Effect of glycerol-water binary mixtures on the structure and dynamics of protein solutions.

We have performed 20 ns of fully atomistic molecular dynamics simulations of Hen Egg-White Lysozyme in 0, 10, 20, 30, and 100% by weight of glycerol in water to better understand the microscopic physics behind the bioprotection offered by glycerol to naturally occuring biological systems. The solvent exposure of protein surface residues changes when glycerol is introduced. The dynamic behavior of the protein, as quantified by the incoherent intermediate scattering function, shows a nonmonotonic dependence on glycerol content.

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures.

We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity.

The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces.

We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues.

Separation and characterization of metallosupramolecular libraries by ion mobility mass spectrometry.

The self-assembly of Zn(II) ions and bis(terpyridine) (tpy) ligands carrying 120° or 180° angles between their metal binding sites was utilized to prepare metallosupramolecular libraries with the connectivity. These combinatorial libraries were separated and characterized by ion mobility mass spectrometry (IM MS) and tandem mass spectrometry (MS(2)). The 180°-angle building blocks generate exclusively linear complexes, which were used as standards to determine the architectures of the assemblies resulting from the 120°-angle ligands.

Design, synthesis, and traveling wave ion mobility mass spectrometry characterization of iron(II)- and ruthenium(II)-terpyridine metallomacrocycles.

New metallomacrocycles composed of 2,2':6',2″-terpyridine (tpy) ligands and Ru(II) or Fe(II) transition metal ions were prepared by stepwise directed assembly and characterized by 2D diffusion NMR spectroscopy (DOSY), electrospray ionization traveling wave ion mobility mass spectrometry (ESI TWIM MS), and molecular modeling. The supramolecular polymers synthesized include a homonuclear all-Ru hexamer as well as heteronuclear hexamer and nonamer with alternating Ru/Ru/Fe metal centers. ESI MS yields several charge states from each supramacromolecule.

How does the coupling of secondary and tertiary interactions control the folding of helical macromolecules?

The authors study how the simultaneous presence of short-range secondary and long-range tertiary interactions controls the folding and collapse behavior of a helical macromolecule. The secondary interactions stabilize the helical conformation of the chain, while the tertiary interactions govern its overall three-dimensional shape. The authors have carried out Monte Carlo simulations to study the effect of chain length on the folding and collapse behavior of the chain.

Inertial suppression of protein dynamics in a binary glycerol-trehalose glass.

The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples.

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations.

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass.

Coupling between helix-coil and coil-globule transitions in helical polymers.

We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which could be a helix, a random coil, an amorphous globule, or one of various other globular states which carry residual helical strands.

Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations.

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein.

Role of hydrogen bonds in the fast dynamics of binary glasses of trehalose and glycerol: a molecular dynamics simulation study.

Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature.

Statistical mechanics of worm-like polymers from a new generating function.

We present a mathematical approach to the worm-like chain model of semiflexible polymers. Our method is built on a novel generating function from which all the properties of the model can be derived. Moreover, this approach satisfies the local inextensibility constraint exactly.