "label" of a special pathognomonic entity. This computer work is supported by a relational data bank (Oracle) and an optical disk. Two examples for the effectiveness of the computer in problem solving are presented. It is concluded that RNV, even in the very competitive class of first-order functional imaging, enjoys a preferred position. The future indeed seems brighter because labeled isonitriles offer the chance for the combination of perfusion-motion imaging of the myocardium.

Coronary Disease↗
PubMed2001

Improved immunoturbidimetric assay for cystatin C.

An immunoturbidimetric assay for cystatin C was optimized with respect to assay imprecision. After investigating the optimum pH, polyethylene glycol concentration and specimen volume, two modifications were introduced: an increase in specimen volume to 25 microL; and an extension of the pre-incubation period to 240 s. These modifications produced an assay with between-batch imprecision (coefficient of variation, n = 10 or 11) ranging from 3-9% at 0.72 mg/L to 1.3% at 5.29 mg/L. The assay was susceptible to interference from lipaemia and haemolysis but not bilirubinaemia in both the original and modified protocol. Extending the pre-incubation to 240 s improved tolerance to common interferences and retained assay applicability in the routine clinical setting.

Acid-Base Equilibrium↗
PubMedDate not supplied

Analysis of the pH-dependencies of the association and dissociation kinetics of HIV-1 protease inhibitors.

The kinetic constants for the interactions between HIV-1 protease and a selection of inhibitors were determined at different pH-values using a biosensor based interaction assay. Since this technique does not involve a substrate, it was possible to determine the pH-dependencies of the association and dissociation rates of an inhibitor, without the complication of a pH-dependent enzyme-substrate/product equilibrium. The importance of these interactions was evaluated by correlating the free energy changes upon association and dissociation of inhibitors with the predicted change in electrostatic properties of the interacting groups as a result of altered pH. It was found that the kinetic parameters varied with pH in a unique manner for all inhibitors, demonstrating that the kinetic features were associated with the specific structure of each inhibitor. Association and dissociation had different pH-profiles, indicating that the two processes proceeded by different pathways/mechanisms. The energy barrier for dissociation of the enzyme-indinavir complex increased with pH from 4.1 to 7.4, while it was generally reduced for the other inhibitors as the pH was increased from 5.1 to 7.4. The pH-dependent interactions involved in the recognition/binding of inhibitors and in the stabilization of the complex were identified by analysing three-dimensional structures of enzyme-inhibitor complexes. The interaction between the pyridine nitrogen of indinavir with Arg-8 was hypothesized to be responsible for the unique pH-dependency of indinavir. The analysis revealed features of interactions that are significant for understanding enzyme function and for optimization of new drug leads. It also highlighted the importance of environmental conditions on interactions.

HIV Protease↗
PubMed2002

Engineering receptors and antibodies for biosensors.

Biosensor sensitivity and selectivity depend essentially on the properties of the biorecognition elements to be used for analyte binding. Two principally different applications are considered, (1) effects monitoring with biological components as targets for bioeffective substances, among them endocrine disruptors; and (2) immunochemical analysis employing antibodies as binding proteins for a wide variety of analytes such as pesticides. Genetic engineering provides an elegant way not only for providing unlimited amounts of biorecognition molecules but also for the alteration of existing properties and the supplementation with additional functions. Instrumental applications were carried out with the optical sensor BIAcore. The first example deals with the characterization of receptors. For this purpose, the human estrogen receptor alpha was used. Binding studies were carried out with natural as well as xenoestrogens. An equilibrium dissociation constant K(d) of 2.3x10(-10) (M) was derived for 17beta-estradiol. A competition assay was performed with a bovine serum albumin (BSA)-17beta-estradiol conjugate, immobilized at the optical sensor surface, and the free estrogen. The signals obtained represent estradiol equivalents. This format was transferred to a microplate-based enzyme-linked receptor assay. It reached a detection limit of 0.02 microg l(-1) 17beta-estradiol and proved suitable for the detection of natural and synthetic estrogens as well as xenoestrogens in field studies. The second example is targeted at kinetic and affinity measurements of recombinant antibody fragments derived from antibody libraries with s-triazine selectivities. Different strategies for the synthesis of antibody fragment libraries, followed by the selection of specific antibody variants, were examined. An antibody library was derived from a set of B cells. Chain shuffling of the heavy and light chains provided the best binders. An enzyme linked immunosorbent assay (ELISA) was achieved for atrazine with an IC(50) of 0.9 microg l(-1) and a detection limit of 0.2 microg l(-1). The close relations between the optimization of recombinant antibodies by evolutionary strategies and genetic algorithms are considered.

Algorithms↗
PubMed1995

Preparation and preclinical evaluation of humanised A33 immunoconjugates for radioimmunotherapy.

A humanised IgG1/k version of A33 (hA33) has been constructed and expressed with yields up to 700 mg l-1 in mouse myeloma NS0 cells in suspension culture. The equilibrium dissociation constant of hA33 (KD = 1.3 nM) was shown to be equivalent to that of the murine antibody in a cell-binding assay. hA33 labelled with yttrium-90 using the macrocyclic chelator 12N4 (DOTA) was shown to localise very effectively to human colon tumour xenografts in nude mice, with tumour levels increasing as blood concentration fell up to 144 h. A Fab' variant of hA33 with a single hinge thiol group to facilitate chemical cross-linking has also been constructed and expressed with yields of 500 mg l-1. Trimaleimide cross-linkers have been used to produce a trivalent Fab fragment (hA33 TFM) that binds antigen on tumour cells with greater avidity than hA33 IgG. Cross-linkers incorporating 12N4 or 9N3 macrocycles have been used to produce hA33 TFM labelled stably and site specifically with yttrium-90 or indium-111 respectively. These molecules have been used to demonstrate that hA33 TFM is cleared more rapidly than hA33 IgG from the circulation of animals but does not lead to accumulation of these metallic radionuclides in the kidney. 90Y-labelled hA33 TFM therefore appears to be the optimal form of the antibody for radioimmunotherapy of colorectal carcinoma.

Amino Acid Sequence↗

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