A Nuclear Magnetic Resonance study of the reversible denaturation of hydrated lysozyme

The understanding of the physical processes that occur below the threshold of protein thermal denaturation is of fundamental importance. In this thermal region proteins undergo a reversible folding/unfolding process whose evolution depends upon temperature and time. When the kinetics of the folding is altered, the specific biological activity of the protein is altered as well and aggregation phenomena usually intervene. The most important role in driving these processes is played by the solvent and water is certainly the solvent par excellence. It is well known that proteins become biologically active with no less than a water monolayer covering their surface. The knowledge of the physical properties of this monolayer is of basic importance to prevent folding alterations. We present a proton Nuclear Magnetic Resonance study at very high resolution of the thermodynamic properties of lysozyme hydration water as a function of temperature and time in the thermal region of the reversible denaturation.     

NMR investigation of degradation processes of ancient and modern paper at different hydration levels

The degradation process of cellulose-made materials was investigated by means of nuclear magnetic resonance (NMR) spectroscopy, with particular emphasis on the role of water and on the hydration mechanism of cellulose fibrils. To accomplish this, the structure and dynamics of water within ancient and modern samples with different aging histories were investigated. The results mainly indicated that hydrolytic and oxidative reactions provoked the formation of acidic by-products. Furthermore, degradation processes were enhanced by higher amounts of water giving a progressive consumption of the amorphous regions of the cellulose. We propose NMR experiments as a benchmark for characterization of the degradation state of paper, as well as for investigating the effectiveness of restoration treatments.     

Slow dynamics of supercooled hydration water in contact with lysozyme: examining the cage effect at different length scales

ABSTRACT

We study by computer simulation the dynamics of hydration water in solution with lysozyme upon approaching the glassy state of water. We calculate the self-density correlation function at different wavelengths to test the Mode Coupling Theory (MCT) of glassy dynamics at different length scales. The results show a strict and clear relation of the behaviour of the structural relaxation with the cage effect. We find a good agreement with the predictions of the MCT in the short and medium scale range, while at increasing length scales the interaction of water molecules with the protein's substrate induces deviations from the MCT behaviour, as found in previous studies. Besides at low temperatures the slow dynamics deviates from MCT due to hopping processes, similar to the bulk, as witnessed by a crossover from a fragile behaviour to a strong behaviour. We show that this deviation is evident at all length scales. Interestingly, we find that in the fragile region the confining cage decreases in radius with temperature while in the strong region it appears stable.     

Water and lysozyme: Some results from the bending and stretching vibrational modes

The dynamic or glass transition in biomolecules is important to their functioning. Also essential is the transition between the protein native state and the unfolding process. To better understand these transitions, we use Fourier transform infrared spectroscopy to study the vibrational bending and stretching modes of hydrated lysozymes across a wide temperature range. We find that these transitions are triggered by the strong hydrogen bond coupling between the protein and hydration water. More precisely, we demonstrate that in both cases the water properties dominate the evolution of the system. We find that two characteristic temperatures are relevant: in the supercooled regime of confined water, the fragile-to-strong dynamic transition occurs at T_L, and in the stable liquid phase, T*≃315±5K characterizes the behavior of both isothermal compressibility K_T (T,P) and the coefficient of thermal expansion a_P (T,P).     

水溶液中结合水的定义与量化

水溶液中溶质的结合水具有不同于远离溶质的自由水的结构和性质.结合水的存在对水和溶质结构和动力学性质均具有显著甚至决定性的影响.然而,对结合水动力学和热力学性质的定量理解在诸多方面一直存在争议甚至严重分歧,其中重点包括如何定义和量化结合水,如何表征结合水和自由水的动力学差别,结合水如何参与生物大分子各种生物功能过程,以及溶质或界面影响结合水结构与性质的途径等.给出结合水定义的物理学依据和量化方法,是深入理解上述问题的第一步.本文简述了各种不同谱学方法定义结合水的基本原理及量化的困难,强调具有不同时间和空间响应尺度的测试方法所得结合水数不必完全可比.此外,系列水溶液物性随浓度升高会明显改变其浓度依赖关系,相应拐点浓度常被用于量化稀溶液中的溶质结合水数.我们近期研究的水溶液玻璃化转变温度-浓度关系,为结合水的定义、量化和水溶液的三区划分提供了物理依据,同时揭示了上述利用性质-浓度关系拐点浓度量化结合水方法的不足.     

Dynamical properties of water in living cells

With the aim of studying the effect of water dynamics on the properties of biological systems, in this paper, we present a quasi-elastic neutron scattering study on three different types of living cells, differing both in their morphological and tumor properties. The measured scattering signal, which essentially originates from hydrogen atoms present in the investigated systems, has been analyzed using a global fitting strategy using an optimized theoretical model that considers various classes of hydrogen atoms and allows disentangling diffusive and rotational motions. The approach has been carefully validated by checking the reliability of the calculation of parameters and their 99% confidence intervals. We demonstrate that quasi-elastic neutron scattering is a suitable experimental technique to characterize the dynamics of intracellular water in the angstrom/picosecond space/time scale and to investigate the effect of water dynamics on cellular biodiversity.     

Ectoine hydration,aggregation and influence on water structure

Neutron diffraction with isotopic H/D substitution on water, augmented by Empirical Potential Structure Refinement has been applied to extract the hydration properties of the osmolyte zwitterionic ectoine at 1.5?M concentration. This has evidenced differences between the hydration of COO^? and NH groups, both in terms of number of water molecules involved in the hydration shell and of three-dimensional symmetry. Signatures of ectoine–ectoine contacts, due to hydrogen bonds, have been found, as possible precursors of ectoine aggregation at higher concentrations. The influence of ectoine on the water structure is ascribed to the dipolar electric field generated by the exposed charges of ectoine.     

Analysis of cold denaturation mechanism of β‐lactoglobulin and comparison with thermal denaturation from Raman spectroscopy investigations

Cold‐ and heat‐induced β‐lactoglobulin (BLG) transformations have been analyzed in the presence of 4 M urea, from Raman spectroscopy investigations carried out simultaneously in the low wavenumber range (10–400 cm⁻¹) and in the amide I region (1500–1800 cm⁻¹). These investigations show common features between the denaturation processes at low and high temperatures. The denatured states are reached via an intermediate state characterized by a soft tertiary structure without detectable conformational changes. This intermediate is intimately connected with a tetrahedral hydrogen‐bond structure of water which extends over a limited range. It is shown that the disruption of the hydrogen‐bond network of D₂O has an important consequence on the solvent dynamics, which controls protein dynamics and is characterized by an anharmonic behavior. By monitoring the amide I mode, conformational changes are detected at low temperature (below 5 °C) and determined to be similar to those detected at high temperature in the presence of urea near 65 °C, and in the absence of urea near 80 °C. The conformational changes are described as a loss of α‐helix structures and a concomitant formation of β‐sheets. The temperature dependence of the amide I wavenumber in BLG dissolved in the 4 M urea aqueous solution was interpreted on the basis of a two‐state model, leading to the protein stability curve related to its molecular conformation. Copyright © 2011 John Wiley & Sons, Ltd.     

Fragile to strong crossover and Widom line in supercooled water: A comparative study

The aim of this paper is to discuss the relationship between the dynamics and thermodynamics of water in the supercooled region. Reviewed case studies comprehend bulk water simulated with the SPC/E, TIP4P and TIP4P/2005 potentials, water at protein interfaces, and water in solution with electrolytes. Upon supercooling, the fragile to strong crossover in the α-relaxation of water is found to occur when the Widom line emanating from the liquid-liquid critical point is crossed. This appears to be a general characteristic of supercooled water, not depending on the applied interaction potential and/or different local environments.     

Interface water-induced hydrophobic carbon chain unfolding in water

The folding and unfolding of the carbon chain, which is the basic constitutional unit of polymers,are important to the performance of the material. However, it is difficult to regulate conformational transition of the carbon chain, especially in an aqueous environment. In this paper, we propose a strategy to regulate the conformational transition of the carbon chain in water based on the all-atom molecular dynamics simulations. It is shown that the unfolded carbon chain will spontaneously collapse into the folded state, while the folded carbon chain will unfold with an external electric field. The regulation ability of the electric field is attributed to the electric field-induced redistribution of interface water molecules near the carbon chain. The demonstrated method of regulating conformational transition of the carbon chain in water in this study provides an insight into regulating hydrophobic molecules in water, and has great potential in drug molecule design and new polymer material development.     

Molecular dynamics and quantum chemical approaches in the study of the hydration of protonated cyclohexyldiamines

Explicit hydration of the neutral and charged cyclohexylamine and of the cyclohexyldiamine isomers in their mono- or diprotonated forms is investigated through classical molecular dynamics (MD) simulations in aqueous solutions combined with DFT calculations in amine–water complexes. The MD studies performed in the monoamines reveal that the structure of the hydration shell around the neutral amino group (NH₂) is quite distinct from that around the charged one (NH₃⁺). On average, the number of water molecules surrounding the two groups is calculated to be ～2 and 3–4, respectively. The variation of the hydration structure prompted by the groups’ proximity is discussed based on the data found for the mono- and diprotonated diamines. To have a more detailed picture of the water molecules’ arrangement around the amino groups and of the amine–water hydrogen bonds, geometry optimisations in hydrates with up to six water molecules are carried out at the B3LYP/aug-cc-pVDZ level. Complexation energies are also computed. The main findings emerging from these calculations are found to be very helpful to rationalise the mutual influence of the amino groups and therefore to better elucidate the MD findings. The complementary nature of the two research methods is emphasised as an excellent tool in order to closely examine the hydration of polyamines, as exemplified for the cyclohexyldiamines.     

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Changes in protein structure and dynamics as a function of hydration from (1)H second moments

We report the proton second moment obtained directly from the Free Induction Decay (FID) of the NMR signal of variously hydrated bovine serum albumin (BSA) and hen egg white lysozyme (HEWL) and from the width of the NMR Z-spectrum of the cross-linked protein gels of different concentrations. The second moment of the proteins decreases in a continuous stepwise way as a function of increasing water content, which suggests that the structural and dynamical changes occur in small incremental steps. Although the second moment is dominated by the short range distances of nearest neighbors, the changes in the second moment show that the protein structure becomes more open with increasing hydration level. A difference between the apparent liquid content of the sample as found from decomposition of the FID and the analytically determined water content demonstrates that water absorbed in the early stages of hydration is motionally immobilized and magnetically indistinguishable from rigid protein protons while at high hydration levels some protein side-chain protons move rapidly contributing to liquid-like component of the NMR signal.     

Probing interfacial dynamics of water in confined nanoporous systems by NMRD

The confined dynamics of water molecules inside a pore involves an intermittence between adsorption steps near the interface and surface diffusion and excursions in the pore network. Depending on the strength of the interaction in the layer(s) close to the surface and the dynamical confinement of the distal bulk liquid, exchange dynamics can vary significantly. The average time spent in the surface proximal region (also called the adsorption layer) between a first entry and a consecutive exit allows estimating the level of ‘nanowettablity’ of water. As shown in several seminal works, NMRD is an efficient experimental method to follow such intermittent dynamics close to an interface. In this paper, the intermittent dynamics of a confined fluid inside nanoporous materials is discussed. Special attention is devoted to the interplay between bulk diffusion, adsorption and surface diffusion on curved pore interfaces. Considering the nano or meso length scale confinement of the pore network, an analytical model for calculating the inter-dipolar spin–lattice relaxation dispersion curves is proposed. In the low-frequency regime (50?KHz–100?MHz), this model is successfully compared with numerical simulations performed using a 3D-off lattice reconstruction of Vycor glass. Comparison with experimental data available in the literature is finally discussed.     

Local and global dynamics in the glass-forming di-isobutyl phthalate as studied by H NMR

Spin-lattice relaxation times T₁ and T_1ρ as well as ¹H NMR spectra have been employed to study the dynamics of the glass-forming di-isobutyl phthalate in the temperature range extending from 100 K, through the glass transition temperature T_g, up to 340 K. Below T_g NMR relaxation is governed by local dynamics and may be attributed to rotation of methyl groups at low temperatures and to motion of isobutyl groups in the intermediate temperature interval. Above T_g the main relaxation mechanism is provided by overall molecular motion. The observed relaxation behavior is explained by motional models assuming asymmetrical distributions of correlation times. The motional parameters obtained from Davidson-Cole distribution, which yields the best fit of the data at all temperatures are given.     

1H spin–lattice relaxation in water solution of 209Bi counterparts of Gd3+contrast agents

ABSTRACT

¹H spin–lattice relaxation studies of water solutions of Bismuth-ethylenediamine-tetraacetic acid (Bi-EDTA), Bismuth-ethylenediamine-tetrakis(methylenephosphonic) acid (Bi-EDTP), Bismuth-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (Bi-DOTA), Bismuth-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonic acid) (Bi-DOTP) and Bismuth-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid (Bi-DO3A) have been performed in order to compare Quadrupole Relaxation Enhancement (QRE) effects with Paramagnetic Relaxation Enhancement (PRE) from the perspective of exploiting the first one as a novel contrast mechanism for Magnetic Resonance Imaging (MRI). The selected compounds can be considered as ²⁰⁹Bi counterparts of Gd³⁺ complexes. The relaxation experiments have been performed in a broad frequency range of 5?kHz–30?MHz. The relaxation contribution associated with QRE has been extracted from the data and compared with PRE. Similarities and differences between the two effects have been discussed.     

良导体导热系数实验中稳态时间、稳态温度与水流量的相关性

通过改变参数进行实验测定,分析了稳态法测量良导体导热系数实验中系统达到稳态的时间、水流量、稳定温度及测得导热系数结果的准确性等相关问题,提供了可供参考的经验数据,对学生实验过程有指导作用.     

Dynamical and structural properties of adsorbed water molecules at the TiO2 rutile-(110) surface: interfacial hydrogen bonding probed by ab-initio molecular dynamics

ABSTRACT

Ab-initio molecular dynamics (AIMD) simulations have been carried out to study a range of different and energetically-accessible adsorbed-water configurations and motifs for their vibrational and structural characteristics, in contact with rutile-(110) interfaces at 100?K. The radial pair distribution function between the titanium atoms at the interface and the hydrogen and oxygen atoms in the water monolayer show an orientation of the water molecules parallel to the surface of titania, and with hydrogen atoms pointed in the opposite direction to the surface. In some cases, a distinctive vibrational frequency region between 2500 and 3000?cm^?1 has also been observed, due to a strong dispersion interaction between water molecules. This behaviour is also seen in experimental studies of thin-film water coverage on TiO₂ surfaces.