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PubMed1978

Accumulation pharmacokinetics of tobramycin.

Tobramycin pharmacokinetics is usually described by a one-compartment model, but this model fails to account for both the incomplete urinary recovery and prolonged post-treatment persistence noted with this drug. We examined the multiple-dose behavior of tobramycin in 35 treated patients with stable renal function, using peak and trough serum concentrations, urine recovery, and postmortem tissue analysis. Serum concentrations rose slowly throughout treatment and declined in two phases after the drug was stopped. The first-phase half-life correlated well with renal function, but the second averaged 146 h and was poorly related to creatinine clearance. A two-compartment model was used to describe the biphasic decline in serum concentrations and to calculate the amount of drug in the tissue compartment at all times during and after treatment. Predicted tissue amounts rose continually throughout treatment in all study patients. In 5 patients, the total amount of tobramycin in the body after the final dose was recovered in the urine, but urine had to be collected for 10 to 20 days to achieve complete recovery of the drug. In four patients, the predicted tissue amount was recovered from postmortem tissues. Regardless of the dose, tobramycin accumulated in the tissues of all patients receiving this antibiotic. The two-compartment pharmacokinetic model explains both the rising peak and trough concentrations during treatment and the detection of the drug in serum and urine long after the last dose.

Adult↗

PubMed1998

Modelling the kinetics of antigen-antibody reactions at particle enhanced optical immunoassays.

Functionalized latexes coated by antibodies are used in diagnostic tests for the detection of antigens in biological fluids. A simple kinetic model is presented which is related to the optical monitoring of the formation of specific complexes between antigen and antibody amplified by latex beads. The antibodies are chemically coupled onto chloromethylstyrene (CMST) particles. The kinetic model is able to describe the immunoprecipitin curves of immunolatex beads. The number of fitting parameters is relatively reduced (only three), and the meaning of these parameters can be interpreted in terms of the chemical equilibrium constant, the percentage of active IgG on the latex beads, and optical response. The model explains very well the optical response of immunolatex prepared by covalent coupling of antibodies on polymer carriers.

Animals↗

PubMed2005

Multiple role adaptation among women who have children and re-enter nursing school in Taiwan.

This study assessed multiple role adaptation within maternal and student roles among female RNs who had children and returned to school for baccalaureate degrees in Taiwan. Using Roy's Adaptation Model as the theoretical framework, relationships were explored among demographic (number of children, age of youngest child, employment status), physical (sleep quality, health perception, activity), and psychosocial factors (self-identity, role expectation, role involvement, social support) and multiple role adaptation (role accumulation). The sample included 118 mother-students who had at least one child younger than age 18 and who were studying in nursing programs in Taiwan. The highest correlation was found between activity and role accumulation followed by significant correlations between sleep quality, health perception, maternal role expectation, and age of youngest child and role accumulation. In regression analyses, the complete model explained 46% of the variance in role accumulation. Implications for education and future research are identified.

Adaptation, Psychological↗

PubMed1999

Intersegment hydrogen bonds as possible structural determinants of the N/Q/R site in glutamate receptors.

Specific electrophysiological and pharmacological properties of ionic channels in NMDA, AMPA, and kainate subtypes of ionotropic glutamate receptors (GluRs) are determined by the Asn (N), Gln (Q), and Arg (R) residues located at homologous positions of the pore-lining M2 segments (the N/Q/R site). Presumably, the N/Q/R site is located at the apex of the reentrant membrane loop and forms the narrowest constriction of the pore. Although the shorter Asn residues are expected to protrude in the pore to a lesser extent than the longer Gln residues, the effective dimension of the NMDA channel (corresponding to the size of the largest permeant organic cation) is, surprisingly, smaller than that of the AMPA channel. To explain this paradox, we propose that the N/Q/R residues form macrocyclic structures (rings) stabilized by H-bonds between a NH(2) group in the side chain of a given M2 segment and a C==O group of the main chain in the adjacent M2 segment. Using Monte Carlo minimization, we have explored conformational properties of the rings. In the Asn, but not in the Gln ring, the side-chain oxygens protruding into the pore may facilitate ion permeation and accept H-bonds from the blocking drugs. In this way, the model explains different electrophysiological and pharmacological properties of NMDA and non-NMDA GluR channels. The ring of H-bonded polar residues at the pore narrowing resembles the ring of four Thr(75) residues observed in the crystallographic structure of the KcsA K(+) channel.

Arginine↗

PubMed1999

The simple reaction time to changes in direction of visual motion.

Recently Dzhafarov et al. presented a model explaining data on simple reaction time (RT) to unidimensional velocity changes. The authors suggested that having a motion with an initial velocity V0, the velocity change detection system is reinitialized by means of a "subtractive normalization" process. Therefore, any abrupt change from V0 to V1 is detected as if it were the onset of motion with a speed equal to /V1-V0/. They derived that the RT is a function of /V1-V0/(-2/3). We tested this model for the case of two-dimensional velocity changes. Our subjects observed a random dot pattern that moved horizontally, then changed the direction of motion by an angle alpha in the range between 6 degrees and 180 degrees without changing the speed V. Speeds of 4 and 12 deg/s were used. The subjects reacted as quickly as possible to the direction change. The RTs asymptotically decreased with increasing alpha; with 12 deg/s speed the RTs were shorter than those obtained with 4 deg/s. It was shown that the data can be well described as a function of /V1-V0/(-2/3)=(2Vsin(alpha/2))(-2/3). An extension of the "subtractive normalization" hypothesis for the case of two-dimensional velocity changes is proposed. It is based on the assumption that the velocity vector V1 after the change is decomposed into two orthogonal components. Alternative explanations based on the use of position or orientation cues are shown to contradict the data.

Humans↗

PubMed1990

Action of a transposable element in coding sequence fusions.

The original Casadaban technique for isolating fused cistrons encoding hybrid beta-galactosidase proteins used a Mucts62 prophage to align the upstream coding sequence and lacZ prior to selection. Kinetic analysis of araB-lacZ fusion colony emergence indicated that the required DNA rearrangements were regulated and responsive to conditions on selection plates. This has been cited as an example of "directed mutation." Here we show genetically that the MuA and integration host factor (IHF) transposition functions are involved in the formation of hybrid araB-lacZ cistrons and propose a molecular model for how fusions can form from the initial strand-transfer complex. These results confirm earlier indications of direct Mu involvement in the fusion process. The proposed model explains how rearranged Mu sequences come to be found as interdomain linkers in certain hybrid cistrons and indicates that the fusion process involves a spatially and temporally coordinated sequence of biochemical reactions.

Base Sequence↗

PubMed2004

Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301 D-R.

Strains of the phytopathogenic bacterium Pseudomonas syringae pv. syringae secrete a family of structurally closely related peptide derivatives dubbed syringolins, of which syringolin A is the major variant. The function of syringolins in the interaction of P. syringae pv. syringae with their host plants presently is unknown. It is hypothesized that they may constitute virulence factors. However, syringolins are determinants recognized and reacted to by nonhost plant species, and syringolin A has been shown to induce hypersensitive death of cells colonized by powdery mildew in wheat and, thus, to reprogram a compatible interaction into an incompatible one. Syringolin A is an unusual derivative of a tripeptide that contains a 12-membered ring consisting of the amino acids 5-methyl-4-amino-2-hexenoic acid and 3,4-dehydrolysine, two nonproteinogenic amino acids. Here we report the cloning, sequencing, and analysis of genes involved in the biosynthesis of syringolin A. The genes encode proteins consisting of modules typical for nonribosomal peptide synthetases and type I polyketide synthetases, as well as proteins likely involved in the transcriptional regulation of syringolin A biosynthesis and in syringolin A export. The structure and arrangement of the modules lead to the formulation of a model explaining the synthesis of the tripeptide, including the formation of the two nonproteinogenic amino acids in the ring structure of syringolin A.

Amino Acid Sequence↗

PubMed2003

Lattice model for the kinetics of rupture of fluid bilayer membranes.

We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility (for expansion) K, the thickness 2h(t) of the hydrophobic part of the bilayer, the hydrophobicity sigma, and a parameter gamma characterizing the tail rigidity of the lipids. The model is a lattice model which incorporates strain relaxation, and considers the nucleation of pores at constant area, constant temperature, and constant particle number. The particle number is conserved by allowing multiple occupancy of the sites. An equilibrium "phase diagram" is constructed as a function of temperature and strain with the total pore surface and distribution as the order parameters. A first-order rupture line is found with increasing tension, and a continuous increase in protopore concentration with rising temperature till instability. The model explains current results on saturated and unsaturated phosphatidylcholine lipid bilayers and thicker artificial bilayers made of diblock copolymers. Pore size distributions are presented for various values of area expansion and temperature, and the fractal dimension of the pore edge is evaluated.

Biophysical Phenomena↗

PubMed2003

The binding site of acetylcholine receptor: from synthetic peptides to solution and crystal structure.

Our group has been employing short synthetic peptides, encompassing sequences from the acetylcholine receptor (AChR) alpha-subunit for the analysis of the binding site of the AChR. A 13-mer peptide mimotope, with similar structural motifs to the AChR binding region, was selected by alpha-bungarotoxin (alpha-BTX) from a phage-display peptide library. The solution structure of a complex between this library-lead peptide and alpha-BTX was solved by NMR spectroscopy. On the basis of this NMR study and on structure-function analysis of the AChR binding site, and in order to obtain peptides with higher affinity to alpha-BTX, additional peptides resulting from systematic residue replacement in the lead peptide were designed and characterized. Of these, four peptides, designated high-affinity peptides (HAPs), homologous to the binding region of the AChR, inhibited the binding of alpha-BTX to the AChR with an IC(50) of 2 nM. The solution and crystal structures of complexes of alpha-BTX with HAP were solved, demonstrating that the HAP fits snugly to alpha-BTX and adopts a beta-hairpin conformation. The X-ray structures of the bound HAP and the homologous loop of the acetylcholine binding protein (AChBP) are remarkably similar. Their superposition results in a model indicating that alpha-BTX wraps around the receptor binding-site loop and, in addition, binds tightly at the interface of two of the receptor subunits, where it inserts a finger into the ligand-binding site. Our proposed model explains the strong antagonistic activity of alpha-BTX and accommodates much of the biochemical data on the mode of interaction of alpha-BTX with the AChR.

Animals↗

PubMed2004

A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect.

Previous work on group I introns has suggested that a central base triple might be more important for the first rather than the second step of self-splicing, leading to a model in which the base triple undergoes a conformational change during self-splicing. Here, we use the well-characterized L-21 ScaI ribozyme derived from the Tetrahymena group I intron to probe the effects of base-triple disruption on individual reaction steps. Consistent with previous results, reaction of a ternary complex mimicking the first chemical step in self-splicing is slowed by mutations in this base triple, whereas reaction of a ternary complex mimicking the second step of self-splicing is not. Paradoxically, mechanistic dissection of the base-triple disruption mutants indicates that active site binding is weakened uniformly for the 5'-splice site and the 5'-exon analog, mimics for the species bound in the first and second step of self-splicing. Nevertheless, the 5'-exon analog remains bound at the active site, whereas the 5'-splice site analog does not. This differential effect arises despite the uniform destabilization, because the wild-type ribozyme binds the 5'-exon analog more strongly in the active site than in the 5'-splice site analog. Thus, binding into the active site constitutes an additional barrier to reaction of the 5'-splice site analog, but not the 5'-exon analog, resulting in a reduced reaction rate constant for the first step analog, but not the second step analog. This threshold model explains the self-splicing observations without the need to invoke a conformational change involving the base triple, and underscores the importance of quantitative dissection for the interpretation of effects from mutations.

Animals↗

PubMed2006

Kinesin's biased stepping mechanism: amplification of neck linker zippering.

A physically motivated model of kinesin's motor function is developed within the framework of rectified Brownian motion. The model explains how the amplification of neck linker zippering arises naturally through well-known formulae for overdamped dynamics, thereby providing a means to understand how weakly-favorable zippering leads to strongly favorable plus-directed binding of a free kinesin head to microtubule. Additional aspects of kinesin's motion, such as head coordination and rate-limiting steps, are directly related to the force-dependent inhibition of ATP binding to a microtubule bound head. The model of rectified Brownian motion is presented as an alternative to power stroke models and provides an alternative interpretation for the significance of ATP hydrolysis in the kinesin stepping cycle.

Adenosine Triphosphate↗

PubMed2003

Pre-eclampsia, the placenta and the maternal systemic inflammatory response--a review.

The central role of the placenta in the pathogenesis of pre-eclampsia is undisputed. The evidence that maternal syndrome of pre-eclampsia is caused by a maternal systemic inflammatory response (MSIR) is reviewed. The polymorphic nature of the inflammatory network explains the diversity of the varied signs of this condition. A key observation is that an MSIR is also a feature of normal third trimester pregnancy, but less severe than in pre-eclampsia. Hence pre-eclampsia is simply the extreme end of a continuum common to all pregnancies, with multiple contributing factors. Evidence is presented that apoptotic or necrotic debris shed from the syncytial surface of the placenta constitutes the inflammatory stimulus in all pregnancies. This model explains many features of pre-eclampsia including its occurrence with either larger placentae or small oxidatively stressed placentae. The clinical implications are that in terms of diagnosis or prediction there can never be a clear distinction between normal and abnormal. No test, predictive or diagnostic, can be expected to distinguish absolutely between different degrees of a problem that is common to all pregnancies. The possibility that the MSIR associated with third trimester pregnancy is nothing more than the maternal price for sustaining gestation is considered. Insulin resistance is a feature of normal pregnancy and also of systemic inflammatory states in non-pregnant individuals. It has been previously proposed that the insulin resistance of pregnancy is an important adaptation to divert maternal glucose to meet the needs of the foetus. Hence the MSIR, by causing maternal insulin resistance, may have substantial foetal advantages so long as it is not too severe.

Endothelium, Vascular↗

PubMed1993

The conformation of the sarcin/ricin loop from 28S ribosomal RNA.

The sarcin/ricin loop is a highly conserved sequence found in the RNA of all large ribosomal subunits. The cytotoxins alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in that loop. Once it has been attacked, ribosomes no longer interact with elongation factors properly, and translation stops. We have determined the conformation of the sarcin/ricin loop by multinuclear NMR spectroscopy using E73, a 29-nucleotide RNA that has the sarcin/ricin loop sequence and that is sensitive to both toxins in vitro. The sarcin/ricin loop has a compact structure that contains several purine.purine base pairs, a GAGA tetraloop, and a bulged guanosine adjacent to a reverse Hoogsteen A.U pair. It is stabilized by an unusual set of cross-strand base-stacking interactions and imino proton to phosphate oxygen hydrogen bonds. In addition to having interesting structural features, this model explains many of the biochemical observations made about the loop's structure and its reactivity with cytotoxins, and it sheds light on the loop's interactions with elongation factors.

Animals↗

PubMed1993

Solution of the ribosome riddle: how the ribosome selects the correct aminoacyl-tRNA out of 41 similar contestants.

Three tRNA binding sites, the A, P and E sites, have been demonstrated on ribosomes of bacterial, archaebacterial and eukaryotic origin. In all these cases the first and the third site, the A and the E site, are allosterically coupled in the sense of a negative co-operativity. Therefore, the allosteric three-site model seems to be a generally valid description of the ribosomal elongation phase, where in a cycle of reactions the nascent peptide chain is prolonged by one amino acid. The molecular concept of the allosteric three-site model explains the astonishing ability of the ribosome to select the correct substrate out of a large number of very similar substrates, and it provides a framework within which the mechanisms of the elongation factors could be understood.

Allosteric Regulation↗

PubMed2006

Exploring the energy landscape of a small RNA hairpin.

The energy landscape of a small RNA tetraloop hairpin is explored by temperature jump kinetics and base-substitution. The folding kinetics are single-exponential near the folding transition midpoint T(m). An additional fast phase appears below the midpoint, and an additional slow phase appears above the midpoint. Stem mutation affects the high-temperature phase, while loop mutation affects the low-temperature phase. An adjusted 2-D lattice model reproduces the temperature-dependent phases, although it oversimplifies the structural interpretation. A four-state free energy landscape model is generated based on the lattice model. This model explains the thermodynamics and multiphase kinetics over the full temperature range of the experiments. An analysis of three variants shows that one of the intermediate RNA structures is a stacking-related trap affected by stem but not loop modification, while the other is an early intermediate that forms some stem and loop structure. Even a very fast-folding 8-mer RNA with an ideal tetraloop sequence has a rugged energy landscape, ideal for testing analytical and computational models.

Kinetics↗

PubMed2005

C-174G polymorphism in the promoter of the interleukin-6 gene is associated with insulin resistance.

OBJECTIVE: The C-174G promoter polymorphism of the interleukin (IL)-6 gene was found to influence transcriptional activity and plasma IL-6 levels in humans. We addressed the question of whether the C-174G IL-6 polymorphism contributes to variation of insulin sensitivity. RESEARCH DESIGN AND METHODS: Two cohorts of subjects were genotyped. Cohort 1 includes 275 nondiabetic subjects who underwent a euglycemic-hyperinsulinemic clamp. Cohort 2 includes 77 patients with morbid obesity who underwent laparoscopic adjustable gastric banding (LAGB). RESULTS: The genotypes were consistent with Hardy-Weinberg equilibrium proportions. In cohort 1, insulin sensitivity was reduced in carriers of the -174G/G genotype as compared with subjects carrying the C allele (P = 0.004). Carriers of -174G/G displayed significantly higher plasma IL-6 levels in comparison with carriers of the C allele. In a stepwise linear regression analysis, the C-174G polymorphism was independently associated with insulin sensitivity; however, after inclusion of plasma IL-6 concentrations, the polymorphism was excluded from the model explaining insulin sensitivity variability, thus suggesting that the polymorphism was affecting insulin sensitivity by regulating IL-6 plasma levels. IL-6 mRNA levels were measured by real-time RT-PCR in subcutaneous fat obtained from obese patients of cohort 2 during LAGB. Carriers of -174G/G showed increased IL-6 expression compared with subjects carrying the C allele (P = 0.04). There was a significant correlation between adipose IL-6 mRNA expression and insulin resistance assessed by homeostasis model assessment (rho = 0.28, P = 0.014). CONCLUSIONS: These results indicate that the -174G/G genotype of the IL-6 gene may contribute to variations in insulin sensitivity.

Adipose Tissue↗

PubMed1999

Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8 A resolution: mechanistic implications.

Serine hydroxymethyltransferase (SHMT) catalyzes the reversible cleavage of serine to form glycine and single carbon groups that are essential for many biosynthetic pathways. SHMT requires both pyridoxal phosphate (PLP) and tetrahydropteroylpolyglutamate (H4PteGlun) as cofactors, the latter as a carrier of the single carbon group. We describe here the crystal structure at 2.8 A resolution of rabbit cytosolic SHMT (rcSHMT) in two forms: one with the PLP covalently bound as an aldimine to the Nepsilon-amino group of the active site lysine and the other with the aldimine reduced to a secondary amine. The rcSHMT structure closely resembles the structure of human SHMT, confirming its similarity to the alpha-class of PLP enzymes. The structures reported here further permit identification of changes in the PLP group that accompany formation of the geminal diamine complex, the first intermediate in the reaction pathway. On the basis of the current mechanism derived from solution studies and the properties of site mutants, we are able to model the binding of both the serine substrate and the H4PteGlun cofactor. This model explains the properties of several site mutants of SHMT and offers testable hypotheses for a more detailed mechanism of this enzyme.

Amino Acid Sequence↗

PubMed2005

Model for acetylene reduction by nitrogenase derived from density functional theory.

The catalytic cycle of acetylene reduction at the FeMo cofactor of nitrogenase has been investigated on the basis of density functional theory. C2H2 binds to the same site as N2, but it binds to a less reduced state of the cofactor. In a manner similar to that of N2 binding, one of the sulfur bridges opens during acetylene binding. The model explains the strong noncompetitive inhibition of N2 reduction by C2H2 and the weak competitive inhibition of C2H2 reduction by N2. Our proposed mechanism is consistent with experimentally observed stereoselectivity and the ability of C2H2 to suppress H2 production by nitrogenase.

Acetylene↗