Mixtures of cationic copolymers and oppositely charged surfactants: effect of polymer charge density and ionic strength on the adsorption behavior at the silica-aqueous interface.

This study addresses polymer-surfactant interactions at solid-liquid interfaces and how these can be manipulated by modulating the association between ionic surfactant and oppositely charged polymer, with a particular focus on electrostatic interactions. For this purpose, the interaction of a series of cationic copolymers of vinylpyrrolidone and quaternized vinylimidazol with sodium dodecyl sulfate (SDS) at the silica-aqueous interface was followed by in situ ellipsometry. To reveal the nature of the interaction, we performed measurements for different copolyion charge densities, in the absence and presence of added salt. The path-dependence of the interaction was studied by comparing the adsorption under two different conditions, adsorption from premixed solutions and sequential addition of surfactant to the polymer solution, but the same end state. The reversibility of the adsorption process was studied by following the effect of dilution on the adsorbed layer. All copolyions adsorbed to both silica and hydrophobized silica, revealing the importance of both hydrophobic and electrostatic attractive interactions. On both types of surface, an increase in adsorbed amount was found on lowering the fraction of charged units. An increased ionic strength gave an increased adsorbed amount in all cases, but especially on hydrophobic surfaces. The adsorbed amount on silica from mixtures of the copolyions with SDS peaked at an SDS concentration corresponding closely to the concentration of cationic charges of the different polyions. Around the region of charge equivalence, there was also a phase separation in the bulk. At higher concentrations of SDS, a redissolution in the bulk, and a decrease in adsorbed amount, occurred as a result of excess SDS binding to the complexes. For the most highly charged polyions, we observed a decrease in adsorbed amount, and a shift in the adsorption maxima to lower SDS concentrations, with increasing ionic strength.

Activity and dynamics of an enzyme, pig liver esterase, in near-anhydrous conditions.

Water is widely assumed to be essential for life, although the exact molecular basis of this requirement is unclear. Water facilitates protein motions, and although enzyme activity has been demonstrated at low hydrations in organic solvents, such nonaqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an enzyme, pig liver esterase, to catalyze alcoholysis as an anhydrous powder, in a reaction system of defined water content and where the substrates and products are gaseous. At hydrations of 3 (±2) molecules of water per molecule of enzyme, activity is several orders-of-magnitude greater than nonenzymatic catalysis. Neutron spectroscopy indicates that the fast (≤nanosecond) global anharmonic dynamics of the anhydrous functional enzyme are suppressed. This indicates that neither hydration water nor fast anharmonic dynamics are required for catalysis by this enzyme, implying that one of the biological requirements of water may lie with its role as a diffusion medium rather than any of its more specific properties.

REACH coarse-grained normal mode analysis of protein dimer interaction dynamics.

The REACH (realistic extension algorithm via covariance Hessian) coarse-grained biomolecular simulation method is a self-consistent multiscale approach directly mapping atomistic molecular dynamics simulation results onto a residue-scale model. Here, REACH is applied to calculate the dynamics of protein-protein interactions. The intra- and intermolecular fluctuations and the intermolecular vibrational densities of states derived from atomistic molecular dynamics are well reproduced by the REACH normal modes. The phonon dispersion relations derived from the REACH lattice dynamics model of crystalline ribonuclease A are also in satisfactory agreement with the corresponding all-atom results. The REACH model demonstrates that increasing dimer interaction strength decreases the translational and rotational intermolecular vibrational amplitudes, while their vibrational frequencies are relatively unaffected. A comparative study of functionally interacting biological dimers with crystal dimers, which are formed artificially via crystallization, reveals a relation between their static structures and the interprotein dynamics: i.e., the consequence of the extensive interfaces of biological dimers is reduction of the intermonomer translational and rotational amplitudes, but not the frequencies.

Hydration-dependent dynamical transition in protein: protein interactions at approximately 240 K.

Interprotein motions in low and fully hydrated carboxymyoglobin crystals are investigated using molecular dynamics simulation. Below approximately 240 K, the calculated dynamic structure factor exhibits a peak arising from interprotein vibration. Above approximately 240 K, the intermolecular fluctuations of the fully hydrated crystal increase drastically, whereas the low-hydration model exhibits no transition. Autocorrelation function analysis shows the transition to be dominated by the activation of diffusive intermolecular motion. The potential of mean force for the interaction remains quasiharmonic. The results indicate useful experimental avenues on protein:protein interactions to be explored using next-generation neutron sources.

Coarse-grained force field for the nucleosome from self-consistent multiscaling.

A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtained from a 5-ns all-atom molecular dynamics (MD) simulation, and were refined to produce agreement with the all-atom MD simulation. This self-consistent multiscale approach yields a coarse-grained model that is capable of reproducing equilibrium structural properties calculated from a 50-ns all-atom MD simulation. This coarse-grained model speeds up nucleosome simulations by a factor of 10(3) and is expected to be useful in examining biologically relevant dynamical nucleosome phenomena on the microsecond timescale and beyond.

Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.