The extent and nature of thermal fluctuations in the innovative class of cross-linked polymers called cyclodextrin nanosponges (CDNS) are investigated, on the picosecond time scale, through elastic and quasielastic neutron scattering experiments. Nanosponges are complex 3D polymer networks where covalent bonds connecting different cyclodextrin (CD) units and intra- and inter-molecular hydrogen-...

Coiled coils are a major motif in proteins and orchestrate multimerization of various complexes important for biological processes. Inhibition of coiled coil-mediated interactions has significant biomedical potential. However, general approaches that afford short peptides with defined coiled coil conformation remain elusive. We evaluated several strategies to stabilize minimal helical bundles, ...

Recent high-resolution soft X–ray resonant inelastic X-ray scattering technique enables us to distinguish valence electronic structure of water molecules having different hydrogen-bond configurations in the liquid phase. Moreover, in the elastic region, well-separated multiple vibrational structures appear, which corresponds to the internal OH stretch vibration in the ground state. Both the val...

We have performed a series of 10 ns Molecular Dynamics simulations of the sodium octanoate micelle in aqueous solution in the constant NpT ensemble, at p = 1 bar and T = 300 K. Two molecular topologies were studied, one with all internal degrees of freedom and the other constraining bond stretching and angle bending degrees of freedom. Two Lennard-Jones parameters for sodium ions, namely the OP...

We study a variety of dilute annealed lattice spin systems. For site diluted problems with many internal spin states, we uncover a new phase characterized by the occupation and vacancy of staggered sublattices. In cases where the uniform system has a low temperature phase, the staggered states represent an intermediate phase. Furthermore, in many of these cases, we show that (at least part of) ...

We have recently reported the isolation from rabbit alveolar macrophages of a receptor which retained its ligand-binding activity for the third component of complement (C3) and for its major proteolytic derived activation fragment (C3b). The isolated receptor demonstrated a greater ability to bind C3b than an equimolar amount of C3. C3b differs from C3 in at least two ways: it is a proteolytic ...

Chain Fold It is a usual way to tabulate the torsion (dihedral) angles for each residue to reconstruct protein structure using standard covalent bond length and angles. The backbone can be further represented by virtual bond between Cα-atoms. The mainchain is fully described by the virtual dihedral angle αi defined by four successive Cα atoms and the virtual bond angle. This description is used...

We have identified three new families of insulin homologs in Caenorhabditis elegans. In two of these families, concerted mutations suggest that an additional disulfide bond links B and A domains, and that the A-domain internal disulfide bond is substituted by a hydrophobic interaction. Homology modeling remarkably confirms these predictions and shows that despite this atypical disulfide bond pa...

We develop a resummed thermodynamic perturbation theory for bond cooperativity in associating fluids by extension of Wertheim's multi-density formalism. We specifically consider the case of an associating hard sphere with two association sites and both pairwise and triplet contributions to the energy, such that the first bond in an associated cluster receives an energy -ε((1)) and each subseque...

Isoelectronic C=F(+) and C=O bonds contained in fluoro-substituted carbenium ions, aldehydes, and ketones are investigated with regard to their bond properties by utilizing the vibrational spectra of these molecules. It is demonstrated that bond dissociation energies (BDEs), bond lengths, vibrational stretching frequencies, and bond densities are not reliable descriptors of the bond strength. T...