Rational design and selection of bivalent peptide ligands of thrombin incorporating P4-P1 tetrapeptide sequences: from good substrates to potent inhibitors

The tetrapeptide Phe-Asn-Pro-Arg is a structurally optimized sequence for binding to the active site of thrombin. By conjugating this tetrapeptide or some variants to a C-terminal fragment of hirudin, we were able to generate a series of new bivalent inhibitors of thrombin containing only genetically encodable natural amino acids. We found that synergistic binding to both the active site and an exosite of thrombin can be enhanced through substitutions of amino acid residues at the P3 and P3' sites of the active-site directed sequence, Phe(P4)-Xaa(P3)-Pro(P2)-Arg(P1)-Pro(P1')-Gln(P2')-Yaa(P3'). Complementary to rational design, a phage library was constructed to explore further the residue requirements at the P4, P3 and P3' sites for bivalent and optimized two-site binding. Very significantly, panning of the phage library has led to thrombin-inhibitory peptides possessing strong anti-clotting activities in the low nanomolar range and yet interfering only partially the catalytic active site of thrombin. Modes of action of the newly discovered bivalent inhibitors are rationalized in light of the allosteric properties of thrombin, especially the interplay between the proteolytic action and regulatory binding occurring at thrombin surfaces remote from the catalytic active site.     

Opportunistic Software Systems Development: Making Systems from What's Available

Despite all the difficulties encountered in each incarnation of software reuse, we persist along the path of trying to figure out how we're going to create systems that meet the ever-increasing demand for capability and, with it, complexity and sheer size. Opportunistic software systems development is a reality today and for the foreseeable future, as the five articles in IEEE Software 's November/December 2008 special issue on OSSD demonstrate. This special issue aims to gather together insights into the viability, or perhaps the inevitability, of OSSD and to bring forward the most effective practices known today. Another goal is to point the way to what needs to be done to make OSSD more accessible to all practitioners. The editors hope to help the software community realize the importance of this new trend and the many aspects of it that have yet to be conquered.     

Alpha-helical regions of the protein molecule as organic nanotubes

An α-helical region of protein molecule was considered in a model of nanotube. The molecule is in conditions of quantum excitations. Such model corresponds to a one-dimensional molecular nanocrystal with three molecules in an elementary cell at the presence of excitation. For the analysis of different types of conformational response of the α-helical area of the protein molecule on excitation, the nonlinear response of this area to the intramolecular quantum excitation caused by hydrolysis of adenosine triphosphate (ATP) is taken into account. It has been established that in the simplest case, three types of excitation are realized. As estimates show, each of them ‘serves’ different kinds of protein. The symmetrical type of excitation, most likely, is realized in the reduction of traversal-striped skeletal muscles. It has the highest excitation energy. This well protects from casual actions. Antisymmetric excitations have intermediate energy (between symmetrical and asymmetrical). They, most likely, are realized in membranous and nucleic proteins. It is shown that the conformational response of the α-helical region of the protein is (in angstroms) a quantity of order N _c /5, where N _c is the number of spiral turns. For the number of turns typical in this case: N _c  ~ 10, displacement compounds are a quantity of order 2 Å. It qualitatively corresponds to observable values. Asymmetrical excitations have the lowest energy. Therefore, most likely, they are realized in enzymatic proteins. It was shown that at this type of excitation, the bending of the α-helix is formally directed to the opposite side with respect to the antisymmetric excitations. Also, it has a greater value than the antisymmetric case for N _c  ≤ 14 and smaller for N _c  > 14.

PACS

92C05

MCS

36.20.Ey     

Kinematic calibration of Orthoglide-type mechanisms from observation of parallel leg motions

The paper proposes a new calibration method for parallel manipulators that allows efficient identification of the joint offsets using observations of the manipulator leg parallelism with respect to the base surface. The method employs a simple and low-cost measuring system, which evaluates deviation of the leg location during motions that are assumed to preserve the leg parallelism for the nominal values of the manipulator parameters. Using the measured deviations, the developed algorithm estimates the joint offsets that are treated as the most essential parameters to be identified. The validity of the proposed calibration method and efficiency of the developed numerical algorithms are confirmed by experimental results. The sensitivity of the measurement methods and the calibration accuracy are also studied.     

Comparison of fast radiation-annealed and isothermally annealed 75As+-implanted layers on silicon wafers

An investigation of fast radiation annealing (FRA) of ⁷⁵As⁺ -implanted silicon is presented which explores the influence of the following factors on the properties of the implanted layers compared with those of the same material subjected to an isochronal anneal under isothermal furnace annealing (IFA) conditions: the FRA power density (effectively the average temperature of the wafer); the orientation of the implanted layer with respect to the FRA source (face up to the source or face down); the implant dose and energy; the time schedule for the anneal; the distance of the wafer from the source and from a water-cooled platen. All experiments are conducted in a normal laboratory environment without the benefit of clean air. The principle variables studied are the spreading resistance profile and the sheet resistance. Significant differences are observed between IFA and FRA material. The most dramatic is that diffusion in the face-up FRA material is significantly less than that in the face-down FRA material. No explanation has been obtained to date for this difference. Devices made from these layers were tested. Excellent device results have been obtained on both types of annealed material.     

Enhanced stiffness modeling of manipulators with passive joints

The paper presents a methodology to enhance the stiffness analysis of serial and parallel manipulators with passive joints. It directly takes into account the influence of external and internal loadings on the manipulator configuration and, consequently, on its Jacobians and Hessians. The main contributions of this paper are the introduction of a non-linear stiffness model for the manipulators with passive joints, a relevant numerical technique for computing the Cartesian stiffness and stability criteria for configurations of the kinematic chains. Within the developed technique, the manipulator elements are presented as pseudo-rigid bodies separated by multidimensional virtual springs and perfect passive joints. Simulation examples are presented that deal with parallel manipulators of the Ortholide family and demonstrate the ability of the developed methodology to describe non-linear behavior of the manipulator structure such as a sudden change of the elastic instability properties (buckling).     

Building Many-Core Processor-to-DRAM Networks with Monolithic CMOS Silicon Photonics

Silicon photonics is a promising technology for addressing memory bandwidth limitations in future many-core processors. This article first introduces a new monolithic silicon-photonic technology, which uses a standard bulk CMOS process to reduce costs and improve energy efficiency, and then explores the logical and physical implications of leveraging this technology in processor-to-memory networks.     

Monitoring of a pharmaceutical nanomilling process using grating light reflection spectroscopy

An optical diagnostic method, grating light reflection spectroscopy (GLRS), has been demonstrated for the in situ monitoring of properties of heterogeneous matrices in industrial processes. The technique is based on measurements near the critical points of intensity and phase in waves reflected from a transmission diffraction grating in contact with a diagnostic sample. The features contained in the reflection spectrum near these thresholds allow for the simultaneous determination of the real and imaginary parts of the dielectric function of the sample. Using these data, the milling progress of highly concentrated fluid suspensions is observed as the material is milled from approximately 40 mm to 160 nm in diameter. A theoretical model that closely resembles experimentally determined spectra was constructed and applied in combination with principal components analysis (PCA) to demonstrate that GLRS can be used to closely monitor changes in the mean particle size of the nanomilled drug product.     

Tailored magnetic nanoparticles for direct and sensitive detection of biomolecules in biological samples

We developed nanoparticles with tailored magnetic properties for direct and sensitive detection of biomolecules in biological samples in a single step. Thermally blocked nanoparticles obtained by thermal hydrolysis, functionalized with specific ligands, are mixed with sample solutions, and the variation of the magnetic relaxation due to surface binding is used to detect the presence of biomolecules. The binding significantly increases the hydrodynamic volume of nanoparticles, thus changing their Brownian relaxation frequency which is measured by a specifically developed AC susceptometer. The system was tested for the presence of Brucella antibodies, a dangerous pathogen causing brucellosis with severe effects both on humans and animals, in serum samples from infected cows and the surface of the nanoparticles was functionalized with lipopolysaccharides (LPS) from Brucella abortus. The hydrodynamic volume of LPS-functionalized particles increased by 25-35% as a result of the binding of the antibodies, measured by changes in the susceptibility in an alternating magnetic field. The method has shown high sensitivity, with detection limit of 0.05 microg x mL(-1) of antibody in the biological samples without any pretreatment. This magnetic-based assay is very sensitive, cost-efficient, and versatile, giving a direct indication whether the animal is infected or not, making it suitable for point-of-care applications. The functionalization of tailored magnetic nanoparticles can be modified to suit numerous homogeneous assays for a wide range of applications.