CGEMA and VGAP: a Colour Graphics Editor for Multiple Alignment using a Variable GAP penalty. Application to the muscarinic acetylcholine receptor

Summary Today, more than 40 protein amino acid (AA) sequences of membrane receptors coupled to guanine nucleotide binding proteins (G-proteins) are available. For those working in the field of medicinal chemistry, these sequences present a new type of information that should be taken into consideration. To make maximal use of sequence data it is essential to be able to compare different protein sequences in a similar way to that used for small molecules. A prerequisite, however, is the availability of a processing environment that enables one to handle sequences in an easy way, both by hand and by computer. In order to meet these ends, the package CGEMA (Colour Graphics Editor for Multiple Alignment) was developed in our laboratory. The programme uses a user-definable colour coding for the different AAs. Sequences can be aligned by hand or by computer, using VGAP, and both approaches can be combined. VGAP is a novel in-house written alignment programme with a variable gap penalty that also handles consecutive alignments using one sequence as a probe. In addition, secondary structure prediction tools are available.From the 20 protein sequences, available for the muscarinic acetylcholine receptor, 13 different sequences were selected, covering the subtypes m1 to m5. By comparing the sequences, two major groups are revealed that correspond to those found by considering the transducing system coupled to the various receptor subtypes. Different parts of the protein sequences are identified as characterizing the subtype and binding the ligands, respectively.     

Monopropionate analogues of DOTA4- and DTPA5-: kinetics of formation and dissociation of their lanthanide(III) complexes

The replacement of an acetate function of the macrocyclic DOTA4-(DO3A-Nprop4-) or the acyclic DTPA5- in terminal position (DTTA-Nprop5-) has been recently shown to result in a significant increase of the water exchange rate on the Gd3+ complexes, which makes these chelates potential contrast agents for MRI applications. Here, two novel and straightforward synthetic routes to H4DO3A-Nprop are described. Protonation constants of DO3A-Nprop4- and stability constants with several alkaline earth and transition metal ions have been determined by potentiometry. For each metal, the thermodynamic stability constant is decreased in comparison to the DOTA chelates. The formation reaction of LnDO3A-Nprop- complexes (Ln=Ce, Gd and Yb) proceeds via the rapid formation of a diprotonated intermediate and its subsequent deprotonation and rearrangement in a slow, OH- catalyzed process. The stability of the LnH2DO3A-Nprop* intermediates is similar to those reported for the corresponding DOTA analogues. The rate constants of the OH- catalyzed deprotonation step increase with decreasing lanthanide ion size, and are slightly higher than for DOTA complexes. The kinetic inertness of GdDTTA-Nprop2- was characterized by the rates of its exchange reactions with Zn2+ and Eu3+. The rate of the reaction between GdDTTA-Nprop2- and Zn2+ increases with Zn2+ concentration, while it is independent of pH, implying that the exchange takes place predominantly via direct attack of the metal ion on the complex. In the Eu3+ exchange, the rate decreases with increasing concentration of the exchanging ion which is accounted for by the transitional formation of a dinuclear GdDTTA-NpropEu+ species. The kinetic inertness of the monopropionate GdDTTA-Nprop2- is decreased in comparison to GdDTPA2-: all rate constants, characterizing the dissociation reaction via either proton- or metal-catalyzed pathways being higher by 1-2 orders of magnitude. Similarly, a study of the acid-catalyzed dissociation of the macrocyclic CeDO3A-Nprop- showed a partial loss of the kinetic inertness with regard to the tetraacetate derivative CeDOTA-.     

The effects of the column pressure drop on retention and efficiency in packed and open tubular supercritical fluid chromatography

The effects of the pressure drop across the column on retention and efficiency in SFC have been studied. Numerical methods are described which enable the prediction of hold-up time and pressure drop in both packed and open tubular columns. Predictions of both hold-up time and pressure drop are in good agreement with experimental data. The density gradient along the column can be calculated using the numerical methods and a procedure is described which enables the calculation of the overall capacity factors of the solutes from the density profile in the column. Significant variations of the capacity factor are observed along the column. The effect of the density gradient along the column on local diffusivity and dispersion is studied. The column efficiency in systems with significant pressure drops is affected by changes in: the linear velocity of the mobile phase; the diffusion coefficients; and the capacity factors of the solutes along the column. The overall efficiency of the chromatographic system can be calculated if, as is the case for open tubular columns, adequate plate height equations are available.     

Formation of β-distonic oxonium ions: Study of ROCH2CH2OR′ radical cations

Radical cations derived from the ethers ROCH₂CH₂OR′ (R, R′ = H, CH₃, C₂₅) were studied, since β-distonic oxonium ions are often prepared from ionized ethers of glycol. The first step in the fragmentation is a 1,5-transfer of an α-hydrogen to oxygen of a terminal alkoxy group leading to a δ-distonic oxonium ion. This step is thermo-neutral and reversible in the ROCH₂CH₂OH radical cations and exothermic and irreversible in the dialkyl ether radical cations. Depending on R and R,′ these δ-distonic oxonium ions fragment by three reactions: the loss of an alcohol or a water molecule, the formation of a β-distonic oxonium ion ˙CH₂CH₂O(H)⁺R and a 1,4-H migration between carbon atoms. Competition between these processes is discussed.     

Bifunctional activation of amine-boranes by the W/Pd bimetallic analogs of “frustrated Lewis pairs”

The reaction between basic [(PCP)Pd(H)] (PCP = 2,6-(CH₂P(t-C₄H₉)₂)₂C₆H₄) and acidic [LWH(CO)₃] (L = Cp (1a), Tp (1b); Cp = η⁵-cyclopentadienyl, Tp = κ³-hydridotris(pyrazolyl)borate) leads to the formation of bimolecular complexes [LW(CO)₂(μ-CO)⋯Pd(PCP)] (4a, 4b), which catalyze amine-borane (Me₂NHBH₃, ^tBuNH₂BH₃) dehydrogenation. The combination of variable-temperature (¹H, ³¹P{¹H}, ¹¹B NMR and IR) spectroscopies and computational (ωB97XD/def2-TZVP) studies reveal the formation of an η¹-borane complex [(PCP)Pd(Me₂NHBH₃)]⁺[LW(CO₃)]⁻ (5) in the first step, where a BH bond strongly binds palladium and an amine group is hydrogen-bonded to tungsten. The subsequent intracomplex proton transfer is the rate-determining step, followed by an almost barrierless hydride transfer. Bimetallic species 4 are easily regenerated through hydrogen evolution in the reaction between two hydrides.

Bimetallic complexes [LW(CO)₂(μ-CO)⋯Pd(PCP)] cooperatively activate amine-boranes for their dehydrogenation via N–H proton tunneling at RDS and H₂ evolution from two neutral hydrides.     

Tetraazamacrocycles lipophiles : synthese et application a l'extraction de Cu (II), Cd (II) et Pb (II)

The synthesis of three lipophilic n-dodecyl tetraazacycloalkanes is described. Extraction of Cu(II), Cd(II) and Pb(II) is related.     

Structure of New 2-Oxo-2,8-dihydro-[l,2,4]oxadiazolo-[2,3-a]pyrimidinecarbamates

The structure of new 2-oxo-2,8-dihydro-[l,2,4]oxadiazolo-[2,3-a]pyrimidine-carbamates 1 was established by correlating the IR. and NMR. data with these of analogous compounds. A X-ray crystallographic analysis of 1c gave an unequivocal proof of structural assignment.     

Boundedness of a class of bi-parameter square functions in the upper half-space

We consider a class of bi-parameter kernels and related square functions in the upper half-space, and give an efficient proof of a boundedness criterion for them. The proof uses modern probabilistic averaging methods and is based on controlling double Whitney averages over good cubes.