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PubMed1991

Asymmetric Boltzmann machines.

We study asymmetric stochastic networks from two points of view: combinatorial optimization and learning algorithms based on relative entropy minimization. We show that there are non trivial classes of asymmetric networks which admit a Lyapunov function L under deterministic parallel evolution and prove that the stochastic augmentation of such networks amounts to a stochastic search for global minima of L. The problem of minimizing L for a totally antisymmetric parallel network is shown to be associated to an NP-complete decision problem. The study of entropic learning for general asymmetric networks, performed in the non equilibrium, time dependent formalism, leads to a Hebbian rule based on time averages over the past history of the system. The general algorithm for asymmetric networks is tested on a feed-forward architecture.

Algorithms↗
PubMed1989

Solubilization and characterisation of the cholecystokininB binding site from pig cerebral cortex.

Cholecystokinin (CCK) binding sites were solubilized from pig cerebral cortical membranes with digitonin (2%, w/v) in the presence of Na+ (120 mM) and Mg2+ (5 mM). Scatchard plot transformation of equilibrium binding data obtained with 125I-CCK-8S gave an apparent dissociation constant (Kd) of 0.6 nM, comparable to that obtained in membranes in the presence of these cations. Hill coefficients close to unity suggested the presence of a single population of receptor sites. Competitive inhibition studies with pentagastrin, gastrin(1-17)S and the CCKA receptor antagonist L-364,718 indicated that the solubilized receptor sites were of the B-type (CCKB), with the same pharmacological profile as that observed in membranes. Optimal specific binding of 125I-CCK-8S to membrane-bound and solubilized receptors was obtained in the presence of divalent cations. Both the membrane-bound and the solubilized receptor activity were attenuated by guanylyl-imidodiphosphate (Gpp(NH)p) indicating that the brain CCKB receptors are coupled to G proteins.

Animals↗
PubMed2006

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile.

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH2CH2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6-311++G* basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C2h and C2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G* basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Models, Chemical↗
PubMed2003

Kinetic analysis of interactions between bispecific monoclonal antibodies and immobilized antigens using a resonant mirror biosensor.

A resonant mirror biosensor (IAsys) protocol is described for the comparative kinetic analysis of the ability of monoclonal antibodies (Mabs) and bispecific antibodies (Babs) to bind immobilized antigens. The protocol has been optimized and validated using the panel of affinity-purified antibodies, including two parental Mabs, one specific to human immunoglobulin G (hIgG) and another specific to horseradish peroxidase (HRP), and a Bab derived thereof by cell fusion (anti-hIgG/HRP Bab). The real-time kinetic analysis of antigen-antibody interactions using this protocol allows to demonstrate the differences in the avidity of bivalently binding Mabs and monovalent Babs. As shown in our previous study [J. Immunol. Methods 261 (2002) 103], the observed equilibrium association constants (Kass) determined by IAsys using this protocol yield figures almost overlapping with those obtained by solid-phase radioimmunoassay (RIA). The described protocol is suited for the investigation of the effects of valency on the binding properties of antibodies. It also may be applied for the selection of Mabs and Babs with desired features, for different fields of application.

Animals↗
PubMedDate not supplied

Improvement of exogenous DNA nuclear importation by nuclear localization signal-bearing vectors: a promising way for non-viral gene therapy?

Several vectors have been developed in order to target genes to specific cells. Virus-based vectors lead to a high transfection efficiency in vitro, but display important disadvantages such as pathological risks, which they expose to patients. Plasmid-associated chemical vectors lack these disadvantages, but allow only a very low efficiency of transgene expression. Most of the non-viral-based gene transfer techniques developed until now mainly focused their efforts to overcome the problem of DNA entry into the cell. Some recent works, however, have begun to investigate the nucleus entry problem and suggest that the trafficking of DNA from cytosol to the nucleus may be improved by using the nuclear localization signal (NLS) found in some nuclear proteins. If the vector contains one or several NLS, either as covalently or non-covalently DNA-linked peptides, a competition may take place between the rate of dissociation of the DNA-vector complexes and the rate of loading of the complexes to the NLS-mediated nucleus importation machinery. This equilibrium may be displaced towards the importation pathway by the use of NLS-bearing proteins instead of peptides. The possibility of recruiting normal endogenous cellular pathways of nuclear uptake to promote entry of exogenously applied DNA through the nuclear pore complex would, thus, seem promising. Nevertheless, attempts to improve the transport of DNA to the nucleus through the use of NLSs have achieved limited success. Although these systems show improved transgene expression, little is known about how they function in transfected cells, and the optimal formulation for gene expression is yet to be determined.

Active Transport, Cell Nucleus↗
PubMed2006

1H NMR Study of the influence of hemin vinyl-->methyl substitution on the interaction between the C-terminus and substrate and the "aging" of the heme oxygenase from Neisseria meningitidis: induction of active site structural heterogeneity by a two-fold symmetric hemin.

Solution 1H NMR has been used to characterize the active site molecular and electronic structure of the cyanide-inhibited 2,4-dimethyldeuterohemin complex of the heme oxygenase from Neisseria meningitidis (NmHO) with respect to the mode of interaction of the C-terminus with the substrate and the spontaneous "aging" of NmHO that results in the cleavage of the C-terminal Arg208-His209 dipeptide. The structure of the portion involving residues Ala12-Phe192 is found to be essentially identical to that of the protohemin complex in either solution or crystal. However, His207 from the C-terminus is found to interact strongly with the substrate 1CH3, as opposed to the 8CH3 in the protohemin complex. The different mode of interaction of His207 with the alternate substrates is attributed to the 2-vinyl group of protohemin sterically interfering with the optimal orientation of the proximal helix Asp27 carboxylate that serves as acceptor to the strong H-bond by the peptide of His207. The 2,4-dimethyldeuterohemin HO complex "ages" in manner similary to that of protohemin, (Liu, Y., Ma, L.-H., Satterlee, J.D., Zhang, X., Yoshida, T., and La Mar, G. N., (2006) Biochemistry 45, 3875-3886) with mass spectrometry and N-terminal sequencing indicating that the Arg208-His209 dipeptide is cleaved. The 2,4-dimethyldeuterohemin complex of WT HO populates an equilibrium isomer stabilized in low phosphate concentration for which the axial His imidazole ring is rotated by approximately 20 degrees from that in the WT. The His ring reorientation is attributed to Asp24 serving as the H-bond acceptor to the His207 peptide NH, rather than to the His23 ring NdeltaH as in the crystals. The functional implications of the altered C-terminal interaction with substrate modification are discussed.

Binding Sites↗
PubMed1998

A study on gelatin capsule brittleness: moisture tranfer between the capsule shell and its content.

Variation in moisture content of the capsule shells either due to the change of storage conditions or the moisture transfer between the capsule shell and its contents may lead to undesired physical properties, such as capsule brittleness and stickiness. DMP 504, a developmental bile-acid sequestrant, is a strongly basic anion-exchange polymer which contains randomly distributed primary, secondary, tertiary, and quaternary amine groups in their hydrochoride salt form. The alkylammonium groups which comprise this polymer form a random network containing a high level of branching and a low level of cross-linking. DMP 504 is very hygroscopic and has a tendency to gain or lose moisture with ease. The transfer of moisture from the capsule shell to DMP 504 powder contained in a hard gelatin capsule can be expected, and if a low water content of the capsule shell is achieved, the capsules become brittle and fracture easily. The sorption isotherm for DMP 504 was generated by storing the drug substance under various relative humidity conditions. After equilibrium, the moisture contents for the samples of individual isotherm points were measured by thermogravimetric analyses. This report applies the sorption-desorption moisture transfer (SDMT) model to predict the equilibrium relative humidity in a system containing DMP 504 in hard gelatin capsules and to establish target loss on drying values for DMP 504 and the capsule shell. Application of this SDMT model resulted in finding a solution to the brittleness problem. The moisture levels of capsule shells and contents for two formulations in a 12-month stability program are also reported here. Results of this study further demonstrate that the SDMT model can be used as a tool to guide the formulator to select optimal initial moisture contents for the empty capsule shell and the formulation to avoid the incidence of brittle capsule problems.

Absorption↗
PubMed1995

Trypsin-mediated semisynthesis of salmon calcitonin.

Salmon calcitonin, CT(1-32).NH2, was synthesised by the trypsin-mediated coupling of the peptide fragments CT(1-24) and CT(25-32).NH2, prepared by conventional Fmoc solid-phase chemistry. Optimal conditions regarding reaction time course, pH, proportion of catalyst, substrate concentration and composition of the reaction medium were determined from initial studies on the coupling of CT(1-11) to CT(12-24) and of CT(12-24) to CT(25-32).NH2. For the final successful semisynthesis, we found that it was unnecessary to protect lysine residues not involved in the coupling, and that secondary hydrolysis at these sites could be prevented by increasing the pH of the reaction medium. The reaction achieved equilibrium after 30-45 min, with overall conversion of around 30% of the initial amount of CT(1-24) substrate into product. Yields were depressed due to cyclisation of the CT(1-24) substrate via air-oxidation of the Cys1 and Cys7 residues.

Amino Acid Sequence↗
PubMed1987

High affinity L-aspartate transport in chick small intestine.

Epithelial cells isolated from chick small intestine were used to study the mechanism of L-aspartate transport. Two kinetically distinct uptake systems of high (Km' = 16 microM) and low (Km'' = 2.7 mM) affinity are observed. This paper examines the cation dependence and membrane potential sensitivity of the high affinity system. Unidirectional influx studies indicate that extracellular Na+ is an absolute requirement for transport function. Flux is optimal when K+ is present intracellularly, however this cation is not required for Na+-dependent L-aspartate uptake. In the absence of K+, flux enhancement is observed when the intracellular pH is acidic. In contrast, acidic intracellular pH is inhibitory in cells that are preequilibrated with K+. Sodium ([Na+]o greater than [Na+]i gradients, and potassium ([K+]o less than [K+]i) or proton ([H+]o less than [H+]i) gradients can independently energize the Na+-dependent accumulation of L-aspartate above equilibrium levels, suggesting that Na+ and L-aspartate cotransport occurs with concomitant K+ or H+ antiport. L-Aspartate influx is insensitive to membrane potential changes created by inwardly directed anion gradients in the presence or absence of intracellular K+. A model is presented that is consistent with electroneutral Na+-coupled transfer with an ion antiport site of low specificity.

Animals↗
PubMed1982

A unique "mini" pepsinogen isolated from bullfrog esophageal glands.

The evolutionary homology of pepsinogens was further evaluated by isolating and characterizing the pepsinogen of the esophageal glands of Rana catesbeiana. Like other pepsinogens, this esophageal enzyme was activated by acid; the resulting pepsin was optimally active between pH 1.4 and 2.0, and was irreversibly denatured above pH 7.0. Chromatography on DEAE-cellulose at pH 7.0 separated four acid protease fractions corresponding to pepsinogens B, D, A, and C. Hydroxylapatite chromatography of the major peptic fraction, pepsinogen A, followed by rechromatography on DEAE-cellulose at pH 8.5 yielded pure pepsinogen A which was free of detectable contaminants. Estimation of molecular weight by gel filtration on Sephadex G-75, by polyacrylamide gel electrophoresis in 0.1% SDS and by sedimentation equilibrium gave values of 31,500, 33,500, and 33,700, respectively. These studies suggest that the difference between bullfrog and other pepsinogens is located in a 90 to 110 amino acid (Mr 9,000 to 11,000) region of the molecule which must be remote from the catalytic and immunogenic sites. This lower molecular weight pepsinogen should thus provide a simpler molecular model for study of the catalytic and immunogenic properties. The pepsinogen from bullfrog gastric mucosa was found to have similar properties which suggested that gastric and esophageal pepsinogens of bullfrog are derived from a common ancestral origin. This archetypic pepsinogen may have undergone deletions late in evolution to render modern bullfrog pepsinogen structurally dissimilar from other described pepsinogens. The modern bullfrog enzyme has retained peptic enzymatic activity despite these evolutionary changes.

Amino Acids↗
PubMed1999

Synthesis of superporous hydrogels: hydrogels with fast swelling and superabsorbent properties.

We have been interested in the synthesis of hydrogels with fast swelling kinetics and superabsorbent properties. To increase the water absorption rate, interconnected pores were introduced to the hydrogels. Since the pore size in the dried hydrogels is in the order of hundreds of micrometers, these hydrogels are called "superporous" hydrogels. Superporous hydrogels were synthesized by crosslinking polymerization of various vinyl monomers in the presence of gas bubbles formed by the chemical reaction of acid and NaHCO3. The polymerization process was optimized to capture the gas bubbles inside the synthesized hydrogels. The use of the NaHCO3/acid system allowed easy control of timing for gelation and foam formation. We found that PF127 was the best foam stabilizer for most of the monomer systems used in our study. Scanning electron microscope (SEM) pictures showed interconnected pores forming capillary channels. The capillary channels, which were critical for fast swelling, were preserved during drying by dehydrating water-swollen hydrogels with ethanol before drying. The ethanol-dehydrated superporous hydrogels reached equilibrium swelling within minutes. The equilibrium swelling time could be reduced to less than a minute with the use of a wetting agent. In our study, water moisture was used as a wetting agent since the amount of moisture content in the dried hydrogels easily could be controlled. Preparation of superporous hydrogels using the right blowing system, foam stabilizer, drying method, and wetting agent makes it possible to reduce the swelling time to less than a minute regardless of the size of the dried gels. The superporous hydrogels can be used where fast swelling and superabsorbent properties are critical.

Absorption↗
PubMed2002

Development of (R)-4-hydroxymandelonitrile synthesis in an aqueous-organic biphasic stirred tank batch reactor.

A relatively new hydroxynitrile lyase-catalyzed reaction was optimized to be suitable for rapid and efficient development of a full-scale production process. The conversion of 4-hydroxybenzaldehyde into (R)-4-hydroxymandelonitrile, catalyzed by Prunus amygdalus hydroxynitrile lyase, was carried out in a biphasic system of aqueous buffer (pH 5.5) and methyl tert-butyl ether and is described with a process model. The process model consists of a description of the reaction kinetics, mass transfer kinetics, and mass balances for both the aqueous and the organic phase. Values are determined for the equilibrium constant, the enzyme kinetic parameters, the lumped mass transfer coefficient for benzaldehyde, and the partition coefficients. By using estimated prices of enzyme and reactor use, the optimum aqueous phase volume fraction and required enzyme concentration were calculated at a temperature of 20 degrees C for a batch-operated stirred tank reactor. According to the process model it was possible to convert 90% of the 4-hydroxybenzaldehyde into (R)-4-hydroxymandelonitrile with 95% enantiomeric excess. The price optimum for this reaction was found at an aqueous phase volume of 17% of the total volume. The required enzyme concentration to meet the targets was 28.6 g/L aqueous phase. At the predicted optimum, the synthesis was performed experimentally and the results were in accordance with the simulation regarding the extent of conversion and the enantiomeric excess.

Aldehyde-Lyases↗
PubMed1985

Treatment of cystic echinococcosis (Echinococcus granulosus) with mebendazole: assessment of bound and free drug levels in cyst fluid and of parasite vitality in operative specimens.

Chemotherapy of the larval stage of Echinococcus granulosus in man with high oral doses of mebendazole has only been partly successful. In order to improve effective pharmacotherapy of this disease with mebendazole, the optimal time for blood sampling has been assessed and the mebendazole concentrations acting on the parasite have been compared with their viability. The optimal time for blood sampling was analysed in 14 patients during longterm treatment with mebendazole. The plasma level 4 h after the morning dose exhibited the best correlation with the average 24-h concentration, suggesting that the plasma level should be monitored 4 h after the morning dose. In 22 patients undergoing surgery for hydatid disease, the mebendazole concentration in cyst fluid was significantly correlated with its plasma level 4 h after the morning dose. In 13 of them the free drug concentration was determined by equilibrium dialysis and it was almost identical with the free mebendazole concentration in plasma. Results of viability tests in 12 cases revealed viable cysts in 6 cases and possibly viable cysts in 6 other cases. Even patients treated for more than 12 months still had viable cysts.

Adult↗
PubMed1991

Optimal growth schedule of pathogens within a host: switching between lytic and latent cycles.

We have studied the optimal growth schedule of a pathogen, which maximizes the total number of transmissions from an infected host to other individuals until host death or recovery. It is assumed that both transmission rate f(N) and host mortality increase with the number of pathogens, N. The model predicts that the optimal growth schedule of pathogens strongly depends on the curvature of f(N): If f(N) increases faster than linearly with N, the pathogens should always reproduce at the maximum speed. By contrast, if f(N) saturates with N, the optimal schedule is composed of (1) a brief initial stage of infection, in which the pathogens proliferate at the maximum speed (productive cycle), (2) followed by the long latent period with the "stationary infection level," N* (latent cycle), (3) which may end when the pathogens start rapid proliferation triggered either by the host's senescence ("programmed break") or by the sudden rise in the host's mortality ("incidental break"). The latter may be caused by the double infection of another strain. We also examine the Nash equilibrium schedule of pathogen growth in the presence of multiple infections.

Age Factors↗
PubMed1993

Conformational studies on some Cl'-branched beta-D-nucleosides by 1H-NMR spectroscopy and molecular mechanics calculations.

Solution structures of 1-(beta-D-psicofuranosyl)thymine (HMT) (5) and 1-(1'-cyano-beta-D-ribofuranosyl)-thymine (CNT) (6) based on 3JH,H coupling constants (1H-NMR at 500 MHz) and nOe enhancement studies were further refined by molecular mechanics calculations using the AMBER force field. These complementary NMR-molecular mechanics studies helped us to define the torsion angles inside the NMR-defined conformational hyperspace. Atom-centered monopole charges were derived for molecular mechanics calculations by fitting the molecular electrostatic potential on freely optimized geometries of 5 and 6 using HF/3-21G level of theory by GAUSSIAN 92 program. The conformation of 5 and 6 can be summarized as follows: (i) the pseudorotational analyses showed that the North conformer is predominant in both 5 (> 70%) and 6 (97%). While the molecular mechanics could correctly predict the energetic preference of North over South type puckered sugar moiety for 5 and 6 it could not provide any clue to the fact that the 1'-CN group in CNT (6) drives the pseudorotational equilibrium more effectively towards North than 1'-CH2OH in HMT (5). (ii). The NMR-observed preference of anti over syn conformation across the glycosyl bond in 5 and 6 was correctly shown by the energetic preference of anti conformers by approx. 10 kJ/mol. (iii) The populations of the staggered rotamers across C4'-C5' (gamma +, gamma t and gamma -) calculated from 3J4'5' and 3J4'5" coupling constants from NMR spectroscopy show that gamma + and gamma t rotamers are preferred. Molecular mechanics calculations are also in an excellent agreement here with the results of solution studies: in 5 gamma + and gamma t rotamers are equally populated and a small energy difference in potential energy is established, while in 6 the larger energy difference in potential energy is found which reflects a higher preference for gamma + rotamer in solution. The energetic preferences found among the lowest energy conformers of 5 (North-gamma +/gamma t-anti-epsilon t1) and 6 (North-gamma +/gamma t-anti) in molecular mechanics calculations are in an excellent agreement with the preferences of the major conformers found by NMR spectroscopy in solution.

Magnetic Resonance Spectroscopy↗
PubMed2006

Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii.

The pyrimidine reductase of the riboflavin biosynthetic pathway (MjaRED) specified by the open reading frame MJ0671 of Methanocaldococcus jannaschii was expressed in Escherichia coli using a synthetic gene. The synthetic open reading frame that was optimized for expression in E. coli directed the synthesis of abundant amounts of the enzyme with an apparent subunit mass of 25 kDa. The enzyme was purified to apparent homogeneity and was shown to catalyze the conversion of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate at a rate of 0.8 micromol min(-1) mg(-1) at pH 8.0 and at 30 degrees C. The protein is a homodimer as shown by sedimentation equilibrium analysis and sediments at an apparent velocity of 3.5 S. The structure of the enzyme in complex with the cofactor nicotinamide adenine dinucleotide phosphate was determined by X-ray crystallography at a resolution of 2.5 Angstroms. The folding pattern resembles that of dihydrofolate reductase with the Thermotoga maritima ortholog as the most similar structure. The substrate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, was modeled into the putative active site. The model suggests the transfer of the pro-R hydrogen of C-4 of NADPH to C-1' of the substrate.

Amino Acid Sequence↗
PubMed1997

Guidelines in selecting ligand concentrations for the determination of binding constants by affinity capillary electrophoresis.

This study examined various factors that affect the selection of ligand concentrations when using affinity capillary electrophoresis (ACE) for the determination of equilibrium constants in free solution. Two groups of model systems were used in this work: the binding of nitrophenols to alpha- or beta-cyclodextrin and the binding of D- or L-tryptophan to human serum albumin (HSA). Both systems gave 1:1 binding behavior in the ACE studies and good fits to previous equations derived to describe the shift in analyte mobility that occurs as the ligand concentration of the running buffer is varied. Some practical factors limiting the range of ligand levels that could be used in such studies included the relative amount of injected analyte, ligand solubility and the ligand's background signal. More fundamental factors included the size of the equilibrium constant for the system being investigated, the relative range of mobilities over which the analyte peak might be observed, the precision of the mobility measurements and the number of analytes present in the sample. Equations and graphs were developed for illustrating each of these latter items and their role in determining the range of ligand concentrations that could be used in ACE binding constant measurements. The results predicted by these equations and graphs showed good agreement with those observed experimentally, and should prove useful in optimizing ACE conditions for other solutes and ligands.

Cyclodextrins↗
PubMed1976

A Ca2+-activated protease possibly involved in myofibrillar protein turnover. Partial characterization of the purified enzyme.

The purified Ca2+-activated protease (CAF) isolated from porcine skeletal muscle and capable of removing Z-disks from intact myofibrils is optimally active on either myofibril or casein substrates at pH 7.5 and in the presence of 1 mM Ca2+ and at least 2 mM 2-mercaptoethanol. No CAF activity is detected when 1 mM Mg2+, Mn2+, Ba2+, Co2+, Ni2+, and Fe2+ are added singly. When added with 1 mM Ca2+, Co2+, Cu2+, Ni2+, and Fe2+ inhibit, whereas Mg2+, Mn2+, and Ba2+ have no effect on CAF activity. CAF is irreversibly inhibited by iodoacetate but is unaffected by soybean trypsin inhibitor. S0/20,W=5.90 S, and sedimentation equilibrium molecular weight - 112 000 for purified CAF. Because purified CAF migrates as two polypeptide chains with molecular weights of 80 000 and 30 000 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the CAF molecule must consist of one each of these two polypeptide chains. Approximate molecular dimensions of 38 X 220 A can be calculated for CAF from calibrated gel permeation column data or from S0/20,W and the molecular weight. Amino acid composition and physical properties of purified CAF distinguish it from the known catheptic enzymes and from other proteases found in blood or in granulocytes. Purified CAF removes Z-disks the 400-A periodicity associated with troponin in the I band and partly degrades M lines but causes no other ultrastructurally detectable effects when incubated with myofibrils. These results agree with the earlier finding that purified CAF degrades troponin, tropomyosin, and C-protein but has no effect on myosin, actin, or alpha-actinin, and suggest that CAF may have a physiological role in disassembly of intact myofibrils during metabolic turnover of myofibrillar proteins.

Amino Acids↗