The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage

The ultrafast-folding 20-residue Trp-cage protein is quickly becoming a new benchmark for molecular dynamics studies. Already several all-atom simulations have probed its equilibrium and kinetic properties. In this work an all-atom Go model is used to accurately represent the side-chain packing and native atomic contacts of the Trp-cage. The model reproduces the hallmark thermodynamics cooperativity of small proteins. Folding simulations observe that in the fast-folding dominant pathway, partial alpha-helical structure forms before hydrophobic core collapse. In the slow-folding secondary pathway, partial core collapse occurs before helical structure. The slow-folding rate of the secondary pathway is attributed to the loss of side-chain rotational freedom, due to the early core collapse, which impedes the helix formation. A major finding is the observation of a low-temperature kinetic intermediate stabilized by a salt bridge between residues Asp-9 and Arg-16. Similar observations [R. Zhou, Proc. Natl. Acad. Sci. U.S.A. 100, 13280 (2003)] were reported in a recent study using an all-atom model of the Trp-cage in explicit water, in which the salt-bridge stabilized intermediate was hypothesized to be the origin of the ultrafast-folding mechanism. A theoretical mutation that eliminates the Asp-9-Arg-16 salt bridge, but leaves the residues intact, is performed. Folding simulations of the mutant Trp-cage observe a two-state free-energy landscape with no kinetic intermediate and a significant decrease in the folding rate, in support of the hypothesis.     

Rapid synthesis of the N-methylwelwitindolinone skeleton

An efficient, convergent synthesis of the core bicyclo[4.3.1]decane ring system of welwitindolinones is described. Key steps in the synthesis include an intramolecular palladium-catalyzed enolate arylation reaction to create the desired bicyclic skeleton and a Curtius rearrangement to install the bridgehead isocyanate unit. [reaction: see text]     

Lewis adducts of the side-on end-on dinitrogen-bridged complex [{(NPN)Ta}2(mu-H)2(mu-eta 1:eta 2-N2)] with AlMe3, GaMe3, and B(C6F5)3: synthesis, structure, and spectroscopic properties

Reaction of the side-on end-on dinitrogen complex [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-N(2))] (1; in which NPN=(PhNSiMe(2)CH(2))(2)PPh), with the Lewis acids XR(3) results in the adducts [{(NPN)Ta}(2)(mu-H)(2)(mu-eta(1):eta(2)-NNXR(3))], XR(3)=GaMe(3) (2), AlMe(3) (3), and B(C(6)F(5))(3) (4). The solid-state molecular structures of 2, 3, and 4 demonstrate that the N-N bond length increases relative to those found in 1 by 0.036, 0.043, and 0.073 A, respectively. In solution complexes 2-4 are fluxional as evidenced by variable-temperature (1)H NMR spectroscopy. The (15)N{(1)H} NMR spectra of 2-4 are reported; furthermore, their vibrational properties and electronic structures are evaluated. The vibrational structures are found to be closely related to that of the parent complex 1. Detailed spectroscopic analysis on 2-4 leads to the identification of the theoretically expected six normal modes of the Ta(2)N(2) core. On the basis of experimental frequencies and the QCB-NCA procedure, the force constants are determined. Importantly, the N-N force constant decreases from 2.430 mdyn A(-1) in 1 to 1.876 (2), 1.729 (3), and 1.515 mdyn A(-1) (4), in line with the sequence of N-N bond lengths determined crystallographically. DFT calculations on a generic model of the Lewis acid adducts 2-4 reveal that the major donor interaction between the terminal nitrogen atom and the Lewis acid is mediated by a sigma/pi hybrid molecular orbital of N(2), corresponding to a sigma bond. Charge analysis performed for the adducts indicates that the negative charge on the terminal nitrogen atom of the dinitrogen ligand increases with respect to 1. The lengthening of the N-N bond observed for the Lewis adducts is therefore explained by the fact that charge donation from the complex fragment into the pi* orbitals of dinitrogen is increased, while electron density from the N-N bonding orbitals p(sigma) and pi(h) is withdrawn due to the sigma interaction with the Lewis acid.     

Extended Peptide Nucleic Acid Nucleobases Based on Isoorotic Acid for the Recognition of A–U Base Pairs in Double-Stranded RNA

Peptide nucleic acids (PNA) with extended isoorotamide containing nucleobases ( I _o ) were designed for binding A–U base pairs in double-stranded RNA. Isothermal titration calorimetry and UV thermal melting experiments revealed improved affinity for A–U using the Io scaffold in PNA. PNAs having four sequential Io extended nucleobases maintained high binding affinity.     

NMR analysis of lignins in CAD-deficient plants. Part 1. Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins

Peroxidase/H2O2-mediated radical coupling of 4-hydroxycinnamaldehydes produces 8-O-4-, 8-5-, and 8-8-coupled dehydrodimers as has been documented earlier, as well as the 5-5-coupled dehydrodimer. The 8-5-dehydrodimer is however produced kinetically in its cyclic phenylcoumaran form at neutral pH. Synthetic polymers produced from mixtures of hydroxycinnamaldehydes and normal monolignols provide the next level of complexity. Spectral data from dimers, oligomers, and synthetic polymers have allowed a more substantive assignment of aldehyde components in lignins isolated from a CAD-deficient pine mutant and an antisense-CAD-downregulated transgenic tobacco. CAD-deficient pine lignin shows enhanced levels of the typical benzaldehyde and cinnamaldehyde end-groups, along with evidence for two types of 8-O-4-coupled coniferaldehyde units. The CAD-downregulated tobacco also has higher levels of hydroxycinnamaldehyde and hydroxybenzaldehyde (mainly syringaldehyde) incorporation, but the analogous two types of 8-O-4-coupled products are the dominant features. 8-8-Coupled units are also clearly evident. There is clear evidence for coupling of hydroxycinnamaldehydes to each other and then incorporation into the lignin, as well as for the incorporation of hydroxycinnamaldehyde monomers into the growing lignin polymer. Coniferaldehyde and sinapaldehyde (as well as vanillin and syringaldehyde) co-polymerize with the traditional monolignols into lignins and do so at enhanced levels when CAD-deficiency has an impact on the normal monolignol production. The implication is that, particularly in angiosperms, the aldehydes behave like the traditional monolignols and should probably be regarded as authentic lignin monomers in normal and CAD-deficient plants.     

Structural principles and amorphouslike thermal conductivity of Na-doped Si clathrates

The postulated low thermal conductivity and the possibility of altering the electronic conductivity of metal-doped clathrates with semiconducting host elements have stimulated great interest in exploring these compounds as promising thermoelectric materials. The electronic and thermal properties of the prototypical Na xSi (46) system are studied in detail here. It is shown that, despite the fact that the Na/Si clathrate is metallic, its thermal conductivity resembles that of an amorphous solid. A theoretical model is developed to rationalize the structural stability of the peculiar structural topology, and a general scheme for rational design of high efficiency thermoelectric materials is presented.     

Interaction of Two Charges in a Uniform Magnetic Field: II. Spatial Problem

The interaction of two charges moving in ℝ³ in a magnetic field B can be formulated as a Hamiltonian system with six degrees of freedom. Assuming that the magnetic field is uniform and the interaction potential has rotation symmetry, we reduce this system to one with three degrees of freedom. For special values of the conserved quantities, choices of parameters or restriction to the coplanar case, we obtain systems with two degrees of freedom. Specialising to the case of Coulomb interaction, these reductions enable us to obtain many qualitative features of the dynamics. For charges of the same sign, the gyrohelices either “bounce-back”, “pass-through”, or exceptionally converge to coplanar solutions. For charges of opposite signs, we decompose the state space into “free” and “trapped” parts with transitions only when the particles are coplanar. A scattering map is defined for those trajectories that come from and go to infinite separation along the field direction. It determines the asymptotic parallel velocities, guiding centre field lines, magnetic moments and gyrophases for large positive time from those for large negative time. In regimes where gyrophase averaging is appropriate, the scattering map has a simple form, conserving the magnetic moments and parallel kinetic energies (in a frame moving along the field with the centre of mass) and rotating or translating the guiding centre field lines. When the gyrofrequencies are in low-order resonance, however, gyrophase averaging is not justified and transfer of perpendicular kinetic energy is shown to occur. In the extreme case of equal gyrofrequencies, an additional integral helps us to analyse further and prove that there is typically also transfer between perpendicular and parallel kinetic energy.