Weak self-interactions of globular proteins studied by small-angle X-ray scattering and structure-based modeling

We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty acid-binding protein (IFABP) is determined from SAXS measurements at multiple concentrations, from Monte Carlo simulations with a coarse-grained structure-based interaction model, and from analytic approximate solutions of two idealized colloidal interaction models without adjustable parameters. By combining these approaches, we find that the structure factor is essentially determined by hard-core and screened electrostatic interactions. Other soft short-ranged interactions (van der Waals and solvation-related) are either individually insignificant or tend to cancel out. The structure factor is also not significantly affected by charge fluctuations. For Mb and IFABP, with small net charge and relatively symmetric charge distribution, the structure factor is well described by a hard-sphere model. For BPTI, with larger net charge, screened electrostatic repulsion is also important, but the asymmetry of the charge distribution reduces the repulsion from that predicted by a charged hard-sphere model with the same net charge. Such charge asymmetry may also amplify the effect of shape asymmetry on the protein-protein potential of mean force.Comment: 15 pages, 8 figure

Structure and kinetics of chemically cross-linked protein gels from small-angle X-ray scattering

Glutaraldehyde (GA) reacts with amino groups in proteins, forming intermolecular cross-links that, at sufficiently high protein concentration, can transform a protein solution into a gel. Although GA has been used as a cross-linking reagent for decades, neither the cross-linking chemistry nor the microstructure of the resulting protein gel have been clearly established. Here we use small-angle X-ray scattering (SAXS) to characterise the microstructure and structural kinetics of gels formed by cross-linking of pancreatic trypsin inhibitor, myoglobin or intestinal fatty acid-binding protein. By comparing the scattering from gels and dilute solutions, we extract the structure factor and the pair correlation function of the gels. The protein gels are spatially heterogeneous, with dense clusters linked by sparse networks. Within the clusters, adjacent protein molecules are almost in contact, but the protein concentration in the cluster is much lower than in a crystal. At the $\sim$1 nm SAXS resolution, the native protein structure is unaffected by cross-linking. The cluster radius is in the range 10 - 50 nm, with the cluster size determined mainly by the availability of lysine amino groups on the protein surface. The development of structure in the gel, on time scales from minutes to hours, appears to obey first-order kinetics. Cross-linking is slower at acidic pH, where the population of amino groups in the reactive deprotonated form is low. These results support the use of cross-linked protein gels in NMR studies of protein dynamics and for modeling NMR relaxation in biological tissue.Comment: 16 pages, 11 figure

Beurteilung der Nährstoffversorgung bei hochleistenden Tieren – hier Mastbroiler – mit Öko-Futtermitteln

Das Ziel der beiden Versuche des Forschungsauftrages 02OE023 „Beurteilung der Nährstoffversorgung bei hochleistenden Tieren – hier Mastbroiler – mit Öko-Futtermitteln“ bestand darin, den Einfluss einer gestaffelten Protein- und Energieversorgung langsamwachsender Broiler auf Wachstumsmerkmale und Ganzkörperzusammensetzung zu prüfen. Für die Untersuchungen standen 469 (Versuch 1) bzw. 384 (Versuch 2) männliche Broiler der Herkunft Hubbard ISA 257 zur Verfügung. Die Versuche, die eine Länge von 56 bzw. 84 Tage hatten, wurden in ein, zwei oder drei Phasen (1. – 35., 36. – 56., 57. – 84. Tag) eingeteilt. Die Broiler erreichten im Versuch 2 Mastendmassen von über 4 kg nach 84 Tagen durch eine hohe Proteinversorgung von 23 % im Starterfutter (0,4 % Methionin) vom 1. – 35. Lebenstag sowie 21 % (0,37 % Methionin) im Nachfolgefutter, um insbesondere eine bedarfsgerechtere Methioninkonzentration im Futter, das sich aus Futtermitteln aus dem ökologischen Landbau zusammensetzte, zu realisieren. Eine Energiekonzentration von 12 MJ ME pro kg (Trockensubstanz) wurde dabei dem höheren Energiebedarf der bewegungsaktiven Broiler gerecht. Eine Fütterung der langsamwachsenden Broiler in zwei oder drei Phasen (1. - 35., 36. – 56., 57. – 84. Tag) und einer damit verbundenen besseren Anpassung der Proteinkonzentration im Futter an den Bedarf der Tiere erwies sich als geeignete Fütterungstechnik. Nach einer intensiven Fütterung der Broiler mit höheren Proteingehalten im ökologischen Futter bzw. durch Fütterung eines optimierten kommerziellen Futters zeigte sich, dass das der tägliche Zuwachs der Broiler nach 56 Tagen Mast rückgängig war. Der Futteraufwand, der bei den herkömmlich gefütterten Broilern bis zum 56. Tag bei 1,8 kg/kg und den intensiv-ökologisch gefütterten Broilern bei 2,0 kg/kg lag, verschlechterte sich in den folgenden 4 Wochen auf 3,2 kg/kg bzw. 3,4 kg/kg. Erste Hinweise auf eine mögliche Bedeutung für den Einsatz von Kräutern, die ätherische Öle mit einem hohen Anteil an Carvacrol enthalten, im ökologischen Broilerfutter gaben die Wachstumsergebnisse der Broiler, deren Futter mit einem 1 % getrocknetem Bohnenkraut angereichert war

Linguistics

Contains reports on three research projects.National Science Foundation (Grant GP-2495)National Institutes of Health (Grant MH-04737-04)U. S. Air Force. Electronics Systems Division (Contract AFl9(628)-2487)National Aeronautics and Space Administration (Grant NsG-496

Linguistics

Contains reports on two research projects.National Institute of Mental Health (Grant 5 P01 MH-13390-05)National Institute of Mental Health (Grant 5 TO1 HD-00111-06

Speech Communication

Contains research objectives and reports on two research objectives.U.S. Air Force (Air Force Cambridge Research Center, Air Research and Development Command) under Contract AF19(604)-6102National Science Foundatio

Realfast: Real-Time, Commensal Fast Transient Surveys with the Very Large Array

Radio interferometers have the ability to precisely localize and better characterize the properties of sources. This ability is having a powerful impact on the study of fast radio transients, where a few milliseconds of data is enough to pinpoint a source at cosmological distances. However, recording interferometric data at millisecond cadence produces a terabyte-per-hour data stream that strains networks, computing systems, and archives. This challenge mirrors that of other domains of science, where the science scope is limited by the computational architecture as much as the physical processes at play. Here, we present a solution to this problem in the context of radio transients: realfast, a commensal, fast transient search system at the Jansky Very Large Array. Realfast uses a novel architecture to distribute fast-sampled interferometric data to a 32-node, 64-GPU cluster for real-time imaging and transient detection. By detecting transients in situ, we can trigger the recording of data for those rare, brief instants when the event occurs and reduce the recorded data volume by a factor of 1000. This makes it possible to commensally search a data stream that would otherwise be impossible to record. This system will search for millisecond transients in more than 1000 hours of data per year, potentially localizing several Fast Radio Bursts, pulsars, and other sources of impulsive radio emission. We describe the science scope for realfast, the system design, expected outcomes, and ways real-time analysis can help in other fields of astrophysics.Comment: Accepted to ApJS Special Issue on Data; 11 pages, 4 figure

Linguistics

Contains research objectives and reports on three research projects.National Institute of Mental Health (Grant 5 P01 MH-13390-05)National Institutes of Health (Grant 5 TO1 HD-00111-07

Linguistics

Contains reports on three research projects.National Science Foundatio