Protein-protein interaction based on pairwise similarity

<p>Abstract</p> <p>Background</p> <p>Protein-protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS) method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines.</p> <p>Results</p> <p>To assess the ability of the proposed method to recognize the difference between "<it>interacted</it>" and "<it>non-interacted</it>" proteins pairs, we applied it on different datasets from the available yeast <it>saccharomyces cerevisiae </it>protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction.</p> <p>Conclusion</p> <p>Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.</p

20–25 Gbit/s low-power inductor-less single-chip optical receiver and transmitter frontend in 28 nm digital CMOS

The design of an analog frontend including a receiver amplifier (RX) and laser diode driver (LDD) for optical communication system is described. The RX consists of a transimpedance amplifier, a limiting amplifier, and an output buffer (BUF). An offset compensation and common-mode control circuit is designed using switched-capacitor technique to save chip area, provides continuous reduction of the offset in the RX. Active-peaking methods are used to enhance the bandwidth and gain. The very low gate-oxide breakdown voltage of transistors in deep sub-micron technologies is overcome in the LDD by implementing a topology which has the amplifier placed in a floating well. It comprises a level shifter, a pre-amplifier, and the driver stage. The single-chip frontend, fabricated in a 28 nm bulk-digital complementary metal–oxide–semiconductor (CMOS) process has a total active area of 0.003 mm² , is among the smallest optical frontends. Without the BUF, which consumes 8 mW from a separate supply, the RX power consumption is 21 mW, while the LDD consumes 32 mW. Small-signal gain and bandwidth are measured. A photo diode and laser diode are bonded to the chip on a test-printed circuit board. Electro-optical measurements show an error-free detection with a bit error rate of 10⁻¹² at 20 Gbit/s of the RX at and a 25 Gbit/s transmission of the LDD

Interactions of aromatic mannosyl disulfide derivatives with Concanavalin A: synthesis, thermodynamic and NMR spectroscopy studies

α-D-Mannopyranosyl units were attached to an aromatic scaffold through disulfide linkages to obtain mono- to trivalent glycosylated ligands for lectin binding studies. Isothermal titration calorimetric (ITC) measurements indicated that binding affinities of these derivatives to Concanavalin A (Con A) were comparable to or slightly higher than that of methyl α-D-mannopyranoside (Ka values in the range of 104 M−1). The stoichiometries of the lectin-ligand complexes were in agreement with the formal valencies (1-3) of the respective ligands indicating cross-linking in interactions with the di- and trivalent derivatives. Multivalency effects could not, however, be observed with the latter. These ligands were shown to bind to the carbohydrate binding site of Con A using saturation transfer difference (STD) NMR competition experiments