Synthesis of Non-natural Xyloglucans by Polycondensation of 4,6-Dimethoxy-1,3,5-triazin-2-yl Oligosaccharide Monomers Catalyzed by Endo-β-1,4-glucanase

Summary: A cellotetraose-backboned hepta-saccharide (XXXG) (a capital X represents a glucopyranose residue that is substituted with a xylopyranose through an α-1,6 glycosidic bond, and a capital G represents a non-substituted glucopyranose residue) and a nona-saccharide (XLLG) (a capital L represents a glucopyranose residue that is substituted with a galactopyranoseβ(1-2)xylopyranose through an α-1,6 glycosidic bond) have directly been converted to the corresponding 4,6-dimethoxy-1,3,5-triazin-2-yl derivatives (DMT-β-XXXG 1 and DMT-β-XLLG 2 , respectively) by the action of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methyl morpholinium chloride (DMT-MM). The selective nucleophilic attack of the anomeric hydroxyl group to DMT-MM has been achieved in water without using any protection of the hydroxyl groups. The resulting activated oligosaccharide derivatives ( 1 and 2 ) were found to polymerize catalyzed by an endo-β-1,4-glucanase as catalyst. The polymerization took place in a complete regio- and stereo-selective manner, affording non-natural polysaccharides having a XXXG-repeating unit and a XLLG-repeating unit, respectively, in the main chain. It is extremely difficult to construct such definite repeating structures via the conventional synthetic routes including protection-deprotection procedures.     

$${\mathbb{Z}_2\mathbb{Z}_4}$$-linear codes: rank and kernel

A code C{{\mathcal C}} is \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-additive if the set of coordinates can be partitioned into two subsets X and Y such that the punctured code of C{{\mathcal C}} by deleting the coordinates outside X (respectively, Y) is a binary linear code (respectively, a quaternary linear code). The corresponding binary codes of \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-additive codes under an extended Gray map are called \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear codes. In this paper, the invariants for \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear codes, the rank and dimension of the kernel, are studied. Specifically, given the algebraic parameters of \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear codes, the possible values of these two invariants, giving lower and upper bounds, are established. For each possible rank r between these bounds, the construction of a \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear code with rank r is given. Equivalently, for each possible dimension of the kernel k, the construction of a \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear code with dimension of the kernel k is given. Finally, the bounds on the rank, once the kernel dimension is fixed, are established and the construction of a \mathbbZ₂\mathbbZ₄{{\mathbb{Z}_2\mathbb{Z}_4}}-linear code for each possible pair (r, k) is given.     

Assessing induced folding of an intrinsically disordered protein by site-directed spin-labeling electron paramagnetic resonance spectroscopy

We used site-directed spin-labeling electron paramagnetic resonance (EPR) spectroscopy to study the induced folding of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)). Four single-site N(TAIL) mutants (S407C, S488C, L496C, and V517C), located in three conserved regions, were prepared and labeled with a nitroxide paramagnetic probe. We could monitor the gain of rigidity that N(TAIL) undergoes in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol (TFE) or one of its physiological partners, namely, the C-terminal domain (XD) of the viral phosphoprotein. The mobility of the spin label grafted at positions 488, 496, and 517 was significantly reduced upon addition of XD, contrary to that of the spin label bound to position 407, which was unaffected. Furthermore, the EPR spectra of spin-labeled S488C and L496C bound to XD in the presence of 30% sucrose are indicative of the formation of an alpha-helix in the proximity of the spin labels. Such an alpha-helix had been already identified by previous biochemical and structural studies. Using TFE we unveiled a previously undetected structural propensity within the N-terminal region of N(TAIL) and showed that its C-terminal region "resists" gaining structure even at high TFE concentrations. Finally, we for the first time showed the reversibility of the induced folding process that N(TAIL) undergoes in the presence of XD. These results highlight the suitability of site-directed spin-labeling EPR spectroscopy to identify protein regions involved in binding and folding events, while providing insights at the residue level.     

Revisiting acido-basicity of the MgO surface by periodic density functional theory calculations: role of surface topology and ion coordination on water dissociation

Low-coordinated (LC) ions at the MgO surface (noted Mg2+LC and O2-LC with L = 1-5), located on monatomic and diatomic steps, corners, step divacancies, and kinks, have been modeled thanks to periodic density functional theory (DFT) calculations (VASP). Ions of lowest coordination induce the strongest surface geometry relaxation and the highest surface energies. The hydration energies of these sites and thermodynamic stabilities of the resulting surfaces were studied. The factors controlling the interaction strength between water and the surface are the possibility for the hydroxyl group to adopt a bridging geometry between two Mg2+ cations in concave areas of the surface, such as the bottom of the monatomic step, and at second order the surface atomic coordination, and especially the presence of three-coordinated ions. The Lewis basicity and acidity of O2-LC and Mg2+LC, respectively, increase as their coordination number decreases, which implies the same trend for the Br?nsted basicity of the Mg2+-O2- pair toward water. However, this trend can be changed if pairs leading to the formation of bridging OH groups are involved, typically on monatomic steps or in step divacancies where O2C-H and O3C-H are obtained, respectively, instead of the expected O1C-H. Thanks to thermodynamic calculations, the state of the surface as a function of temperature can be determined at a given pressure, unraveling the roles of surface topology and ions coordination.     

A synthetic entry to furo[2,3-b]pyridin-4(1H)-ones and related furoquinolinones via iodocyclization

[reaction: see text] N-Methyl-4-alkoxy-3-alkynylpyridin-2(1H)-ones readily undergo iodine-promoted 5-endo-heteroannulation under mild conditions to 3-iodofuropyridinium triiodide salts in moderate to good yields. The latter may be dealkylated in situ upon exposure to an iodide anion to provide the corresponding 3-iodofuro[2,3-b]pyridin-4(1H)-ones. The same strategy applies to the formation of furo[2,3-b]quinolin-4(9H)-ones.     

Quantum transport of slow charge carriers in quasicrystals and correlated systems

We show that the semiclassical model of conduction breaks down if the mean free path of charge carriers is smaller than a typical extension of their wave function. This situation is realized for sufficiently slow charge carriers and leads to a transition from a metalliclike to an insulatinglike regime when scattering by defects increases. This explains the unconventional conduction properties of quasicrystals and related alloys. The conduction properties of some heavy fermions or polaronic systems, where charge carriers are also slow, present a deep analogy.     

Velocity locking of incoherent nonlinear wave packets

We show both theoretically and experimentally in an optical fiber system that a set of incoherent nonlinear waves irreversibly evolves to a specific equilibrium state, in which the individual wave packets propagate with identical group velocities. This intriguing process of velocity locking can be explained in detail by simple thermodynamic arguments based on the kinetic wave theory. Accordingly, the selection of the velocity-locked state is shown to result from the natural tendency of the isolated wave system to approach the state that maximizes the nonequilibrium entropy.     

Song of the dunes as a self-synchronized instrument

Since Marco Polo it has been known that some sand dunes have the peculiar ability to emit a loud sound with a well-defined frequency, sometimes for several minutes. The origin of this sustained sound has remained mysterious, partly because of its rarity in nature. It has been recognized that the sound is not due to the air flow around the dunes but to the motion of an avalanche, and not to an acoustic excitation of the grains but to their relative motion. By comparing singing dunes around the world and two controlled experiments, in the laboratory and the field, we prove that the frequency of the sound is the frequency of the relative motion of the sand grains. Sound is produced because moving grains synchronize their motions. The laboratory experiment shows that the dune is not needed for sound emission. A velocity threshold for sound emission is found in both experiments, and an interpretation is proposed.     

Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.     

Model storage,exchange and integration

The field of Computational Systems Neurobiology is maturing quickly. If one wants it to fulfil its central role in the new Integrative Neurobiology, the reuse of quantitative models needs to be facilitated. The community has to develop standards and guidelines in order to maximise the diffusion of its scientific production, but also to render it more trustworthy. In the recent years, various projects tackled the problems of the syntax and semantics of quantitative models. More recently the international initiative BioModels.net launched three projects: (1) MIRIAM is a standard to curate and annotate models, in order to facilitate their reuse. (2) The Systems Biology Ontology is a set of controlled vocabularies aimed to be used in conjunction with models, in order to characterise their components. (3) BioModels Database is a resource that allows biologists to store, search and retrieve published mathematical models of biological interests. We expect that those resources, together with the use of formal languages such as SBML, will support the fruitful exchange and reuse of quantitative models.