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A parallel tempering method was developed for the reconstruction of porous media using information extracted from 2D digitized microscopy images. The method affords significant improvement over simulated annealing, can be easily parallelized, and works generally for isotropic and anisotropic structures. Inclusion of the pore size distribution function in the reconstruction method was decisive for best results. The validity of the results has been checked by comparing cluster size distribution functions, percolation, and transport properties between original and reconstructed images. [ABSTRACT FROM AUTHOR]

A molecular description of protein-surface interactions could open new avenues in bionanotechnology and provide a deeper understanding of in vivo phase boundary biophysics. However, current experimental techniques can provide only inferential or incomplete information about the protein-surface interface. We present a novel computational method for modeling the interactions of proteins with solid surfaces using comprehensive sampling and an atomistic description. The approach relies on an all-atom Monte Carlo plus-minimization search algorithm that rapidly and simultaneously optimizes rigid-body and side-chain conformations. We apply the method to the statherin-hydroxyapatite system, an evolved protein-surface interaction that is likely to have one or a few specific structural solutions. The algorithm converges on a set of low energy, entropically favorable structures that are consistent with previous experimental results, namely protein-surface intermolecular distances acquired by solid-state NMR. The simulations isolate particular residues as being primary contributors to the adsorption free energy (hydrogen bonding, van der Waals, and electrostatic energies), in agreement with previous mutagenesis, deletion, and single amino acid experiments. We also report the discovery of a molecular recognition motif where the N-terminal alpha-helix of statherin places all four of its basic residues to match the periodicity of open phosphate triad clusters across the [001] monoclinic face of the hydroxyapatite surface. Results suggest new experiments that could further elucidate the structural features of this important biological system.

Hydrophobic interaction chromatography (HIC) is known to be potentially denaturing to proteins, but the effects of mobile phase conditions on chromatographic behavior are not well understood. In this study, we apply a model describing the effects of secondary protein unfolding equilibrium on chromatographic behavior, including the effects of salt concentration on both stability and adsorption. We use alpha-lactalbumin as a model protein that in the presence and absence of calcium, allows evaluation of adsorption parameters for folded and unfolded species independently. The HIC adsorption equilibrium under linear binding conditions and solution phase protein stability have been obtained from a combination of literature and new experiments. The effect of salt concentration on protein stability and the rate constant for unfolding on the chromatographic surface have been determined by fitting the model to isocratic chromatography data under marginally stable conditions. The model successfully describes the effects of added calcium and ammonium sulfate. The results demonstrate the importance of considering the effects on stability of mobile phase modifiers when applying HIC to marginally stable

Experiments and simulations have been carried out for several polar protected peptides in reversed phase chromatography in order to demonstrate how simulation can describe the effects of varying temperature and cosolvent fraction. Comparisons of adsorption chemical potentials from mesoscopic simulations and experimental chromatographic retention data show very good agreement with only one temperature-independent solvent parameter from a single peptide. Such simulations should help guide the design of chromatography experiments with biomolecules and predict retention, including conditions for which empirical correlations such as hydrophobicity scales and molecular descriptors have not been developed.

Mesoscopic simulations using Langevin dipoles on a lattice for the solvent and calculated partial charges for the solute have been used to estimate free energies of adsorption from data on reversed-phase chromatography on nine protected peptides covering a wide range of structures. There is a single parameter, the effective solvent dipole moment, that is fit to data for one peptide and used to predict properties of the other eight peptides. Good agreement of adsorption chemical potentials, including order of chromatographic retention times, is found for calculations that are Boltzmann-averaged over a set of orientations. In addition, the results suggest that there are preferential orientations for each peptide at the model hydrophobic chromatographic surface. Estimation methods for adsorption based on molecular descriptors and hydrophobicity scales are shown to be unreliable for these systems. With refinements and extensions, this simulation method should be applicable to solvents containing salt, such as in hydrophobic interaction chromatography, and to larger solutes including proteins.