Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase

The enzyme phenylalanine hydroxylase (PAH) is defective in the inherited disorder phenylketonuria. PAH, a tetrameric enzyme, is highly regulated and displays positive cooperativity for its substrate, Phe. Whether Phe binds to an allosteric site is a matter of debate, despite several studies worldwide. To address this issue, we generated a dimeric model for Phe–PAH interactions, by performing molecular docking combined with molecular dynamics simulations on human and rat wild-type sequences and also on a human G46S mutant. Our results suggest that the allosteric Phe-binding site lies at the dimeric interface between the regulatory and the catalytic domains of two adjacent subunits. The structural and dynamical features of the site were characterized in depth and described. Interestingly, our findings provide evidence for lower allosteric Phe-binding ability of the G46S mutant than the human wild-type enzyme. This also explains the disease-causing nature of this mutant.     

Honeybees establish specific sites on the comb for their waggle dances

Successful honeybee foragers perform dances on the surface of the comb where they interact with nectar receivers and dance followers. We have recorded the sites at which dances take place in large ten-frame hives and in two-frame observation hives. We find that dancing bees are most commonly found on particular combs in large hives and in particular areas on the combs in the observation hives. Although the site where dances take place may change from day to day, dancers will keep to the same site during the foraging period in any one day. Furthermore, if an established dance site is artificially relocated in the hive during the day, dancers seek these sites out before commencing their dances. We conclude that the dance sites are labelled in some way and so promote the congregation of both dancers and dance followers at the same site. Accepted: 27 November 1996     

The effect of winter temperatures on the timing of breeding activity in the common toad Bufo bufo

A 19-year study of a common toad population in south Dorset, UK, was carried out between 1980 and 1998. The daily arrival of sexually mature male and female toads at a breeding pond was recorded each year. The timing of the main arrival of toads at the breeding pond was highly correlated with the mean daily temperatures over the 40 days immediately preceding the main arrival. When the temperatures were higher than average, breeding occurred significantly earlier in the year than if they were either average or lower than average. During the study, the toad breeding seasons were early (2–13 February) in 5 years (1989, 1990, 1993, 1995, 1998), late (16–23 March) in 2 years (1986, 1996) and average (25 February–8 March) during the remaining 12 years. Evidence was found suggesting that common toads have a daylength threshold of about 9 h, below which the migration to the breeding pond does not occur. Evidence was also found indicating that common toads in southern England have a threshold temperature for activity of about 6°C and that the onset of breeding activity is highly correlated with the number of days during the 40 days prior to the main arrival at the breeding pond that were at or above this temperature. Predicting the start of the main breeding migration to a pond in any year may be possible by comparing the pattern of the 40-day running mean daily temperatures from 21 December the preceding year with those from previous years when the start of breeding activity is known. Although all five of the earliest recorded toad breeding years occurred during the last 10 years, and were associated with the occurrence of particularly mild winters, a significant trend towards earlier breeding in recent years compared with previous years was not found. Received: 16 July 1998 / Accepted: 14 September 1998     

Population-specific material properties of the implantation site for transcatheter aortic valve replacement finite element simulations

Patient-specific computational models are an established tool to support device development and test under clinically relevant boundary conditions. Potentially, such models could be used to aid the clinical decision-making process for percutaneous valve selection; however, their adoption in clinical practice is still limited to individual cases. To be fully informative, they should include patient-specific data on both anatomy and mechanics of the implantation site. In this work, fourteen patient-specific computational models for transcatheter aortic valve replacement (TAVR) with balloon-expandable Sapien XT devices were retrospectively developed to tune the material parameters of the implantation site mechanical model for the average TAVR population.Pre-procedural computed tomography (CT) images were post-processed to create the 3D patient-specific anatomy of the implantation site. Balloon valvuloplasty and device deployment were simulated with finite element (FE) analysis. Valve leaflets and aortic root were modelled as linear elastic materials, while calcification as elastoplastic. Material properties were initially selected from literature; then, a statistical analysis was designed to investigate the effect of each implantation site material parameter on the implanted stent diameter and thus identify the combination of material parameters for TAVR patients.These numerical models were validated against clinical data. The comparison between stent diameters measured from post-procedural fluoroscopy images and final computational results showed a mean difference of 2.5 ± 3.9%. Moreover, the numerical model detected the presence of paravalvular leakage (PVL) in 79% of cases, as assessed by post-TAVR echocardiographic examination.The final aim was to increase accuracy and reliability of such computational tools for prospective clinical applications.     

Distinctive communication networks in inactive states of β2-adrenergic receptor: Mutual information and entropy transfer analysis

Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (β₂-AR) unraveled distinct communication pathways. Previously, a so-called “highly” inactive state of the receptor was observed during 1.5 microsecond long molecular dynamics simulation where the largest intracellular loop (ICL3) was swiftly packed onto the G-protein binding cavity, becoming entirely inaccessible. Mutual information quantifying the degree of correspondence between backbone-C_α fluctuations was mostly shared between intra- and extra-cellular loop regions in the original inactive state, but shifted to entirely different regions in this latest inactive state. Interestingly, the largest amount of mutual information was always shared among the mobile regions. Irrespective of the conformational state, polar residues always contributed more to mutual information than hydrophobic residues, and also the number of polar-polar residue pairs shared the highest degree of mutual information compared to those incorporating hydrophobic residues. Entropy transfer, quantifying the correspondence between backbone-C_α fluctuations at different timesteps, revealed a distinctive pathway directed from the extracellular site toward intracellular portions in this recently exposed inactive state for which the direction of information flow was the reverse of that observed in the original inactive state where the mobile ICL3 and its intracellular surroundings drove the future fluctuations of extracellular regions.     

Energy coupling sites in the electron transport chain of Zymomonas mobilis

Abstract Energy-coupling sites in the electron transport chain of the obligately fermentative aerotolerant bacterium Zymomonas mobilis were examined. The H⁺ /O stoichiometry of the electron transport chain in intact bacteria oxidizing ethanol was close to 3.3. Cytoplasmic membrane vesicles coupled NADH oxidation to ATP synthesis. With ascorbate/phenazine methosulfate they showed oxygen uptake which was sensitive to antimycin A, but no significant ATP synthesis could be detected. Cells with a defective coupling site I, prepared by cultivation on a sulfate-deficient medium, showed a decreased rotenone sensitivity of respiration, and they lacked almost all the respiration-driven proton translocation and ATP synthesis. We conclude that, despite the reported composition of the electron transport chain, only energy coupling site 1 was functional in Z. mobilis .     

The CTPase activity of ParB determines the size and dynamics of prokaryotic DNA partition complexes

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