Sequential matching problem

Kurzfassung in englisch We present sequential matching problem (SMP) as the problem of finding maximal matchings in a sequence of bipartite graphs, with a strategy of making maximum number of common edges in two consecutive matchings. One application of SMP is the problem of assigning workers to jobs in different time shifts with a goal of minimizing total number of unnecessary switches between jobs. We analyze various algorithmic techniques for this NP-complete problem. We also analyze the Mixed Integer Programming (MIP)problem formulation with huge number of variables and their solution by branch and price method, a column generation scheme with branch and bound, of implicit pricing of nonbasic variables to generate new columns. We then discuss special branching rules, pricing problems, implementation issues, and computational results. Finally we analyze a simpler version of SMP with only two bipartite graphs which is still NP-complete, and an algorithm to augment the common edges in the maximum matchings

Preparation of azide biosynthetic surrogates of myo-Inositol

As a prelude to biomolecular incorporation studies, practical routes to a series of four regioisomeric azido-deoxy derivatives of inositol that mimic the natural myo-stereochemistry are described. Starting from commercially available myo-inositol, the regioselective and stereoselective introduction of azide functionality was achieved at the C-2, C-3, C-4 and C-5 positions via azide displacement of the corresponding O-sulfonates of suitably protected scyllo-, chiro-, epi- and neo-inositols, respectively. Notably, a final one-pot acetolysis method conveniently allowed for rapid access to pentaacetate azido-deoxy inositols. Investigations on the metabolic incorporation of these myo-inositol azide surrogates in both acetate and free alcohol forms are in progress

Triazolophostins: a library of novel and potent agonists of IP3 receptors.

IP3 receptors are channels that mediate the release of Ca(2+) from the intracellular stores of cells stimulated by hormones or neurotransmitters. Adenophostin A (AdA) is the most potent agonist of IP3 receptors, with the β-anomeric adenine contributing to the increased potency. The potency of AdA and its stability towards the enzymes that degrade IP3 have aroused interest in AdA analogs for biological studies. The complex structure of AdA poses problems that have necessitated optimization of synthetic conditions for each analog. Such lengthy one-at-a-time syntheses limit access to AdA analogs. We have addressed this problem by synthesizing a library of triazole-based AdA analogs, triazolophostins, by employing click chemistry. An advanced intermediate having all the necessary phosphates and a β-azide at the anomeric position was reacted with various alkynes under Cu(i) catalysis to yield triazoles, which upon deprotection gave triazolophostins. All eleven triazolophostins synthesized are more potent than IP3 and some are equipotent with AdA in functional analyses of IP3 receptors. We show that a triazole ring can replace adenine without compromising the potency of AdA and provide facile routes to novel AdA analogs.A. M. V. thanks the University Grants Commission (UGC) India for a Senior Research Fellowship (SRF) during this work. K. M. S. thanks the Department of Science and Technology (DST) India for Swarnajayanti Fellowship, Ramanujan Fellowship and for financial support. C. W. T. and V. K. were supported by the Wellcome Trust, Biotechnology and Biological Sciences Research Council, and the German Academic Exchange Service (V. K.).This is the final published version. It first appeared at http://dx.doi.org/10.1039/C5OB00440

Selective determinants of inositol 1,4,5-trisphosphate and adenophostin A interactions with type 1 inositol 1,4,5-trisphosphate receptors

BACKGROUND AND PURPOSE: Adenophostin A (AdA) is a potent agonist of inositol 1,4,5-trisphosphate receptors (IP 3R). AdA shares with IP 3 the essential features of all IP 3R agonists, namely structures equivalent to the 4,5-bisphosphate and 6-hydroxyl of IP 3, but the basis of its increased affinity is unclear. Hitherto, the 2'-phosphate of AdA has been thought to provide a supra-optimal mimic of the 1-phosphate of IP 3. EXPERIMENTAL APPROACH: We examined the structural determinants of AdA binding to type 1 IP 3R (IP 3R1). Chemical synthesis and mutational analysis of IP 3R1 were combined with 3H-IP 3 binding to full-length IP 3R1 and its N-terminal fragments, and Ca 2+ release assays from recombinant IP 3R1 expressed in DT40 cells. KEY RESULTS: Adenophostin A is at least 12-fold more potent than IP 3 in functional assays, and the IP 3-binding core (IBC, residues 224-604 of IP 3R1) is sufficient for this high-affinity binding of AdA. Removal of the 2'-phosphate from AdA (to give 2'-dephospho-AdA) had significantly lesser effects on its affinity for the IBC than did removal of the 1-phosphate from IP 3 (to give inositol 4,5-bisphosphate). Mutation of the only residue (R568) that interacts directly with the 1-phosphate of IP 3 decreased similarly (by -30-fold) the affinity for IP 3 and AdA, but mutating R504, which has been proposed to form a cation-Π interaction with the adenine of AdA, more profoundly reduced the affinity of IP 3R for AdA (353-fold) than for IP 3 (13-fold). CONCLUSIONS AND IMPLICATIONS: The 2'-phosphate of AdA is not a major determinant of its high affinity. R504 in the receptor, most likely via a cation-Π interaction, contributes specifically to AdA binding

Integron Gene Cassettes: A Repository of Novel Protein Folds with Distinct Interaction Sites

Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.13 page(s

Synthesis of dimeric analogs of adenophostin A that potently evoke Ca2+ release through IP3 receptors.

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are tetrameric intracellular channels through which many extracellular stimuli initiate the Ca2+ signals that regulate diverse cellular responses. There is considerable interest in developing novel ligands of IP3R. Adenophostin A (AdA) is a potent agonist of IP3R and since some dimeric analogs of IP3R ligands are more potent than the corresponding monomer; we considered whether dimeric AdA analogs might provide agonists with increased potency. We previously synthesized traizolophostin, in which a simple triazole replaced the adenine of AdA, and showed it to be equipotent to AdA. Here, we used click chemistry to synthesize four homodimeric analogs of triazolophostin, connected by oligoethylene glycol chains of different lengths. We evaluated the potency of these analogs to release Ca2+ through type 1 IP3R and established that the newly synthesized dimers are equipotent to AdA and triazolophostin.University Grants Commission India (Senior Research Fellowship), Department of Science and Technology India (Swarnajayanti Fellowship, Ramanujan Fellowship), Wellcome TrustThis is the author accepted manuscript. The final version is available from The Royal Society of Chemistry via http://dx.doi.org/10.1039/c6ra19413

Chemical glycosylations for the synthesis of building units of post-translational modifications

In chemical glycosylation reactions, a glycosyl donor couples with a glycosyl acceptor through glycosidic linkage. Most of the products end up with a mixture due to the formation of a stereogenic center at the anomeric carbon. Activation with a suitable Lewis acid and introduction of the non‐participating protecting group on donor and acceptor results in a selective product. Herein, we used a suitably protected donor and acceptor which produced an orthogonally protected building block with α‐selectivity. We used also a donor for the synthesis of modified phosphoribosylated amino acid. The formation of glycoside products can be used to synthesize complex biologically important organic molecules