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Zampanolide (1), a 20-membered macrolide from a Tongan marine sponge, stabilizes microtubules and blocks cells in G2/M of the cell cycle. Zampanolide is cytotoxic in the low nanomolar range and induces microtubule bundles in cells. It leads to tubulin assembly in cells and in purified tubulin preparations and is not a substrate for the P-glycoprotein drug efflux pump. Zampanolide, with only four stereogenic centers, may be amenable to large-scale synthetic preparation. [ABSTRACT FROM AUTHOR]

Calcium ion binding by the four EF-hand motifs of the protein calmodulin (CaM) is a central event in Ca2-based cellular signaling. To understand molecular details of this complex process, isolated Ca2-binding loops can be studied, by use of both experiments and calculations. In this work, we explore the metal specificity of the four Ca2-binding loops of CaM using density functional theory (DFT) quantum chemical calculations and molecular dynamics simulations. We study CaM complexes with the physiologically important ions of calcium (Ca2) and magnesium (Mg2) and also with two other ions, strontium (Sr2) and lanthanum (La3). The former is of interest in the area of radioactive waste bioremediation, whereas the latter is often used as a probe of Ca2-binding sites. We obtain intrinsic metal ion-loop binding energies as well as their components:  vacuum, charge-transfer, solvation, entropy, and deformation terms. A detailed analysis of the results reveals that the total binding energy depends on a delicate balance among these energy components. They, in turn, are determined by the cation's charge and size as well as the amino acid composition and flexibility of the loops and the identity of the metal-chelating residues. [ABSTRACT FROM AUTHOR]

The study of the chemical steps in enzyme-catalyzed reactions represents a challenge for molecular simulation techniques. One concern is how to calculate paths for the reaction. Common techniques include the definition of a reaction coordinate in terms of a small set of (normally) geometrical variables or the determination of minimum energy paths on the potential energy surface of the reacting system. Both have disadvantages, the former because it presupposes knowledge of which variables are likely to be important for reaction and the latter because it provides a static picture and dynamical effects are ignored. In this paper, we employ the transition path sampling method developed by Chandler and co-workers, which overcomes some of these limitations. The reaction that we have chosen is the chorismate-mutase-catalyzed conversion of chorismate into prephenate, which has become something of a test case for simulation studies of enzyme mechanisms. We generated an ensemble of ∼1000 independent transition paths for the reaction in the enzyme and another ∼500 for the corresponding reaction in solution. A large variety of analyses of these paths was performed, but we have concentrated on characterizing the transition state ensemble, particularly the flexibility of its structures with respect to other ligands of the enzyme and the time evolution of various geometrical and energetic properties as the reaction proceeds. We have also devised an approximate technique for locating transition state structures along the paths. [ABSTRACT FROM AUTHOR]

The kinetics of the reaction HBrO2 + HBrO2 → HOBr + BrO3- + H+ is investigated in aqueous HClO4 (0.04−0.9 M) and H2R.4 (0.3−0.9 M) media and at temperatures in the range 15−38 °C. The reaction is found to be cleanly second order in [HBrO2], with the experimental rate constant having the form kexp = k + k‘[H+]. The half-life of the reaction is on the order of a few tenths of a second in the range 0.01 M < [HBrO2]0 < 0.02 M. The detailed mechanism of this reaction is discussed. The activation parameters for k are found to be E‡ = 19.0 ± 0.9 kJ/mol and ΔS‡ = −132 ± 3 J/(K mol) in HClO4, and E‡ = 23.0 ± 0.5 kJ/mol and ΔS‡ = −119 ± 1 J/(K mol) in H2R.4. The activation parameters for k‘ are found to be E‡ = 25.8 ± 0.5 kJ/mol and ΔS‡ = −106 ± 1 J/(K mol) in HClO4, and E‡ = 18 ± 3 kJ/mol and ΔS‡ = −130 ± 11 J/(K mol) in H2R.4. The values ΔfH2980{BrO2(aq)} = 157 kJ/mol and ΔfH2980{HBrO2(aq)} = −33 kJ/mol are estimated using a trend analysis (bond strengths) based on the assumption ΔfH2980{HBrO2(aq)} lies between ΔfH2980{HOBr(aq)} and ΔfH2980{HBrO3(aq)} as ΔfH2980{HClO2(aq)} lies between ΔfH2980{HOCl(aq)} and ΔfH2980{HClO3(aq)}. The estimated value of ΔfH2980{BrO2(aq)} agrees well with calculated gas-phase values, but the estimated value of ΔfH2980{HBrO2(aq)}, as well as the tabulated value of ΔfH2980{HClO2(aq)}, is in substantial disagreement with calculated gas-phase values. Values of ΔrH0 are estimated for various reactions involving BrO2 or HBrO2-i [ABSTRACT FROM AUTHOR]

We prove results that enable the efficient and natural realization of a large class of robust heteroclinic networks in coupled identical cell systems. We also propose some general conjectures that relate a natural and large class of robust heteroclinic networks that occur in networks modelled by equations of Lotka–Volterra type, and certain networks of symmetric systems, to robust heteroclinic networks in coupled cell networks. [ABSTRACT FROM AUTHOR]

The minima hopping algorithm (MHOP) to find global minima on potential energy surfaces is used for protein structure prediction. The energy surface of the protein is represented with an all-atom OPLS force field and an implicit free energy solvation term. The system we studied here is the small 10-residue β-hairpin mini-protein, chignolin. Starting from a completely extended structure, we found minima with <0.5 Å rms coordinate deviation from the geometry-optimized native experimental conformation. A few lowest-energy conformations were used for the calculation of NMR-restraint violations and chemical shifts, and the local minima found during each run leading to the global minimum were connected to trace out a search pathway of the folding process. [ABSTRACT FROM AUTHOR]

The unstirred, ferroin (Fe(phen) 32+) catalyzed Belousov−Zhabotinsky (BZ) reaction is the prototype oscillatory chemical system. Reaction media with added Br −appear red (reduced, low [Fe(phen) 33+]) during an induction period of several minutes, followed by the “spontaneous” formation of “pacemaker” sites, which oscillate between a blue, oxidized state (high [Fe(phen) 33+]) and the red, reduced state and generate target patterns of concentric, outwardly moving waves of oxidation (blue). Auto-oscillatory behavior is also seen in the Oregonator model of Field, Kõrös and Noyes (FKN), a robust, reduced model that captures qualitative BZ kinetics in the auto-oscillatory regime. However, the Oregonator model predicts a blue (oxidized) induction phase. Here we develop a generalized Oregonator-like model with noexplicit bifurcation parameter that yields the observed transition from a red initial state to oscillatory dynamics, and displays a new bifurcation mechanism not seen in the original Oregonator. [ABSTRACT FROM AUTHOR]

Inthis work we have studied two hydridotetraminecobalt(III) complexesusing a mixture of computational techniques. These species were chosenas simple and computationally tractable models of the Co(III)–hydridocompounds that are known to be important intermediates in the catalyticcycles of hydrogen evolution mediated by the cobaloxime complexes.We have performed both static density functional theory (DFT) calculationsof the complexes in implicit solvent and adaptive hybrid DFT/molecularmechanical (MM) molecular dynamics (MD) simulations in explicit solventand compared our results to the experimental structural and spectraldata that are available for one of the compounds. A principal aimof the study has been to provide a benchmark for future work on cobaloximeand other hydrogen-evolving catalysts using adaptive DFT/MM MD methods. [ABSTRACT FROM AUTHOR]

The production of cytotoxic nitric oxide (NO) and conversion into the neuropharmacological agent and potent greenhouse gas nitrous oxide (N2O) is linked with anoxic nitrate catabolism by Salmonella enterica serovar Typhimurium. Salmonella can synthesize two types of nitrate reductase: a membrane-bound form (Nar) and a periplasmic form (Nap). Nitrate catabolism was studied under nitrate-rich and nitrate-limited conditions in chemostat cultures following transition from oxic to anoxic conditions. Intracellular NO production was reported qualitatively by assessing transcription of the NO-regulated genes encoding flavohaemoglobin (Hmp), flavorubredoxin (NorV) and hybrid cluster protein (Hcp). A more quantitative analysis of the extent of NO formation was gained by measuring production of N2O, the end-product of anoxic NO-detoxification. Under nitrate-rich conditions, the nar, nap, hmp, norV and hcp genes were all induced following transition from the oxic to anoxic state, and 20% of nitrate consumed in steady-state was released as N2O when nitrite had accumulated to millimolar levels. The kinetics of nitrate consumption, nitrite accumulation and N2O production were similar to those of wild-type in nitrate-sufficient cultures of a nap mutant. In contrast, in a narG mutant, the steady-state rate of N2O production was ~30-fold lower than that of the wild-type. Under nitrate-limited conditions, nap, but not nar, was up-regulated following transition from oxic to anoxic metabolism and very little N2O production was observed. Thus a combination of nitrate-sufficiency, nitrite accumulation and an active Nar-type nitrate reductase leads to NO and thence N2O production, and this can account for up to 20% of the nitrate catabolized. [ABSTRACT FROM AUTHOR]

The mechanism of the reactions catalyzed by the pyridoxal-phosphate-independent amino acid racemases and epimerases faces the difficult task of deprotonating a relatively low acidicity proton, the amino acid's -hydrogen, with a relatively poor base, a cysteine. In this work, we propose a mechanism for one of these enzymes, glutamate racemase (MurI), about which many controversies exist, and the roles that its active site residues may play. The titration curves and the pK12values of all of the ionizable residues for different structures leading from reactants to products have been analyzed. From these results a concerted mechanism has been proposed in which the Cys70 residue would deprotonate the -hydrogen of the substrate while, at the same time, being deprotonated by the Asp7 residue. To study the consistency of this mechanism classical molecular dynamics (MD) simulations have been carried out along with pK12calculations on the MD-generated structures. [ABSTRACT FROM AUTHOR]

Animals that live in cooperative societies form hierarchies in which dominant individuals reap disproportionate benefits from group cooperation. The stability of these societies requires subordinates to accept their inferior status rather than engage in escalated conflict with dominants over rank. Applying the logic of animal contests to these cases predicts that escalated conflict is more likely where subordinates are reproductively suppressed, where group productivity is high, relatedness is low, and where subordinates are relatively strong. We tested these four predictions in the field on co-foundress associations of the paper wasp Polistes dominulus by inducing contests over dominance rank experimentally. Subordinates with lower levels of ovarian development, and those in larger, more productive groups, were more likely to escalate in conflict with their dominant, as predicted. Neither genetic relatedness nor relative body size had significant effects on the probability of escalation. The original dominant emerged as the winner in all except one escalated contest. The results provide the first evidence that reproductive suppression of subordinates increases the threat of escalated conflict, and hence that reproductive sharing can promote stability of the dominant–subordinate relationship. [ABSTRACT FROM AUTHOR]

Objectives BAY 57-1293 is a helicase–primase inhibitor (HPI) from a new class of antivirals that are highly efficacious in herpes simplex virus (HSV)-1 animal infection models. Resistant mutants with point mutations in the helicase (UL5) were reported to be present in laboratory isolates at a low frequency of approximately 10−6. In contrast, we have shown elsewhere that some laboratory isolates contain resistant variants at higher frequency (10−4). Therefore, we screened 10 recent clinical isolates of HSV-1 for BAY 57-1293-resistant virions. Methods Clinical isolates were screened by a plaque reduction assay in Vero cells to determine the frequency of occurrence of BAY 57-1293-resistant variants. The helicase gene for the resistant variants was sequenced. Results One isolate contained highly resistant variants at 10−4 and another at 10−5. Both variants contained a previously reported BAY 57-1293 resistance mutation (K356N) in UL5 and were > 5000-fold resistant. Conclusions Occurrence of HPI-resistant viruses at high frequency in a clinical isolate is intriguing. Two alternative hypotheses are proposed to explain this phenomenon. It is also surprising that two unrelated clinical isolates contain an identical HPI resistance mutation. These results have important implications for HPI drug-resistance monitoring during subsequent clinical trials. [ABSTRACT FROM AUTHOR]

: Objectives To investigate the mechanism of action of the helicase–primase inhibitors (HPIs) BAY 57-1293 and BILS 22 BS by selection and characterization of drug-resistant herpes simplex virus (HSV)-1 mutants. : Methods HSV-1 mutants were selected using BAY 57-1293 in Vero cells. Resistance mutations identified in the UL5 helicase or UL52 primase genes were validated by marker transfer. Cross-resistance to the structurally distinct BILS 22 BS was measured by ID50 determinations. : Results (i) A single mutation (UL52: A899T) confers 43-fold resistance to BAY 57-1293, but does not confer any resistance to BILS 22 BS. (ii) A double mutant (UL52: A899T and UL5: K356T) is 2500-fold resistant to BAY 57-1293, which is more than 17 times the sum of fold-resistance due to the individual mutations, UL52: A899T (43-fold) and UL5: K356T (100-fold). (iii) Virus containing the single helicase mutation and the double mutant with mutations in both helicase and primase showed equal resistance to BILS 22 BS (70-fold). : Conclusions By measuring the relative inhibitory concentrations required to overcome particular mutations in the helicase and primase proteins, evidence was obtained that BAY 57-1293 interacts with both components of the helicase–primase complex to achieve maximum potency, whereas for BILS 22BS, this may not be the case. Furthermore, our observations suggest that BAY 57-1293 interacts simultaneously with UL5 and UL52. Overall, the results suggest that these two potent HPIs interact differently with the helicase–primase complex. [ABSTRACT FROM AUTHOR]