Comparative molecular modeling of Amphioxus calcium vector protein with calmodulin and troponin C

Calcium vector protein (CaVP), a new protein isolated from Amphioxus muscle, binds in a Ca2+ -rgulated manner to a 27 kd target protein, named CaVPT, whose function has not been elucidated yet. CaVP bears significant sequence homology to both calmodulin and skeletal muscle troponin C, especially in the C-tenninal half of the molecule, which presumably contains the two functional Ca2+ sites. The N-terminal half contains two abortive EF-hands and is intramolecularly crosslinked with a disulfide bond. Using the crystallographic structures of calmodulin and striated muscle troponin C as a framework, we constructed two different three-dimensional models of CaVP and modeled the intramolecular disulfide bridge. The modeling based upon the coordinates of calmodulin yields a Ca2+ -filled sites configuration in the N-terminal half of the molecule, even though no Ca2+ is bound in this half, whereas the troponin C-derived model generates a Ca2+ -empty sites configuration. The models predict that neither in the Ca2+ nor in the Ca2+ -empty sites conformation is there any steric and/or energetic obstacle for the formation of the disulfide bridge and that the disulfide bond is poorly accessible to reducing reagents. The optical properties of the Trp and Tyr residues of CaVP indicate that the calmodulin-derived model represents the most plausible predictio

Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin

Artemia has a complex extracellular hemoglobin of Mr 260,000 comprising two globin chains (Mr 130,000) each of which is a polymer of eight covalently linked domains of Mr 16,000. The primary structure of this polymeric globin was studied to understand how globin folded domains are ordered within a globin chain and, in turn, how the latter associate into a functional hemoglobin molecule. Here we report the amino acid sequence of a second domain, E7 (Mr 16,081, excluding the heme), and interpretations of sequence data by computer-assisted alignment and modeling. This clearly shows that, as with domain E1 (Moens, L. Van Hauwaert, M.-L. De Smet, K. Geelen, D. Verpooten, G. Van Beeumen, J. Wodak, S. Alard, P. & Trotman, C. (1988) J. Biol. Chem. 263, 4679-4685), domain E7 is compatible with a globin folded structure of the β-type chain. Several specific differences of domains E7 and E1 from the classic globins are identified. They possibly can be interpreted in terms of specific requirements for a double octameric functional molecule.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting

The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold’s termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics

Formation and Evolution of Dwarf Elliptical Galaxies - II. Spatially resolved star-formation histories

We present optical VLT spectroscopy of 16 dwarf elliptical galaxies (or dEs) comparable in mass to NGC 205, and belonging to the Fornax cluster and to nearby groups of galaxies. Using ULySS and STECKMAP, we derive radial profiles of the SSP-equivalent ages, metallicities and star-formation histories. The old stellar population of the dEs, which dominates their mass, is likely coeval with that of massive ellipticals or bulges, but the star formation efficiency is lower. Important intermediate age (1-5 Gyr) populations, and frequently tails of star formation until recent times are detected. These histories are reminiscent of their lower mass dSph counterparts of the Local Group. Most galaxies (10/16) show significant metallicity gradients, with metallicity declining by 0.5 dex over one half-light radius on average. These gradients are already present in the old population. The flattened (or discy), rotating objects (6/16) have flat metallicity profiles. This may be consistent with a distinct origin for these galaxies or it may be due to their geometry. The central SSP-equivalent age varies between 1 and 6 Gyr, with the age slowly increasing with radius in the vast majority of objects. The group and cluster galaxies have similar radial gradients and star-formation histories. The strong and old metallicity gradients place important constraints on the possible formation scenarios of dEs. Numerical simulations of the formation of spherical low-mass galaxies reproduce these gradients, but they require a longer time for them to build up. A gentle depletion of the gas, by ram-pressure stripping or starvation, could drive the gas-rich, star-forming progenitors to the present dEs.Comment: 21 pages, 9 figures. Accepted in MNRA

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Heterosubtypic Neutralizing Monoclonal Antibodies Cross-Protective against H5N1 and H1N1 Recovered from Human IgM+ Memory B Cells

Background: The hemagglutinin (HA) glycoprotein is the principal target of protective humoral immune responses to influenza virus infections but such antibody responses only provide efficient protection against a narrow spectrum of HA antigenic variants within a given virus subtype. Avian influenza viruses such as H5N1 are currently panzootic and pose a pandemic threat. These viruses are antigenically diverse and protective strategies need to cross protect against diverse viral clades. Furthermore, there are 16 different HA subtypes and no certainty the next pandemic will be caused by an H5 subtype, thus it is important to develop prophylactic and therapeutic interventions that provide heterosubtypic protection. Methods and Findings: Here we describe a panel of 13 monoclonal antibodies (mAbs) recovered from combinatorial display libraries that were constructed from human IgM+ memory B cells of recent (seasonal) influenza vaccinees. The mAbs have broad heterosubtypic neutralizing activity against antigenically diverse H1, H2, H5, H6, H8 and H9 influenza subtypes. Restriction to variable heavy chain gene IGHV1-69 in the high affinity mAb panel was associated with binding to a conserved hydrophobic pocket in the stem domain of HA. The most potent antibody (CR6261) was protective in mice when given before and after lethal H5N1 or H1N1 challenge. Conclusions: The human monoclonal CR6261 described in this study could be developed for use as a broad spectrum agent for prophylaxis or treatment of human or avian influenza infections without prior strain characterization. Moreover, the CR6261 epitope could be applied in targeted vaccine strategies or in the design of novel antivirals. Finally our approach of screening the IgM+ memory repertoire could be applied to identify conserved and functionally relevant targets on other rapidly evolving pathogens

Calculs de surface et d'énergie dans le domaine des macromolécules

Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Detection of cavities in a set of interpenetrating spheres

A general topological procedure is described that is able to detect cavities of all shapes and sizes in a system of interpenetrating spheres. The procedure is coupled to an analytic algorithm for computing surface areas and volumes, but as such, involves only logical operations and is therefore not subject to numerical imprecision. Its application to the identification of internal cavities in molecular systems is illustrated. Copyright © 1991 John Wiley & Sons, Inc.SCOPUS: ar.jFLWNAinfo:eu-repo/semantics/publishe

Simulation of conformational changes in 2 Zn insulin

SCOPUS: le.jinfo:eu-repo/semantics/publishe

Comparative molecular modeling of Amphioxus calcium vector protein with calmodulin and troponin C

Calcium vector protein (CaVP), a new protein isolated from Amphioxus muscle, binds in a Ca2+-regulated manner to a 27 kd target protein, named CaVPT, whose function has not been elucidated yet. CaVP bears significant sequence homology to both calmodulin and skeletal muscle troponin C, especially in the C-tenninal half of the molecule, which presumably contains the two functional Ca2+sites. The N-terminal half contains two abortive EF-hands and is intramolecularly crosslinked with a disulfide bond. Using the crystallographic structures of calmodulin and striated muscle troponin C as a framework, we constructed two different three-dimensional models of CaVP and modeled the intramolecular disulfide bridge. The modeling based upon the coordinates of calmodulin yields a Ca2+-filled sites configuration in the N-terminal half of the molecule, even though no Ca2+is bound in this half, whereas the troponin C-derived model generates a Ca2+-empty sites configuration. The models predict that neither in the Ca2+nor in the Ca2+-empty sites conformation is there any steric and/or energetic obstacle for the formation of the disulfide bridge and that the disulfide bond is poorly accessible to reducing reagents. The optical properties of the Trp and Tyr residues of CaVP indicate that the calmodulin-derived model represents the most plausible prediction. © 1990 Oxford University Press.SCOPUS: ar.jinfo:eu-repo/semantics/publishe