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. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally observed enhancement of the stability of some enzymes at this particular concentration. Our microscopic analysis suggests. that the formation of a robust intermolecular hydrogen bonding network is most effective at this concentration and is the main mechanism for the suppression of the fast dynamics. (c) 2005 American Insititute of Physics

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. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics. (c) 2005 American Institute of Physics

Rigidity, Secondary Structure, and the Universality of the Boson Peak in Proteins

AbstractComplementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than α-helical proteins; which are softer than β-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications

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. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems. (c) 2006 American Institute of Physics

Widely tunable femtosecond solitonic radiation in photonic crystal fiber cladding

We report on a means to generate tunable ultrashort optical pulses. We demonstrate that dispersive waves generated by solitons within the small-core features of a photonic crystal fiber cladding can be used to obtain femtosecond pulses tunable over an octave-wide spectral range. The generation process is highly efficient and occurs at the relatively low laser powers available from a simple Ti:sapphire laser oscillator. The described phenomenon is general and will play an important role in other systems where solitons are known to exist.Peer reviewed: YesNRC publication: N

Ion transport and structural dynamics in homologous ammonium and phosphoniumbased room temperature ionic liquids

Charge transport and structural dynamics in a homologous pair of ammonium and phosphonium based room temperature ionic liquids (ILs) have been characterized over a wide temperature range using broadband dielectric spectroscopy and quasi-elastic light scattering spectroscopy. We have found that the ionic conductivity of the phosphonium based IL is significantly enhanced relative to the ammonium homolog, and this increase is primarily a result of a lower glass transition temperature and higher ion mobility. Additionally, these ILs exhibit pronounced secondary relaxations which are strongly influenced by the atomic identity of the cation charge center. While the secondary relaxation in the phosphonium IL has the expected Arrhenius temperature dependence characteristic of local beta relaxations, the corresponding relaxation process in the ammonium IL was found to exhibit a mildly non-Arrhenius temperature dependence in the measured temperature range—indicative of molecular cooperativity. These differences in both local and long-range molecular dynamics are a direct reflection of the subtly different inter-ionic interactions and mesoscale structures found in these homologous ILs

Dual-tip-enhanced ultrafast CARS nanoscopy

Coherent anti-Stokes Raman scattering (CARS) and, in particular, femtosecond adaptive spectroscopic techniques (FAST CARS) have been successfully used for molecular spectroscopy and microscopic imaging. Recent progress in ultrafast nanooptics provides flexibility in generation and control of optical near fields, and holds promise to extend CARS techniques to the nanoscale. In this theoretical study, we demonstrate ultrafast subwavelentgh control of coherent Raman spectra of molecules in the vicinity of a plasmonic nanostructure excited by ultrashort laser pulses. The simulated nanostructure design provides localized excitation sources for CARS by focusing incident laser pulses into subwavelength hot spots via two self-similar nanolens antennas connected by a waveguide. Hot-spot-selective dual-tip-enhanced CARS (2TECARS) nanospectra of DNA nucleobases are obtained by simulating optimized pump, Stokes and probe near fields using tips, laser polarization- and pulse-shaping. This technique may be used to explore ultrafast energy and electron transfer dynamics in real space with nanometre resolution and to develop novel approaches to DNA sequencing.Comment: 11 pages, 6 figure