Marco Lagi

The low-temperature dynamic crossover phenomenon in protein hydration water: Simulations vs experiments

A super-Arrhenius-to-Arrhenius dynamic crossover phenomenon has been observed in the translational alpha-relaxation time and in the inverse of the self-diffusion constant both experimentally and by simulations for lysozyme hydration water in the temperature range of TL = 223 +/- 2 K. MD simulations are based on a realistic hydrated powder model, which uses the TIP4P-Ew rigid molecular model for the hydration water. The convergence of neutron scattering, nuclear magnetic resonance and molecular dynamics simulations supports the interpretation that this crossover is a result of the gradual evolution of the structure of hydration water from a high-density liquid to a low-density liquid form upon crossing of the Widom line above the possible liquid-liquid critical point of water.

Logarithmic Decay in Single-Particle Relaxation of Hydrated Lysozyme Powder

We present the self-dynamics of protein amino acids of hydrated lysozyme powder around the physiological temperature by means of molecular dynamics simulations. The self-intermediate scattering functions of the amino acid residue center of mass display a logarithmic decay over 3 decades of time, from 2 ps to 2 ns, followed by an exponential alpha relaxation. This kind of slow dynamics resembles the relaxation scenario within the beta-relaxation time range predicted by mode coupling theory in the vicinity of higher-order singularities. These results suggest a strong analogy between the single-particle dynamics of the protein and the dynamics of colloidal, polymeric, and molecular glass-forming liquids.

Observation of high-temperature dynamic crossover in protein hydration water and its relation to reversible denaturation of lysozyme

The diffusive dynamics of hydration water in lysozyme is studied by high-resolution incoherent quasielastic neutron scattering spectroscopy and molecular dynamics (MD) simulations in a temperature range of 290 K<T<380 K. The hydration level of the protein powder sample is kept at h=0.35 gram of water per gram of dry protein to provide monolayer of water coverage on the protein surfaces. Two lysozyme samples, the H(2)O hydrated and the D(2)O hydrated, are measured in the experiments. The difference spectra of the two are used to extract the diffusive dynamics of the hydration water. The self-diffusion constant D of the hydration water is obtained from the analyses of the low-Q spectra. The Arrhenius plot of the inverse diffusion constant [i.e., log(1/D) versus 1/T] shows a dynamic crossover from a super-Arrhenius behavior at low temperatures to an Arrhenius behavior at high temperatures bordered at T(D)=345+/-5 K. We also observe a pronounced increase in the migration distance d of the hydration water molecules above T(D). We present evidence from the neutron scattering experiment that this dynamic crossover temperature in the hydration water coincides with that of the reversible denaturation of lysozyme determined by specific heat measurements. We further performed MD simulations of hydrated lysozyme powder to offer a plausible reason for this coincidence of the crossover phenomenon with the reversible denaturation of the protein.

Absence of the Density Minimum of Supercooled Water in Hydrophobic Confinement

The surface effect on the peculiar dynamic and thermodynamic properties of supercooled water, such as the density, has been puzzling the scientific community for years. Recently, using the small angle neutron scattering method, we were able to measure the density of H(2)O confined in the hydrophobic mesoporous material CMK-1-14 from room temperature down to the deeply supercooled temperature 130 K at ambient pressure. We found that the well-known density maximum of water is shifted 17 K lower and, more interestingly, that the previously observed density minimum in hydrophilic confinement disappears. Furthermore, the deduced thermal expansion coefficient shows a much broader peak spanning from 240 to 180 K in comparison with the sharp peak at 230 K in hydrophilic confinement. These present results may help in the understanding of the effect of hydrophobic/hydrophilic interfaces on the properties of supercooled confined water.

DNA closed nanostructures: a structural and Monte Carlo simulation study

DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.

Experimental evidence of logarithmic relaxation in single-particle dynamics of hydrated protein molecules

We observe a logarithmic-like decay of the intermediate scattering function (ISF) of the hydrogen atoms in the protein molecule in the time interval from 10 ps to 1 ns. We analyze the ISF, FH(Q,t), in terms of an asymptotic expression proposed by mode coupling theory (MCT). The result clearly shows that this logarithmic stretching of the β-relaxation range is real, substantiating the prediction of the molecular dynamics (MD) simulation results that used the formula proposed by MCT for the analysis of ISF.

Interconnected networks: Structural and dynamic characterization of aqueous dispersions of dioctanoylphosphatidylcholine

Aqueous dispersions of the phospholipid dioctanoylphosphatidylcholine (diC 8PC) phase-separate below a cloud-point temperature, depending on lipid concentration. The lower phase is viscous and rich in lipid. The structure and dynamics of this system were explored via cryo-transmission electron microscopy (cryo-TEM), small-angle X-ray scattering (SAXS), and NMR. The lower phase comprises a highly interconnected tridimensional network of wormlike micelles. A molecular mechanism for the phase separation is suggested.

The Dynamic Response Function χT(Q,t) of Confined Supercooled Water and its Relation to the Dynamic Crossover Phenomenon

Abstract We have made a series of Quasi-Elastic Neutron Scattering (QENS) studies of supercooled water confined in 3-D and 1-D geometries, specifically, interstitial water in aged cement paste (3-D) and water confined in MCM-41-S and Double Wall Nano Tube DWNT (1-D). In addition, we also include the cases of hydration water on protein surface and other biopolymer surfaces (pseudo 2-D). By analyzing the QENS spectra using Relaxing Cage Model (RCM), we are able to extract accurately the self-intermediate scattering function of hydrogen atoms FH(Q,t), at low-Q as a function of temperature T, showing an α-relaxation process at long time. We can then construct the Dynamic Response Function χT(Q,t) = -dFH(Q,t)/dT. χT(Q,t) as a function of t at constant Q shows a single peak at the characteristic α-relaxation time 〈τ〉, the amplitude of which grows as we approach the dynamic crossover temperature TL observed before in each of these geometries. However, the peak height of χT(Q,t) decreases after passing the crossover temperature TL. We make an argument to relate the occurrence of the extremum of the peak height in χT to the existence of the dynamic crossover temperature in each of these cases.

Neutron scattering studies of dynamic crossover phenomena in a coupled system of biopolymer and its hydration water

We have observed a Fragile-to-Strong Dynamic Crossover (FSC) phenomenon of the α-relaxation time and self-diffusion constant in hydration water of three biopolymers: lysozyme, B-DNA and RNA. The mean squared displacement (MSD) of hydrogen atoms is measured by Elastic Neutron Scattering (ENS) experiments. The α-relaxation time is measured by Quasi-Elastic Neutron Scattering (QENS) experiments and the self-diffusion constant by Nuclear Magnetic Resonance (NMR) experiments. We discuss the active role of the FSC of the hydration water in initiating the dynamic crossover phenomenon (so-called glass transition) in the biopolymer. The latter transition controls the flexibility of the biopolymer and sets the low temperature limit of its biofunctionality. Finally, we show an MD simulation of a realistic hydrated powder model of lysozyme and demonstrate the agreement of the MD simulation with the experimental data on the FSC phenomenon in the plot of logarithm of the α-relaxation time vs. 1/T.