Structure determination of Murine Norovirus NS6 proteases with C-terminal extensions designed to probe protease-substrate interactions

Noroviruses are positive-sense single-stranded RNA viruses. They encode an NS6 protease that cleaves a viral polyprotein at specific sites to produce mature viral proteins. In an earlier study we obtained crystals of murine norovirus (MNV) NS6 protease in which crystal contacts were mediated by specific insertion of the C-terminus of one protein (which contains residues P5-P1 of the NS6-7 cleavage junction) into the peptide binding site of an adjacent molecule, forming an adventitious protease-product complex. We sought to reproduce this crystal form to investigate protease–substrate complexes by extending the C-terminus of NS6 construct to include residues on the C-terminal (P′) side of the cleavage junction. We report the crystallization and crystal structure determination of inactive mutants of murine norovirus NS6 protease with C-terminal extensions of one, two and four residues from the N-terminus of the adjacent NS7 protein (NS6 1′, NS6 2′, NS6 4′). We also determined the structure of a chimeric extended NS6 protease in which the P4-P4′ sequence of the NS6-7 cleavage site was replaced with the corresponding sequence from the NS2-3 cleavage junction (NS6 4′ 2|3).The constructs NS6 1′ and NS6 2′ yielded crystals that diffracted anisotropically. We found that, although the uncorrected data could be phased by molecular replacement, refinement of the structures stalled unless the data were ellipsoidally truncated and corrected with anisotropic B-factors. These corrections significantly improved phasing by molecular replacement and subsequent refinement.The refined structures of all four extended NS6 proteases are very similar in structure to the mature MNV NS6—and in one case reveal additional details of a surface loop. Although the packing arrangement observed showed some similarities to those observed in the adventitious protease-product crystals reported previously, in no case were specific protease–substrate interactions observed

The Threshold Pion-Photoproduction of Nucleons In The Chiral Quark Model

In this paper, we show that the low energy theorem (LET) of the threshold pion-photoproduction can be fully recovered in the quark model. An essential result of this investigation is that the quark-pion operators are obtained from the effective chiral Lagrangian, and the low energy theorem does not require the constraints on the internal structures of the nucleon. The pseudoscalar quark-pion coupling generates an additional term at order $\mu=m_{\pi}/M$ only in the isospin amplitude $A^{(-)}$. The role of the transitions between the nucleon and the resonance $P_{33}(1232)$ and P-wave baryons are also discussed, we find that the leading contributions to the isospin amplitudes at $O(\mu^2)$ are from the transition between the P-wave baryons and the nucleon and the charge radius of the nucleon. The leading contribution from the P-wave baryons only affects the neutral pion production, and improve the agreement with data significantly. The transition between the resonance $P_{33}(1232)$ and the nucleon only gives an order $\mu^3$ corrections to $A^{(-)}$

Dispersion Effects in Nucleon Polarisabilities

We present a formalism to extract the dynamical nucleon polarisabilities defined via a multipole expansion of the structure amplitudes in nucleon Compton scattering. In contradistinction to the static polarisabilities, dynamical polarisabilities gauge the response of the internal degrees of freedom of a composed object to an external, real photon field of arbitrary energy. Being energy dependent, they therefore contain additional information about dispersive effects induced by internal relaxation mechanisms, baryonic resonances and meson production thresholds of the nucleon. We give explicit formulae to extract the dynamical electric and magnetic dipole as well as quadrupole polarisabilities from low energy nucleon Compton scattering up to the one pion production threshold and discuss the connection to the definition of static nucleon polarisabilities. As a concrete example, we examine the results of leading order Heavy Baryon Chiral Perturbation Theory for the four leading spin independent iso-scalar polarisabilities of the nucleon. Finally, we consider the possible r{\^o}le of energy dependent effects in low energy extractions of the iso-scalar dipole polarisabilities from Compton scattering on the deuteron.Comment: 17 pages LaTeX2e with 2 figures, using includegraphicx (5 .eps files). Minor corrections, references updated. Contents identical to version to appear in Phys. Rev. C 65, spelling differen

The P_33(1232) resonance contribution into the amplitudes M_{1+}^{3/2},E_{1+}^{3/2},S_{1+}^{3/2} from an analysis of the p(e,e'p)\pi^0 data at Q^2 = 2.8, 3.2, and 4 (GeV/c)^2 within dispersion relation approach

Within the fixed-t dispersion relation approach we have analysed the TJNAF and DESY data on the exclusive p(e,e'p)\pi^0 reaction in order to find the P_{33}(1232) resonance contribution into the multipole amplitudes M_{1+}^{3/2},E_{1+}^{3/2},S_{1+}^{3/2}. As an input for the resonance and nonresonance contributions into these amplitudes the earlier obtained solutions of the integral equations which follow from dispersion relations are used. The obtained values of the ratio E2/M1 for the \gamma^* N \to P_{33}(1232) transition are: 0.039\pm 0.029, 0.121\pm 0.032, 0.04\pm 0.031 for Q^2= 2.8, 3.2, and 4 (GeV/c)^2, respectively. The comparison with the data at low Q^2 shows that there is no evidence for the presence of the visible pQCD contribution into the transition \gamma N \to P_{33}(1232) at Q^2=3-4 GeV^2. The ratio S_{1+}^{3/2}/M_{1+}^{3/2} for the resonance parts of multipoles is: -0.049\pm 0.029, -0.099\pm 0.041, -0.085\pm 0.021 for Q^2= 2.8, 3.2, and 4 (GeV/c)^2, respectively. Our results for the transverse form factor G_T(Q^2) of the \gamma^* N \to P_{33}(1232) transition are lower than the values obtained from the inclusive data. With increasing Q^2, Q^4G_T(Q^2) decreases, so there is no evidence for the presence of the pQCD contribution here too

Photon- and meson-induced reactions on the nucleon

In an unitary effective Lagrangian model we develop a unified description of both meson scattering and photon-induced reactions on the nucleon. Adding the photon to an already existing model for meson-nucleon scattering yields both Compton and meson photoproduction amplitudes. In a simultaneous fit to all available data involving the final states $\gamma N$, $\pi N$, $\pi\pi N$, $\eta N$ and $K \Lambda$ the parameters of the nucleon resonances are extracted.Comment: 57 pages, 14 figures, LaTex (uses Revtex and graphicx). Submitted to Phys. Rev. C. References updated, Fig. 14 change

Low-Energy Compton Scattering of Polarized Photons on Polarized Nucleons

The general structure of the cross section of $\gamma N$ scattering with polarized photon and/or nucleon in initial and/or final state is systematically described and exposed through invariant amplitudes. A low-energy expansion of the cross section up to and including terms of order $\omega^4$ is given which involves ten structure parameters of the nucleon (dipole, quadrupole, dispersion, and spin polarizabilities). Their physical meaning is discussed in detail. Using fixed-t dispersion relations, predictions for these parameters are obtained and compared with results of chiral perturbation theory. It is emphasized that Compton scattering experiments at large angles can fix the most uncertain of these structure parameters. Predictions for the cross section and double-polarization asymmetries are given and the convergence of the expansion is investigated. The feasibility of the experimental determination of some of the struture parameters is discussed.Comment: 41 pages of text, 9 figures; minor revisions prior to publication in Phys. Rev.

Hydraulically-actuated compliant revolute joint for medical robotic systems based on multimaterial additive manufacturing

IEEE International Conference on Robotics and Automation (ICRA), Montréal, Canada, janvier 2019 Research team : AV

Vector meson production and nucleon resonance analysis in a coupled-channel approach for energies m_N < sqrt(s) < 2 GeV II: photon-induced results

We present a nucleon resonance analysis by simultaneously considering all pion- and photon-induced experimental data on the final states gamma N, pi N, 2 pi N, eta N, K Lambda, K Sigma, and omega N for energies from the nucleon mass up to sqrt(s) = 2 GeV. In this analysis we find strong evidence for the resonances P_{31}(1750), P_{13}(1900), P_{33}(1920), and D_{13}(1950). The omega N production mechanism is dominated by large P_{11}(1710) and P_{13}(1900) contributions. In this second part we present the results on the photoproduction reactions and the electromagnetic properties of the resonances. The inclusion of all important final states up to sqrt(s) = 2 GeV allows for estimates on the importance of the individual states for the GDH sum rule.Comment: 41 pages, 26 figures, discussion extended, typos corrected, references updated, to appear in Phys. Rev.

Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design.

Accelerating cures for children with cancer remains an immediate challenge as a result of extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs)-many of which are refractory to current standard-of-care treatments-from high-risk childhood cancers. Here, we genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; and refine our understanding of relapsed disease. In addition, we use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. We anticipate that these data will serve as a resource for pediatric oncology drug development and will guide rational clinical trial design for children with cancer

Compton scattering on the nucleon at intermediate energies and polarizabilities in a microscopic model

A microscopic calculation of Compton scattering on the nucleon is presented which encompasses the lowest energies -- yielding nucleon polarizabilities -- and extends to energies of the order of 600 MeV. We have used the covariant "Dressed K-Matrix Model" obeying the symmetry properties which are appropriate in the different energy regimes. In particular, crossing symmetry, gauge invariance and unitarity are satisfied. The extent of violation of analyticity (causality) is used as an expansion parameter.Comment: 35 pages, 15 figures, using REVTeX. Modified version to be published in Phys. Rev. C, more extensive comparison with data for Compton scattering, all results unchange