Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Targeted mutagenesis of the female-suppressor sygi gene in tetraploid kiwifruit by crispr/cas9

Kiwifruit belong to the genus Actinidia with 54 species apparently all functionally dioecious. The sex-determinants of the type XX/XY, with male heterogametic, operate independently of the ploidy level. Recently, the SyGI protein has been described as the suppressor of female development. In the present study, we exploited the CRISPR/Cas9 technology by targeting two different sites in the SyGI gene in order to induce a stable gene knock-out in two tetraploid male accessions of Actinidia chinensis var. chinensis. The two genotypes showed a regenerative efficiency of 58% and 73%, respectively. Despite not yet being able to verify the phenotypic effects on the flower structure, due to the long time required by tissue-cultured kiwifruit plants to flower, we obtained two regenerated lines showing near fixation of a unique modification in their genome, resulting in both cases in the onset of a premature stop codon, which induces the putative gene knock-out. Evaluation of gRNA1 locus for both regenerated plantlets resulted in co-amplification of a minor variant differing from the target region for a single nucleotide. A genomic duplication of the region in proximity of the Y genomic region could be postulated

NuSTAR + XMM-Newton monitoring of the neutron star transient AX J1745.6-2901

AX J1745.6-2901 is a high-inclination (eclipsing) transient neutron star (NS) Low Mass X-ray Binary (LMXB) showcasing intense ionised Fe K absorption. We present here the analysis of 11 XMM-Newton and 15 NuSTAR new data-sets (obtained between 2013-2016), therefore tripling the number of observations of AX J1745.6-2901 in outburst. Thanks to simultaneous XMM-Newton and NuSTAR spectra, we greatly improve on the fitting of the X-ray continuum. During the soft state the emission can be described by a disk black body ($kT\sim1.1-1.2$ keV and inner disc radius $r_{DBB}\sim14$ km), plus hot ($kT\sim2.2-3.0$ keV) black body radiation with a small emitting radius ($r_{BB}\sim0.5-0.8$ km) likely associated with the boundary layer or NS surface, plus a faint Comptonisation component. Imprinted on the spectra are clear absorption features created by both neutral and ionised matter. Additionally, positive residuals suggestive of an emission Fe K$\alpha$ disc line and consistent with relativistic ionised reflection are present during the soft state, while such residuals are not significant during the hard state. The hard state spectra are characterised by a hard ($\Gamma\sim1.9-2.1$) power law, showing no evidence for a high energy cut off ($kT_e>60-140$ keV) and implying a small optical depth ($\tau<1.6$). The new observations confirm the previously witnessed trend of exhibiting strong Fe K absorption in the soft state, that significantly weakens during the hard state. Optical (GROND) and radio (GMRT) observations suggest for AX J1745.6-2901 a standard broad band SED as typically observed in accreting neutron stars.Comment: Accepted for publication in MNRA

Hydrodynamics of polar liquid crystals

Starting from a microscopic definition of an alignment vector proportional to the polarization, we discuss the hydrodynamics of polar liquid crystals with local $C_{\infty v}$-symmetry. The free energy for polar liquid crystals differs from that of nematic liquid crystals ($D_{\infty h}$) in that it contains terms violating the ${\bf{n}}\to -{\bf{n}}$ symmetry. First we show that these $\mathcal{Z}_2$-odd terms induce a general splay instability of a uniform polarized state in a range of parameters. Next we use the general Poisson-bracket formalism to derive the hydrodynamic equations of the system in the polarized state. The structure of the linear hydrodynamic modes confirms the existence of the splay instability.Comment: 9 pages, corrected typos, added references, revised content, to appear in PR

Fifteen years of XMM-Newton and Chandra monitoring of Sgr A*: Evidence for a recent increase in the bright flaring rate

We present a study of the X-ray flaring activity of Sgr A* during all the 150 XMM-Newton and Chandra observations pointed at the Milky Way center over the last 15 years. This includes the latest XMM-Newton and Chandra campaigns devoted to monitoring the closest approach of the very red Br-Gamma emitting object called G2. The entire dataset analysed extends from September 1999 through November 2014. We employed a Bayesian block analysis to investigate any possible variations in the characteristics (frequency, energetics, peak intensity, duration) of the flaring events that Sgr A* has exhibited since their discovery in 2001. We observe that the total bright-or-very bright flare luminosity of Sgr A* increased between 2013-2014 by a factor of 2-3 (~3.5 sigma significance). We also observe an increase (~99.9% significance) from 0.27+-0.04 to 2.5+-1.0 day^-1 of the bright-or-very bright flaring rate of Sgr A*, starting in late summer 2014, which happens to be about six months after G2's peri-center passage. This might indicate that clustering is a general property of bright flares and that it is associated with a stationary noise process producing flares not uniformly distributed in time (similar to what is observed in other quiescent black holes). If so, the variation in flaring properties would be revealed only now because of the increased monitoring frequency. Alternatively, this may be the first sign of an excess accretion activity induced by the close passage of G2. More observations are necessary to distinguish between these two hypotheses.Comment: Accepted for publication in MNRA

Steady shear flow thermodynamics based on a canonical distribution approach

A non-equilibrium steady state thermodynamics to describe shear flows is developed using a canonical distribution approach. We construct a canonical distribution for shear flow based on the energy in the moving frame using the Lagrangian formalism of the classical mechanics. From this distribution we derive the Evans-Hanley shear flow thermodynamics, which is characterized by the first law of thermodynamics $dE = T dS - Q d\gamma$ relating infinitesimal changes in energy $E$, entropy $S$ and shear rate $\gamma$ with kinetic temperature $T$. Our central result is that the coefficient $Q$ is given by Helfand's moment for viscosity. This approach leads to thermodynamic stability conditions for shear flow, one of which is equivalent to the positivity of the correlation function of $Q$. We emphasize the role of the external work required to sustain the steady shear flow in this approach, and show theoretically that the ensemble average of its power $\dot{W}$ must be non-negative. A non-equilibrium entropy, increasing in time, is introduced, so that the amount of heat based on this entropy is equal to the average of $\dot{W}$. Numerical results from non-equilibrium molecular dynamics simulation of two-dimensional many-particle systems with soft-core interactions are presented which support our interpretation.Comment: 23 pages, 7 figure

Multiple-Point and Multiple-Time Correlations Functions in a Hard-Sphere Fluid

A recent mode coupling theory of higher-order correlation functions is tested on a simple hard-sphere fluid system at intermediate densities. Multi-point and multi-time correlation functions of the densities of conserved variables are calculated in the hydrodynamic limit and compared to results obtained from event-based molecular dynamics simulations. It is demonstrated that the mode coupling theory results are in excellent agreement with the simulation results provided that dissipative couplings are included in the vertices appearing in the theory. In contrast, simplified mode coupling theories in which the densities obey Gaussian statistics neglect important contributions to both the multi-point and multi-time correlation functions on all time scales.Comment: Second one in a sequence of two (in the first, the formalism was developed). 12 pages REVTeX. 5 figures (eps). Submitted to Phys.Rev.