Biomolecular solution X-ray scattering at the National Synchrotron Light Source

A new beamline for simultaneous SAXS/WAXS of biomolecules in solution is described

A comparison between two-scale asymptotic expansions and Bloch wave expansions for the homogenization of periodic structures

in pressInternational audienceIn this paper we make a comparison between the two-scale asymptotic expansion method for periodic homogenization and the so-called Bloch wave method. It is well-known that the homogenized tensor coincides with the Hessian matrix of the first Bloch eigenvalue when the Bloch parameter vanishes. In the context of the two-scale asymptotic expansion method, there is the notion of high order homogenized equation [5] where the homogenized equation can be improved by adding small additional higher order differential terms. The next non-zero high order term is a fourth-order term, accounting for dispersion effects (see e.g. [23], [18], [15]). Surprisingly, this homogenized fourth-order tensor is not equal to the fourth-order tensor arising in the Taylor expansion of the first Bloch eigenvalue, which is often called Burnett tensor. Here, we establish an exact relation between the homogenized fourth-order tensor and the Burnett fourth-order tensor. It was proved in [11] that the Burnett fourth-order tensor has a sign. For the special case of a simple laminate we prove that the homogenized fourth-order tensor may change sign. In the elliptic case we explain the difference between the homogenized and Burnett fourth-order tensors by a difference in the source term which features an additional corrector term. Finally, for the wave equation, the two fourth-order tensors coincide again, so dispersion is unambiguously defined, and only the source terms differ as in the elliptic case

Structure tridimensionnelle de l'aldolase de muscle de lapin à une résolution de 2,1 Å

L'enzyme fructose-diphosphate aldolase (EC.4.1.2.13) est un enzyme abondant du cycle glycolytique catalysant le clivage réversible du D-fructose-1,6-diphosphate en dihydroxyacétone-phosphate et D-glycéraldéhyde-3-phosphate. Les modifications chimiques effectuées pour l'aldolase de classe I ont permis d'identifier certains résidus d'acides aminés impliqués dans la catalyse. Ces études ont également démontré que le mécanisme enzymatique de l'aldolase de classe I implique la formation de deux bases de Schiff et d'un intermédiaire carbanion.L'interprétation du mécanisme enzymatique au niveau moléculaire nécessite la solution de la structure tridimensionnelle de l'aldolase à haute résolution. La structure tridimensionnelle de l'aldolase de muscle de lapin à une résolution de 2.1êA a été déterminée par cristallographie et diffraction aux rayons-X pour la forme cristalline monoclinique de cet enzyme. La correction systématique des intensités de diffraction mesurées à l'aide d'un diffractomètre implique des modèles semi-empiriques pour l'évaluation du bruit de fond, de la transmission et de la décomposition du cristal en présence du faisceau de rayons-X. La corrélation des 185843 intensités mesurées à partir de 72 cristaux en 90036 réflexions uniques (I >0) génère un facteur résiduel de 0.046. La solution du problème des phases utilise un seul dérivé d'atomes lourds. La dualité de phases obtenue de ce dérivé d'atomes lourds est résolue par la symétrie non-cristallographique du tétramère et l'effet moyenne du solvant.L'affinement cristallographique des 11616 atomes en fonction des 85380 réflexions uniques de 10êA à 2.1êA (Fo>3[sigma]) génère un facteur résiduel de 0.166 avec une déviation aux distances et aux angles de liaison de 0.02êA et 1.7[degré] respectivement. Considérant la correction de pertes d'intensité de cette forme cristalline dépassant les 80%, la qualité des résultats obtenus suggère que les modèles semi-empiriques utilisés pour la correction des données de diffraction sont en majeure partie responsables de la solution de la structure tridimensionnelle à la résolution de 2.1êA. L'architecture moléculaire de l'aldolase est composée de huit brins-[béta] et de douze hélices-[alpha].L'organisation spatiale de ces structures secondaires forme un baril-[béta] composé de deux groupes de feuillets-[béta] parallèles. La similitude de structure entre le motif des déshydrogénases et un des deux groupes de feuillets-[béta] suggère une relation d'évolution entre le baril-[béta] et le motif des déshydrogénases. La modélisation de la base de Schiff du D-fructose-1,6-diphosphate avec le résidu lysine 229 suggère un rôle potentiel pour la catalyse enzymatique des résidus d'acides aminés se retrouvant au site actif. La modélisation du substrat effectuée pour une autre forme cristalline de l'aldolase identifie essentiellement les mêmes résidus d'acides d'aminés. Les rôles potentiels suggérés pour la catalyse enzymatique sont différents entre les deux modélisations. La thèse discute des deux mécanismes enzymatiques proposés. La structure tridimensionnelle obtenue pour la région COOH-terminale de deux des quatre sous-unités est en interaction avec un autre tétramère de la maille cristalline. La conservation des principaux résidus d'acides aminés impliqués dans l'interaction de la région COOH-terminale suggère un mécanisme potentiel de polymérisation de tétramères d'aldolase in vivo .L'inhibition connue de l'enzyme glycéraldéhyde-3-phosphate déshydrogénase par les produits d'oxydation de l'aldolase en présence de fructose-1,6-diphosphate et d'hexacyanoferrate (III) démontre une interaction entre ces deux enzymes impliquant un transfert des produits de réaction. La conformation de la région COOH-terminale pour la forme cristalline monoclinique démontre sa mobilité, et permet de proposer un mécanisme de transfert des produits de réaction entre le site actif de l'aldolase et le site actif de la glycéraldéhyde-3-phosphate déshydrogénase

On the possibility of using polycrystalline material in the development of structure-based generic assays

The correlation coefficients calculated between raw powder diffraction profiles can be used to identify ligand-bound/unbound states of lysozyme

Evaluation of Load-To-Strength Ratios in Metastatic Vertebrae and Comparison With Age- and Sex-Matched Healthy Individuals.

Vertebrae containing osteolytic and osteosclerotic bone metastases undergo pathologic vertebral fracture (PVF) when the lesioned vertebrae fail to carry daily loads. We hypothesize that task-specific spinal loading patterns amplify the risk of PVF, with a higher degree of risk in osteolytic than in osteosclerotic vertebrae. To test this hypothesis, we obtained clinical CT images of 11 cadaveric spines with bone metastases, estimated the individual vertebral strength from the CT data, and created spine-specific musculoskeletal models from the CT data. We established a musculoskeletal model for each spine to compute vertebral loading for natural standing, natural standing + weights, forward flexion + weights, and lateral bending + weights and derived the individual vertebral load-to-strength ratio (LSR). For each activity, we compared the metastatic spines' predicted LSRs with the normative LSRs generated from a population-based sample of 250 men and women of comparable ages. Bone metastases classification significantly affected the CT-estimated vertebral strength (Kruskal-Wallis, p < 0.0001). Post-test analysis showed that the estimated vertebral strength of osteosclerotic and mixed metastases vertebrae was significantly higher than that of osteolytic vertebrae (p = 0.0016 and p = 0.0003) or vertebrae without radiographic evidence of bone metastasis (p = 0.0010 and p = 0.0003). Compared with the median (50%) LSRs of the normative dataset, osteolytic vertebrae had higher median (50%) LSRs under natural standing (p = 0.0375), natural standing + weights (p = 0.0118), and lateral bending + weights (p = 0.0111). Surprisingly, vertebrae showing minimal radiographic evidence of bone metastasis presented significantly higher median (50%) LSRs under natural standing (p < 0.0001) and lateral bending + weights (p = 0.0009) than the normative dataset. Osteosclerotic vertebrae had lower median (50%) LSRs under natural standing (p < 0.0001), natural standing + weights (p = 0.0005), forward flexion + weights (p < 0.0001), and lateral bending + weights (p = 0.0002), a trend shared by vertebrae with mixed lesions. This study is the first to apply musculoskeletal modeling to estimate individual vertebral loading in pathologic spines and highlights the role of task-specific loading in augmenting PVF risk associated with specific bone metastatic types. Our finding of high LSRs in vertebrae without radiologically observed bone metastasis highlights that patients with metastatic spine disease could be at an increased risk of vertebral fractures even at levels where lesions have not been identified radiologically

Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library

Bounds on strong field magneto-transport in three-dimensional composites

This paper deals with bounds satisfied by the effective non-symmetric conductivity of three-dimensional composites in the presence of a strong magnetic field. On the one hand, it is shown that for general composites the antisymmetric part of the effective conductivity cannot be bounded solely in terms of the antisymmetric part of the local conductivity, contrary to the columnar case. So, a suitable rank-two laminate the conductivity of which has a bounded antisymmetric part together with a high-contrast symmetric part, may generate an arbitrarily large antisymmetric part of the effective conductivity. On the other hand, bounds are provided which show that the antisymmetric part of the effective conductivity must go to zero if the upper bound on the antisymmetric part of the local conductivity goes to zero, and the symmetric part of the local conductivity remains bounded below and above. Elementary bounds on the effective moduli are derived assuming the local conductivity and effective conductivity have transverse isotropy in the plane orthogonal to the magnetic field. New Hashin-Shtrikman type bounds for two-phase three-dimensional composites with a non-symmetric conductivity are provided under geometric isotropy of the microstructure. The derivation of the bounds is based on a particular variational principle symmetrizing the problem, and the use of Y-tensors involving the averages of the fields in each phase.Comment: 21 page

RODIN project, Topology Optimization 2.0?

RODIN project is an attempt to propose a new kind of topology optimization tools. It has been motivated by the combination of two events: (1) the industrials demands for getting past serious limits identified in the available tools, (2) the advent of a new mathematical approach in the mid 2000's presenting very interesting properties. This project has been launched in July 2012 and is supported by French public funding. It is a collaborative project that gathers ten partners (ranging from academics to software editors and industrials end-users) and firmly aims at overcoming technical and scientific locks in the area of topology optimization. RODIN is therefore an ambitious and risky project that will possibly mark the birth of a new numerical tool

Structural basis of nSH2 regulation and lipid binding in PI3Kα

We report two crystal structures of the wild-type phosphatidylinositol 3-kinase α (PI3Kα) heterodimer refined to 2.9 Å and 3.4 Å resolution: the first as the free enzyme, the second in complex with the lipid substrate, diC4-PIP2, respectively. The first structure shows key interactions of the N-terminal SH2 domain (nSH2) and iSH2 with the activation loop that suggest a mechanism by which the enzyme is inhibited in its basal state. In the second structure, the lipid substrate binds in a positively charged pocket adjacent to the ATP-binding site, bordered by the P-loop, the activation loop and the iSH2 domain. An additional lipid-binding site was identified at the interface of the ABD, iSH2 and kinase domains. The ability of PI3Kα to bind an additional PIP2 molecule was confirmed in vitro by fluorescence quenching experiments. The crystal structures reveal key differences in the way the nSH2 domain interacts with wild-type p110α and with the oncogenic mutant p110αH1047R. Increased buried surface area and two unique salt-bridges observed only in the wild-type structure suggest tighter inhibition in the wild-type PI3Kα than in the oncogenic mutant. These differences may be partially responsible for the increased basal lipid kinase activity and increased membrane binding of the oncogenic mutant

Structure of acostatin, a dimeric disintegrin from Southern copperhead (Agkistrodon contortrix contortrix), at 1.7 Å resolution

Disintegrins are a family of small (4–14 kDa) proteins that bind to another class of proteins, integrins. Therefore, as integrin inhibitors, they can be exploited as anticancer and antiplatelet agents. Acostatin, an αβ heterodimeric disintegrin, has been isolated from the venom of Southern copperhead (Agkistrodon contortrix contortrix). The three-dimensional structure of acostatin has been determined by macromolecular crystallography using the molecular-replacement method. The asymmetric unit of the acostatin crystals consists of two heterodimers. The structure has been refined to an R_(work) and R_(free) of 18.6% and 21.5%, respectively, using all data in the 20–1.7 Å resolution range. The structure of all subunits is similar and is well ordered into N-terminal and C-terminal clusters with four intramolecular disulfide bonds. The overall fold consists of short β-sheets, each of which is formed by a pair of antiparallel β-strands connected by β-turns and flexible loops of different lengths. Conformational flexibility is found in the RGD loops and in the C-terminal segment. The interaction of two N-terminal clusters via two intermolecular disulfide bridges anchors the αβ chains of the acostatin dimers. The C-terminal clusters of the heterodimer project in opposite directions and form a larger angle between them in comparison with other dimeric disintegrins. Extensive interactions are observed between two heterodimers, revealing an αββα acostatin tetramer. Further experiments are required to identify whether the αββα acostatin complex plays a functional role in vivo