Improved protein-ligand docking using GOLD

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol.     

Compressibility and uncoupling of cytochrome P450cam: high pressure FTIR and activity studies

The effect of the hydrostatic pressure on the CO ligand stretch vibration in cytochrome P450cam-CO bound with various substrates is studied by FTIR. The vibration frequency is linearily shifted to lower values with increasing pressure. The slope of the shift gives the isothermal compressibility of the heme pocket and is found to be related to the high-spin state content in an opposite direction to that previously observed from the pressure-induced shift of the Soret band. This opposite behaviour is explained by the dual effect of heme pocket water molecules both on the CO ligand and on electrostatic potentials produced by the protein at the distal side. The latter effect disturbs ligand-distal side contacts which are needed for a specific proton transfer in oxygen activation when dioxygen is the ligand. Their loss results in uncoupled H(2)O(2) formation.     

Inclusion complexation behavior of dyestuff guest molecules by a bridged bis(cyclomaltoheptaose)[bis(beta-cyclodextrin)] with a pyromellitic acid diamide tether

A novel bridged bis(beta-cyclodextrin) with a pyromellitic acid 2,5-diamide tether (2) has been synthesized by reaction of 6(I)-(2-aminoethyleneamino)-6-deoxycyclomaltoheptaose [mono 6-(2-aminoethyleneamino)-6-deoxy-beta-cyclodextrin] with 1,2,4,5-benzenetetracarboxylic dianhydride. Its inclusion complexation behavior with some representative dyestuffs, i.e., Acridine Red (AR), Rhodamine B (RhB), Neutral Red (NR), Brilliant Green (BG), was studied by using UV-absorption, fluorescence, and 2D NMR spectroscopy. Fluorescence titrations have been performed at 25 degrees C in pH 7.2 buffer solution to calculate the binding constants of resulting complexes. These results obtained indicated that bis(beta-cyclodextrin) 2 exhibits the strongly enhanced binding ability with all dye molecules examined compared with natural cyclodextrins. The binding modes of 2 with dye molecules have been deduced by 2D NMR experiments to establish the correlations between molecular conformations and binding constants of inclusion complexation. It is found that the improved binding ability and molecular selectivity of 2 could be attributed to double-cavity cooperative inclusion interaction and the size/shape matching between the host and guest.     

Walking and running at resonance

Humans and other animals can temporarily store mechanical energy in elastic oscillations, f(el), of body parts and in pendulum oscillations, f(p) = const sq.rt (g/L), of legs, length L, or other appendages, and thereby reduce the energy consumption of locomotion. However, energy saving only occurs if these oscillations are tuned to the leg propagation frequency f. It has long been known that f is tuned to the pendulum frequency of the free-swinging leg of walkers. During running the leg frequency increases to some new value f = f(r). We propose that in order to maintain resonance the animal, mass M, actively increases its leg pendulum frequency to the new value f(p,r) =const sq.rt (a(y)/L)=f(r), by giving its hips a vertical acceleration a(y)= F(y)/M. The pendulum frequency is increased if the impact force F(y) of the stance foot is larger than Mg, explaining the observation by Alexander and Bennet-Clark (1976) that F(v) becomes larger than Mg when animals start to run. Our model predictions of the running velocity U(r) as function of L, F(v), are in agreement with measurements of these quantities (Farley et al. 1993). The leg's longitudinal elastic oscillation frequency scales as f(el) = const sq.rt (k/M). Experiments by Ferris et al., (1998) show that runners adjust their leg's stiffness, k, when running on surfaces of different elasticity so that the total stiffness k remains constant. Our analysis of their data suggests that the longitudinal oscillations of the stance leg are indeed kept in tune with the running frequency. Therefore we conclude that humans, and by extension all animals, maintain resonance during running. Our model also predicts the Froude number of walking-running transitions, Fr = U(2)/gL approximately 0.5 in good agreement with measurements.     

Molecular motions and conformational changes of HPPK

6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) belongs to a class of catalytic enzymes involved in phosphoryl transfer and is a new target for the development of novel antimicrobial agents. In the present study, the fundamental consideration is to view the overall structure of HPPK as a network of interacting residues and to extract the most cooperative collective motions that define its global dynamics. A coarse-grained model, harmonically constrained according to HPPK's crystal structure is used. Four crystal structures of HPPK (one apo and three holo forms with different nucleotide and pterin analogs) are studied with the goal of providing insights about the function-dynamic correlation and ligand induced conformational changes. The dynamic differences are examined between HPPK's apo- and holo-forms, because they are involved in the catalytic reaction steps. Our results indicate that the palm-like structure of HPPK is nearly rigid, whereas the two flexible loops: L2 (residues 43-53) and L3 (residues 82-92) exhibit the most concerted motions for ligand recognition and presumably, catalysis. These two flexible loops are involved in the recognition of HPPKs nucleotide and pterin ligands, whereas the rigid palm region is associated with binding of these cognate ligands. Six domains of collective motions are identified, comprised of structurally close but not necessarily sequential residues. Two of these domains correspond to the flexible loops (L2 and L3), whereas the remaining domains correspond to the rigid part of the molecule.     

Reproductive Biology of Southwestern Atlantic Wreckfish, Polyprion americanus (Teleostei: Polyprionidae)

We report on the reproductive biology of southwestern Atlantic wreckfish. Females mature first at 77.9cm total length (TL) (10.4 years) and all are mature by 90cm TL (15.2 years). Males mature first at 74.9cm (9 years) and all are mature by 80cm TL (10.9 years). The wreckfish is a gonochoristic multiple spawner and the gonadal cycle is synchronized at the population level. Spawning occurs from late July to early October along the continental slope (<300m). Ovarian fecundity varies from 3 to 11.9 million (135–311 oocytes×g^–1) and increases exponentially with length. Spawning at western boundary current systems, maintained by homing of adults, is a basic requirement for self-sustaining populations of this species.     

Immobilised activated sludge based biosensor for biochemical oxygen demand measurement

A biochemical oxygen demand (BOD) sensor, based on an immobilised mixed culture of microorganisms in combination with a dissolved oxygen electrode, has been developed for the purpose of on-line monitoring of the biological treatment process for waste and wastewater. The sensor was designed for easy replacement of the biomembrane, thereby making it suitable for short-term use. The drawbacks of activated sludge based sensor, such as short sensor lifetime, were thereby circumvented. The sensor BOD measurements were carried out in the kinetic mode using a flow injection system, resulting in 25 s for one measurement followed by 4–8 min recovery time. Based on the results of normalised sensor responses, the OECD synthetic wastewater was considered to be a more suitable calibration solution in comparison with the GGA solution. Good agreement was achieved between the results of the sensor BOD measurement and those obtained from BOD₅ analysis of a wastewater sample from a food-processing factory. Reproducibility of responses using one sensor was below ±5.6% standard deviation. Reproducibility of responses using different sensors was within acceptable bias limits, viz. ±15% standard deviation.     

Allozyme Variation Patterns and Multiple Hybridization Origins: Clonal Variation Among Four Sibling Parthenogenetic Caucasian Rock Lizards

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D.uzzelli, D.sapphirina, and D.bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D.raddei and D.valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F₁ typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Abscission and thinning of young fruit and thier regulation by plant hormones and bioregulators

Natural abscission of young fruit and its regulation by plant hormones isconsidered and compared to the generally accepted model of senescencetriggered abscission of, for example, leaves or mature fruit. It isconcluded that abscission of young fruit cannot be explained by this model.Alternatively, it is suggested that the senescence triggered initial step inthe classical abscission model should be replaced by a correlativelytriggered step. Polar basipetal IAA transport with its autostimulation andautoinhibition components is the main regulating signal in this correlativeacting system and replaces ethylene as the initial driving force from thesenescence triggered model.Results supporting this model are presented and tested against existingresults from the literature. Finally, this hypothesis is tested as a possibleexplanation of the mode of action of some thinning chemicals orbioregulators. It is speculated how a thinning chemical should be designedto function in a more reliable way, at least as far as its interference with the endogenous hormone system is concerned.