Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.     

Local boundedness of the number of solutions of Plateau’s problem for polygonal boundary curves

In the present article, the author proves two generalizations of his “finiteness-result” (I.H.P. Anal. Non-lineaire, 2006, accepted) which states for any extreme simple closed polygon that every immersed, stable disc-type minimal surface spanning Γ is an isolated point of the set of all disc-type minimal surfaces spanning Γ w.r.t. the C ⁰-topology. First, it is proved that this statement holds true for any simple closed polygon in , provided it bounds only minimal surfaces without boundary branch points. Also requiring that the interior angles at the vertices of such a polygon Γ have to be different from the author proves the existence of some neighborhood O of Γ in and of some integer , depending only on Γ, such that the number of immersed, stable disc-type minimal surfaces spanning any simple closed polygon contained in O, with the same number of vertices as Γ, is bounded by .      

Amine oxidase amperometric biosensor coupled to liquid chromatography for biogenic amines determination

A selective and sensitive method is presented for biogenic amines (BA) determination. The novelty consists in coupling a highly selective electrochemical biosensor to a weak acid cation-exchange column for online detection of amines. A bienzyme design, based on a recently isolated amine oxidase from grass pea and commercial horseradish peroxidase, was used for the biosensor construction. The enzymes were co-immobilized on the surface of a graphite electrode together with the electrochemical mediator (Os-redox polymer). The electrochemical detection was performed at a low applied potential (?50 mV vs. Ag/AgCl, KCl_0.1 M), where biases from interferences are minimal. The separation and determination of six BA, with relevance in food analysis (tyramine, putrescine, cadaverine, histamine, agmatine and spermidine), were investigated. Irrespective of the BA nature, the amine oxidase-based biosensor showed a linear response up to 5 mM, and its sensitivity decreases in the following order: cadaverine, putrescine, spermidine, agmatine, histamine and tyramine. The approach was used to estimate the BA content in fish samples, after their extraction with methanesulfonic acid.     

Separation of rare earth elements by anion-exchange chromatography using ethylenediaminetetraacetic acid as mobile phase

Rare earth elements (REEs) form anionic complexes which can be separated isocratically by anion-exchange chromatography using ethylenediaminetetraacetic acid (EDTA) as the mobile phase. For easy detection and identification, inductively coupled plasma (ICP) MS was used as detection method. From pH 3.5 to 7.5, retention increases from La to Sm and then decreases again up to Lu. Above pH 8.5, the retention of the light lanthanides increased drastically. It seems that the stoichiometry and the charge of the REE-EDTA complexes change with the elution pH. This strange elution behaviour can be easily tuned for particular applications by selecting the elution pH. For example, at pH values between 5.5 and 7.5 most isobaric and polyatomic interferences which occur in ICP-MS detection of the lanthanides are eliminated. A mechanism for the stepwise formation of the REE-EDTA complexes as a function of pH is proposed.     

Nickel‐Catalyzed Carboxylation of Benzylic C−N Bonds with CO2

A user‐friendly Ni‐catalyzed reductive carboxylation of benzylic C?N bonds with CO₂ is described. This procedure outperforms state‐of‐the‐art techniques for the carboxylation of benzyl electrophiles by avoiding commonly observed parasitic pathways, such as homodimerization or β‐hydride elimination, thus leading to new knowledge in cross‐electrophile reactions.     

On the Road Map of Vogel’s Plane

We define “population” of Vogel’s plane as points for which universal character of adjoint representation is regular in the finite plane of its argument. It is shown that they are given exactly by all solutions of seven Diophantine equations of third order on three variables. We find all their solutions: classical series of simple Lie algebras (including an “odd symplectic” one), \({D_{2,1,\lambda}}\) superalgebra, the line of sl(2) algebras, and a number of isolated solutions, including exceptional simple Lie algebras. One of these Diophantine equations, namely \({knm=4k+4n+2m+12,}\) contains all simple Lie algebras, except so\({(2N+1).}\) Among isolated solutions are, besides exceptional simple Lie algebras, so called \({\mathfrak{e}_{7\frac{1}{2}}}\) algebra and also two other similar unidentified objects with positive dimensions. In addition, there are 47 isolated solutions in “unphysical semiplane” with negative dimensions. Isolated solutions mainly belong to the few lines in Vogel plane, including some rows of Freudenthal magic square. Universal dimension formulae have an integer values on all these solutions at least for first three symmetric powers of adjoint representation.