Xiang Qiang Chu

Experimental evidence of fragile-to-strong dynamic crossover in DNA hydration water

We used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H(2)O and D(2)O hydrated samples were measured. The contribution of scattering from DNA is subtracted out by taking the difference of the signals between the two samples. The measurement was made at a series of temperatures from 270 down to 185 K. The relaxing-cage model was used to analyze the quasielastic spectra. This allowed us to extract a Q-independent average translational relaxation time of water molecules as a function of temperature. We observe clear evidence of a fragile-to-strong dynamic crossover (FSC) at T(L)=222+/-2 K by plotting log versus T. The coincidence of the dynamic transition temperature T(c) of DNA, signaling the onset of anharmonic molecular motion, and the FSC temperature T(L) of the hydration water suggests that the change of mobility of the hydration water molecules across T(L) drives the dynamic transition in DNA.

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.

Pressure effects in supercooled water: Comparison between a 2D model of water and experiments for surface water on a protein

Waters behavior differs from that of normal fluids, having more than sixty anomalies. Simulations and theories propose that many of these anomalies result from the coexistence of two liquid phases with different densities. Experiments in bulk water confirm the existence of two local arrangements of water molecules with different densities, but, because of inevitable freezing at low temperature T, cannot ascertain whether the two arrangements separate into two phases. To avoid the freezing, new experiments measure the dynamics of water at low T on the surface of proteins, finding a crossover from a non-Arrhenius regime at high T to a regime that is approximately Arrhenius at low T. Motivated by these experiments, Kumar et al (2008 Phys. Rev. Lett. 100, 105701) investigated, by Monte Carlo simulations and mean field calculations on a cell model for water in two dimensions (2D), the relation of the dynamic crossover with the coexistence of two liquid phases. They show that the crossover in the orientational correlation time r is a consequence of the rearrangement of the hydrogen bonds at low T, and predict that: (i) the dynamic crossover is isochronic, i.e. the value of the crossover time τ L is approximately independent of pressure P; (ii) the Arrhenius activation energy E A (P) of the low-T regime decreases upon increasing P; (iii) the temperature T* (P) at which r reaches a fixed macroscopic time τ* ≥ τ L decreases upon increasing P; in particular, this is true also for the crossover temperature T L (P) at which τ = τ L . Here, we compare these predictions with recent quasi-elastic neutron scattering (QENS) experiments performed by Chu et al on hydrated proteins at different values of P. We find that the experiments are consistent with these three predictions.

Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions

Both the structure and dynamics of biomolecules are known to be essential for their biological function. In the dehydrated state, the function of biomolecules, such as proteins, is severely impeded, so hydration is required for bioactivity. The dynamics of the hydrated biomolecules and their hydration water are related - but how closely? The problem involves several layers of complexity. Even for water in the bulk state, the contribution from various dynamic components to the overall dynamics is not fully understood. In biological systems, the effects of confinement on the hydration water further complicate the picture. Even if the various components of the hydration water dynamics are properly understood, which of them are coupled to the protein dynamics, and how? The studies of protein dynamics over the wide temperature range, from physiological to low temperatures, provide some answers to these question. At low temperatures, both the protein and its hydration water behave as solids, with only vibrational degrees of freedom. As the temperature is increased, non-vibrational dynamic components start contributing to the measurable dynamics and eventually become dominant at physiological temperatures. Thus, the temperature dependence of the dynamics of protein and its hydration water may allow probing various dynamic components separately. In order to suppress the water freezing, the low-temperature studies of protein rely on either low-hydrated samples (essentially, hydrated protein powders), or cryo-protective solutions. Both approaches introduce the hydration environments not characteristic of the protein environments in living systems, which are typically aqueous protein solutions of various concentrations. In this paper, we discuss the coupling between the dynamic components of the protein and its hydration water by critical examining of the existing literature, and then propose that proteins can be studied in an aqueous solution that is remarkably similar in its dynamic properties to pure water, yet does not freeze down to about 200 K, even in the bulk form. The first experiment of this kind using quasielastic neutron scattering is discussed, and more experiments are proposed.

Apparent Decoupling of the Dynamics of a Protein from the Dynamics of its Aqueous Solvent

Studies of the low-temperature dynamics of proteins in aqueous solutions are limited by the crystallization of water. In this work, we use a solution of LiCl in D2O as a solvent for a protein to prevent crystallization and study the dynamics of both the protein and its aqueous solvent by quasielastic neutron scattering (QENS) in the temperature range of 210 to 290 K. Our results reveal that, while the dynamics of the aqueous solvent undergoes a crossover at about 220 K, the dynamics of the protein itself shows no transition at this temperature. The prevailing view is that the β-fluctuations of the protein are governed by the α-fluctuations of the solvent; therefore, observation of the apparent decoupling between the dynamics of the protein and its solvent below the crossover temperature is remarkable.

Dynamic Crossover Phenomenon in Confined Supercooled Water and Its Relation to the Existence of a Liquid‐Liquid Critical Point in Water

We have observed a Fragile‐to‐Strong Dynamic Crossover (FSC) phenomenon of the α‐relaxation time and self‐diffusion constant in confined supercooled water. The α‐relaxation time is measured by Quasielastic Neutron Scattering (QENS) experiments and the self‐diffusion constant by Nuclear Magnetic Resonance (NMR) experiments. Water is confined in 1‐d geometry in cylindrical pores of nanoscale silica materials, MCM‐41‐S and in Double‐Wall Carbon Nanotubes (DWNT). The crossover phenomenon can also be observed from appearance of a Boson peak in Incoherent Inelastic Neutron Scattering experiments. We observe a pronounced violation of the Stokes‐Einstein Relation at and below the crossover temperature at ambient pressure. Upon applying pressure to the confined water, the crossover temperature is shown to track closely the Widom line emanating from the existence of a liquid‐liquid critical point in an unattainable deeply supercooled state of bulk water. Relation of the dynamic crossover phenomenon to the existence of a density minimum in supercooled confined water is discussed. Finally, we discuss a role of the FSC of the hydration water in a biopolymer that controls the biofunctionality of the biopolymer.We have observed a Fragile‐to‐Strong Dynamic Crossover (FSC) phenomenon of the α‐relaxation time and self‐diffusion constant in confined supercooled water. The α‐relaxation time is measured by Quasielastic Neutron Scattering (QENS) experiments and the self‐diffusion constant by Nuclear Magnetic Resonance (NMR) experiments. Water is confined in 1‐d geometry in cylindrical pores of nanoscale silica materials, MCM‐41‐S and in Double‐Wall Carbon Nanotubes (DWNT). The crossover phenomenon can also be observed from appearance of a Boson peak in Incoherent Inelastic Neutron Scattering experiments. We observe a pronounced violation of the Stokes‐Einstein Relation at and below the crossover temperature at ambient pressure. Upon applying pressure to the confined water, the crossover temperature is shown to track closely the Widom line emanating from the existence of a liquid‐liquid critical point in an unattainable deeply supercooled state of bulk water. Relation of the dynamic crossover phenomenon to the existence...

Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA

The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile

Significance Deep-sea microorganisms can adapt to extreme conditions of high temperature and pressure. What makes these organisms survive and reproduce in such critical conditions remains an open question. Here, we use the quasielastic neutron scattering (QENS) technique to study the dynamic behavior of a hyperthermophilic protein that is found in the deep sea. Our results give evidence that high pressure affects the dynamical properties of proteins by distorting the protein energy landscape in ways that are significantly different for hyperthermophilic and mesophilic proteins. Consequently, a general schematic denaturation phase diagram together with energy landscapes for the two different proteins are derived, and this approach can be used as a general picture to understand the effects of pressure on protein dynamics and activities. Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.

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.

Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study

Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.