Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex

Nuclear magnetic resonance (NMR) spectroscopy provides a range of powerful techniques for determining the structures and the dynamics of proteins. The high-resolution determination of the structures of protein-protein complexes, however, is still a challenging problem for this approach, since it can normally provide only a limited amount of structural information at protein-protein interfaces. We present here the determination using NMR chemical shifts of the structure (PDB code 2K5X) of the cytotoxic endonuclease domain from bacterial toxin colicin (E9) in complex with its cognate immunity protein (Im9). In order to achieve this result, we introduce the CamDock method, which combines a flexible docking procedure with a refinement that exploits the structural information provided by chemical shifts. The results that we report thus indicate that chemical shifts can be used as structural restraints for the determination of the conformations of protein complexes that are difficult to obtain by more standard NMR approaches.     

New thermosets obtained from DGEBA and Meldrum acid with lanthanum and ytterbium triflates as cationic initiators

Ytterbium and lanthanum triflates were used as cationic initiators to cure mixtures of diglycidylether of bisphenol A (DGEBA) and Meldrum acid (MA) in several proportions of comonomers and initiators. The evolution of epoxy and lactone groups during curing, and of linear ester formed in the final materials were evaluated by Fourier transform infrared in the attenuated-total-reflection mode (FTIR/ATR).

The global evolution of the curing process was investigated by calorimetric analysis and the activation energy was calculated by isoconversional procedures.

Shrinkage on curing and thermal degradability of the final materials on varying the initiator and the proportion of Meldrum acid in the mixtures were evaluated. The expandable character of MA was confirmed. The materials obtained were more degradable than conventional epoxy resins due to the tertiary ester groups incorporated into the network by copolymerization, especially those obtained with ytterbium triflate. On increasing the proportion of initiator the degradability was also increased.     

Evidence for radical fragmentations from persistent singlet carbenes

Upon warm up, persistent aminohydrazinocarbenes undergo beta-fragmentation reactions. Experimental as well as computational evidences are reported for the involvement of radical processes. This is the first example of a homolytic fragmentation for a persistent singlet carbene.     

Can free energy calculations be fast and accurate at the same time? Binding of low-affinity,non-peptide inhibitors to the SH2 domain of the src protein

The usefulness of free-energy calculations in non-academic environments, in general, and in the pharmaceutical industry, in particular, is a long-time debated issue, often considered from the angle of cost/performance criteria. In the context of the rational drug design of low-affinity, non-peptide inhibitors to the SH2 domain of the (pp60)src tyrosine kinase, the continuing difficulties encountered in an attempt to obtain accurate free-energy estimates are addressed. free-energy calculations can provide a convincing answer, assuming that two key-requirements are fulfilled: (i) thorough sampling of the configurational space is necessary to minimize the statistical error, hence raising the question: to which extent can we sacrifice the computational effort, yet without jeopardizing the precision of the free-energy calculation? (ii) the sensitivity of binding free-energies to the parameters utilized imposes an appropriate parametrization of the potential energy function, especially for non-peptide molecules that are usually poorly described by multipurpose macromolecular force fields. Employing the free-energy perturbation method, accurate ranking, within +/-0.7 kcal/mol, is obtained in the case of four non-peptide mimes of a sequence recognized by the (pp60)src SH2 domain.     

Synthesis of the 4-azatricyclo[5.2.2.0(4,8)]undecan-10-one core of daphniphyllum alkaloid calyciphylline A using a Pd-catalyzed enolate alkenylation

[reaction: see text] The ABC ring system of the natural product calyciphylline A has been synthesized. The key steps were a palladium-catalyzed intramolecular coupling of an amino-tethered vinyl bromide with a ketone using potassium phenoxide as the base to generate the C-ring and a hydroxyl-directed hydrogenation of an exocyclic double bond to give the azatricyclic ketone 1.     

Structural Stability of Planar Polynomial Foliations

We discuss natural notions of structural stability of planar polynomial foliations of fixed degree with respect to perturbation within the same restricted set, within the set of all polynomial vector fields of the same degree, and within the set of smooth vector fields. Characterization theorems for structural stability in the latter two settings are obtained as immediate corollaries of known results. We provide sufficient conditions and separate necessary conditions for structural stability of planar polynomial foliations with respect to perturbation within the set of planar polynomial foliations of the same degree.     

Herman Rings and Arnold Disks

For (,a) C* x C, let f_,a be the rational map defined by f_,a(z)= z² (az+1)/(z+a). If R/Z is a Brjuno number, we let D bethe set of parameters (,a) such that f_,a has a fixed Hermanring with rotation number (we consider that (e²ⁱ,0) D). Resultsobtained by McMullen and Sullivan imply that, for any g D, theconnected component of D(C* x (C/{0,1})) that contains g isisomorphic to a punctured disk. We show that there is a holomorphic injection F:DD such thatF(0) = (e²ⁱ ,0) and , where r is the conformal radius at 0 of the Siegel disk of the quadraticpolynomial z e²ⁱ z(1+z). As a consequence, we show that for a (0,1/3), if f_l,a has afixed Herman ring with rotation number and if m_a is the modulusof the Herman ring, then, as a0, we have e m_a=(r/a) + O(a). We finally explain how to adapt the results to the complex standardfamily z e^(a/2)(z-1/z).     

Structural studies of peri-interactions and bond formation between electron-rich atomic centres and N-phenylcarboxamides or nitroalkenyl groups

Structural studies of peri-interactions with dimethylamino groups in naphthalene systems indicate that the N-phenylcarboxamide group has a through-space electron attracting power closer to that of a carboxylic ester than a N,N-dialkylcarboxamide, while 2-nitroalkenyl groups have a lower through-space electron attracting power. However, addition of a benzoyl group to the 2-position of the nitroethenyl group leads to cyclisation to give a zwitterion, in which the carbanion is stabilised by full conjugation with the nitro group and partial conjugation with the carbonyl group. An interesting case where a steric interaction overrides an electrophile/nucleophile attraction is also described. The limitations to the interpretation of short contact distances from crystallographic measurements are discussed.     

A novel nucleophilic approach to 1-alkyladenosines. A two-step synthesis of [1-15N]adenosine from inosine

A novel ANRORC mechanism in the reaction of 1-(2,4-dinitrobenzenesulfonyl)inosines with amines has allowed the preparation of 1-alkyladenosines and [1-15N]adenosines in a straightforward way from inosines.