Adsorption-induced conformational changes of antifreeze glycoproteins at the ice/water interface

The conformation of antifreeze glycoprotein (AFGP) molecules adsorbed at the ice/water interface was studied by attenuated total reflection (ATR)-FTIR spectroscopy. Measurements were carried out for AFGP/D2O solution films formed on the surface of an ATR prism as a function of temperature. Using the FTIR spectrum from the O-D stretching band of D2O molecules, we monitored the supercooled and frozen states of the film and measured the thickness of the quasi-liquid layer (QLL) at the ice/prism interfaces. The AFGP structure was determined for the liquid, supercooled, and frozen states of the solution film using the amide I band spectra. No noticeable differences in conformation were observed in the solution conformation from room temperature down to the 15 K supercooling studied, whereas the alpha-helical content of AFGP suddenly increased when the supercooled solution film froze at -15 degrees C. This change in conformation can increase the overall interaction between the AFGP molecules and ice surface and allow a stronger adsorption. In contrast, the alpha-helical content of AFGP in the frozen film gradually decreased with increasing temperature and finally returned to its solution-state level at the melting point of D2O ice. This gradual decrease in the alpha-helix content directly correlates with the measured increase in QLL thickness. Finally, we conclude that the differences in the alpha-helix signals between the frozen and supercooled states indicate the conformational change of AFGP molecules upon adsorption at the ice/water interface, emphasizing the importance of the structure-function relationship, even for this highly flexible antifreeze.     

Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity

Certain Arctic and Antarctic ectotherm species have developed strategies for survival under low temperature conditions that, among others, consist of antifreeze glycopeptides (AFGP). AFGP form a class of biological antifreeze agents that exhibit the ability to inhibit ice growth in vitro and in vivo and, hence, enable life at temperatures below the freezing point. AFGP usually consist of a varying number of (Ala‐Ala‐Thr)_n units (n=4–55) with the disaccharide β‐D ‐galactosyl‐(1→3)‐α‐N‐acetyl‐D ‐galactosamine glycosidically attached to every threonine side chain hydroxyl group. AFGP have been shown to adopt polyproline II helical conformation. Although this pattern is highly conserved among different species, microheterogeneity concerning the amino acid composition usually occurs; for example, alanine is occasionally replaced by proline in smaller AFGP. The influence of minor and major sequence mutations on conformation and antifreeze activity of AFGP analogues was investigated by replacement of alanine by proline and glycosylated threonine by glycosylated hydroxyproline. The target compounds were prepared by using microwave‐enhanced solid phase peptide synthesis. Furthermore, artificial analogues were obtained by copper‐catalyzed azide–alkyne cycloaddition (CuAAC): propargyl glycosides were treated with polyproline helix II‐forming peptides comprising (Pro‐Azp‐Pro)_n units (n=2–4) that contained 4‐azidoproline (Azp). The conformations of all analogues were examined by circular dichroism (CD). In addition, microphysical analysis was performed to provide information on their inhibitory effect on ice recrystallization.     

Impact of Borate on Structure of Antifreeze Glycoproteins

Antifreeze glycoproteins (AFGPs) facilitate the survival of various organisms in the polar region by preventing internal ice accumulation via an adsorption-inhibition mechanism. Inhibition of AFGP antifreeze activity by the borate buffers has been widely acknowledged as the direct experimental evidence supporting the hydroxyl, rather than methyl, binding mechanism. On the other hand, perturbation of borate binding on the AFGP configuration, which might have considerable influence on the binding efficiency of not only the hydroxyl but also the methyl groups, has rarely been quantitatively examined. Herein we studied, using molecular dynamics simulations, the perturbation on the configuration of a solvated AFGP8 protein induced by the binding of one single borate anion. Near the freezing point, this binding not only makes the disaccharide groups adjacent to the borate-binding disaccharide close to each other but also affects the entire AFGP8 conformation. The structural changes induced by the binding of borate on different disaccharide sidechains exhibit clear site-specificities and the effect of borate binding on the structural changes is significantly reduced at higher temperatures. Our study is valuable for further understanding the relationship between the structure and antifreeze activity of these antifreeze glycoproteins.     

Can proteins and crystals self-catalyze methyl rotations?

The chi (C(alpha)-C(beta)) torsional barrier in the dipeptide alanine (N-methyl-l-alanyl-N-methylamide) crystal was investigated using ab initio calculations at various levels of theory, molecular mechanics, and molecular dynamics. For one of the two molecules in the asymmetric unit the calculations suggest that rotation around the chi dihedral angle is catalyzed by the crystal environment, reducing by up to approximately 2kT the torsional barrier in the crystal with respect to that in the gas phase. This catalytic effect is present at both low and room temperature and originates from a van der Waals destabilization of the minima in the methyl dihedral potential coming from the nonbonded environment of the side chain. Screening of a subset of the Protein Data Bank with a pharmacophore model reproducing the crystal environment around this side chain methyl identified a protein containing an alanine residue with an environment similar to that in the crystal. Calculations indicate that this chi torsional barrier is also reduced in the protein at low temperature but not at room temperature. This suggests that environment-catalyzed rotation of methyl groups can occur both in the solid phase and in native biological structures, though this effect might be temperature-dependent. The relevance of this catalytic effect is discussed in terms of its natural occurrence and its possible contribution to the low-frequency vibrational modes of molecules.     

Determination of the hydrogen-bonding induced local viscosity enhancement in room temperature ionic liquids via femtosecond time-resolved depleted spontaneous emission

The fluorescence depletion dynamics of Rhodamine 700 (R-700) molecules in room temperature ionic liquids (RTILs) 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF(4)]) and 1-hydroxyethyl-3-methylimidazolium tetrafluoroborate ([HOemim][BF(4)]) were investigated to determine the local viscosity of the microenvironment surrounding the fluorescent molecules, which is induced by strong hydrogen bonding interaction between cationic and anionic components in RTILs. The solvation and rotation dynamics of R-700 molecules in RTILs show slower time constants relative to that in conventional protic solvents with the same bulk viscosity, indicating that the probe molecule is facing a more viscous microenvironment in RTILs than in conventional solvents because of the strong hydrogen bonding interaction between cationic and anionic components. In addition, this effect is more pronounced in hydroxyl-functionalized ionic liquid than in the regular RTIL due to the presence of a hydroxyl group as a strong hydrogen bonding donor. The hydrogen-bonding-induced local viscosity enhancement effect related to the heterogeneity character of RTILs is confirmed by the nonexponential rotational relaxation of R-700 determined by time-correlated single photon counting (TCSPC). The geometry of hydrogen bonding complexes with different components and sizes are further optimized by density functional theory methods to show the possible hydrogen-bond networks. A model of the hydrogen-bonding network in RTILs is further proposed to interpret the observed specific solvation and local viscosity enhancement effect in RTILs, where most of the fluoroprobes exist as the free nonbonding species in the RTIL solutions and are surrounded by the hydrogen-bonding network formed by the strong hydrogen-bonding between the cationic and anionic components in RTIL. The optimized geometry of hydrogen bonding complexes with different components and sizes by density functional theory methods confirms the local viscosity enhancement effect deduced from fluorescence depletion and TCSPC experiments. The calculated interaction energies reveal the existence of the stronger hydrogen bonding network in RTILs (especially in hydroxyl-functionalized ionic liquid) than that in conventional protic solvent, which leads to the enhancement effect of local microviscosity, and therefore leads to the slow solvation and rotation dynamics of probe molecules observed in RTILs.     

Temperature dependence of solvation dynamics of probe molecules in methanol-doped ice and in liquid ethanol

We have studied the solvation statics and dynamics of coumarin 343 and a strong photoacid (pK* approximately 0.7) 2-naphthol-6, 8-disulfonate (2N68DS) in methanol-doped ice (1% molar concentration of methanol) and in cold liquid ethanol in the temperature range of 160-270 K. Both probe molecules show a relatively fast solvation dynamics in ice, ranging from a few tens of picoseconds at about 240 K to nanoseconds at about 160 K. At about 160 K in doped ice, we observe a sharp decrease of the dynamic Stokes shift of both coumarin 343 and 2N68DS. Its value is approximately only 200 cm-1 at approximately 160 K compared to about 1100 cm-1 at T >/= 200 K (at times longer than t > 10 ps). We find a good correlation between the inefficient and slow excited-state proton-transfer rate at low-temperature ice, T < 180 K, and the dramatic decrease of the solvation energy, as measured by the dynamic band shift, at these low temperatures. We find that the average solvation rate in ice is similar to its value in liquid ethanol at all given temperatures in the range of 200-250 K. The surprisingly fast solvation rate in ice is explained by the relatively large freedom of the water hydrogen rotation in ice Ih.     

Polymorphism and dynamics of MBBA as studied by NMR

We report proton NMR experiments on the liquid crystal material N-(p-methoxybenzylidene) p-n-butylaniline (MBBA) at 100MHz in the temperature range 110-350 K. The phase diagram was investigated by means of second moment and spin-lattice relaxation measurements in order to establish connections between dynamics and phase transitions. The results show that in a slow cooling experiment, two processes contribute to the relaxation, a slow ethyl group motion together with reorientation of the methyl groups. For the glassy nematic state, as well as for the phases observed after reheating a quenched sample, only methyl rotation is observed. The correlation times of these various mechanisms were determined and the results compared with those obtained by previous NMR and dielectric analysis.     

Comparison of the Time-resolved Absorption and Phosphorescence from the Tryptophan Triplet State in Proteins in Solution

Measurement of the room temperature Trp triplet state lifetime in proteins by time-resolved phosphorescence can provide valuable information on the structure and dynamics of proteins in solution. Our time-resolved absorption measurements on the long-lived states resulting from electronic excitation of the chromophore demonstrate the presence of more complex behavior than revealed by time-resolved phosphorescence. To provide additional insight into this behavior, a comparative study of time-resolved transient absorption and time-resolved phosphorescence of proteins in solution was carried out. The results show that the time evolution of the long-lived states observed through transient absorption often differs considerably from that observed in time-resolved phosphorescence. In some proteins, the presence of competing reactions complicates the interpretation of the transient absorption measurements (which may affect the phosphorescence yield). A more complete characterization of these processes will likely prove useful in the study of protein structure and dynamics in solution.     

Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water

The microstructure, IR spectrum, as well as rotation dynamics of water molecule in sodium tetrafluoroborate （NaBF4）/water mixture at room temperatures were studied with molecular dynamics simulation. Different concentrations of water （6.25%, 25.0%, 50.0%, 75.0%, 90.0%, and 99.6%） in NaBF4/water mixture were simulated to understand the structure and dynamics. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in both liquids. With increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift whereas the O-H stretch bands show blue shift, and the decay of the reorientation correlation function becomes slower. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the interor intra-molecular modes.     

Lattice- and network-structure in plastic ice

We have investigated structural and energetic characteristics of plastic ice, which was found in a high pressure region such as 10 GPa by molecular dynamics simulation and free energy calculation. It was predicted that plastic ice intervenes between ice VII and liquid water, in which diffusion is suppressed but rotation is allowed. In the present work, the structure in plastic ice is explored from both local and global view points and focus is placed on the local arrangement, the extent of deviation from the ideal lattice position, and the hydrogen-bonded patterns. The roles of the attractive interaction and the repulsive part of Lennard-Jones potential are also examined. It is found that the higher interaction energy in plastic ice induces a large dislocation of water molecules, which eventually conducts a facile rotation. There are a large amount of hydrogen-bonds which do not orient to the tetrahedral directions. These orientational defects give rise to fusion of the two interpenetrating sublattices of ice VII leading to a plastic phase rather than defect-containing ice VII, which results in a unique network structure of the plastic ice.     

Local dynamics of micelles of new long-chain surfactants in aqueous media

The molecular dynamics, organization, and phase state of aqueous solutions of new long-chain cationic surfactants with saturated hydrocarbon radicals (from C₁₆ to C₂₂) containing one or two hydroxyl groups in their polar heads are studied by the spin-probe EPR spectroscopy. In the region of micellar solutions, local mobility of surfactant molecules slightly changes with an increase in the length of hydrocarbon radical, whereas the order parameter of micelles increases notably. The addition of two hydroxyl groups to the polar part of long-chain (C ₂₂) surfactant molecule considerably decreases local mobility and increases the ordering of micellar system compared to the micelles of analogous surfactant with one hydroxyl group. Phase transition from micellar to a solid state is observed in this system with a decrease in temperature. The addition of KCl to aqueous surfactant solution lowers the local mobility, increases the order parameter of micelles, and can cause changes in the phase state of a system. In the presence of salt, the correlation time of probe rotation and its order parameter depend on surfactant concentration. Apparently, this is explained by changes in the shape of micelles upon variations in surfactant concentration.     

Transport properties of 2F <==> F2 in a temperature gradient as studied by molecular dynamics simulations

We calculate transport properties of a reacting mixture of F and F(2) from results of non-equilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, which reduces the entropy production. The heat of transfer for the Soret stationary state was more than 100 kJ mol(-1), meaning that the Dufour and Soret effects are non-negligible in reacting mixtures. This sheds new light on the transport properties of reacting mixtures.     

Molecular simulation of nanoclusters of gas hydrates in a water shell. The mechanical state of the system

The molecular dynamics method is employed to study hydrates of methane (sI), and krypton hydrate (sII), as well as an ice nanocluster in a supercooled water shell. The main attention is focused on the local structure and the mechanical state of two-phase nanosized systems, which is described using the local pressure tensor. Analysis of the temperature dependence of the local pressure allows one to compare two possible mechanisms responsible for the anomalous stability of gas hydrates at ambient pressure. According to the first mechanism, the water shell plays the role of a barrier that prevents the gas from escaping from the hydrate core. The second mechanism implies that the water shell generates additional pressure, which transfers the hydrate to a thermodynamically stable state. Results of molecular dynamics simulation indicate that both mechanisms are simultaneously involved in the stabilization of the hydrate nanocluster.     

Structural studies by 1H and 13C dynamic n.m.r.: Part III alternative protonation sites in carbonyl conjugated enamines of the type R1?C(O)?CH?CH?NR2R3

¹³C magnetic resonance spectra of several enamino ketones with secondary and tertiary amino groups were obtained for trifluoroacetic acid solutions. In both series O-protonation is predominant and the chemical shifts are related to the electron density changes with respect to the parent base. The spectra of the tertiary compounds are interpreted in terms of slow rotation around the C–1? C–2 and C–3? N bonds discernible at room temperature. O-protonated forms of the secondary enamino ketones undergo further reaction on C–2 yielding pyridinium salts. The mechanism of formation of the quaternary salts is interpreted and the additivity parameters of the ¹³C n.m.r. chemical shifts in the pyridinium ions is briefly discussed.     

Vibrational density of states of hydration water at biomolecular sites: hydrophobicity promotes low density amorphous ice behavior

Inelastic neutron scattering experiments and molecular dynamics simulations have been used to investigate the low frequency modes, in the region between 0 and 100 meV, of hydration water in selected hydrophilic and hydrophobic biomolecules. The results show changes in the plasticity of the hydrogen-bond network of hydration water molecules depending on the biomolecular site. At 200 K, the measured low frequency density of states of hydration water molecules of hydrophilic peptides is remarkably similar to that of high density amorphous ice, whereas, for hydrophobic biomolecules, it is comparable to that of low density amorphous ice behavior. In both hydrophilic and hydrophobic biomolecules, the high frequency modes show a blue shift of the libration mode as compared to the room temperature data. These results can be related to the density of water molecules around the biological interface, suggesting that the apparent local density of water is larger in a hydrophilic environment.     

A Photophysical Study of Terphenyl Core Oligosulfonimide Dendrimers Exhibiting High Steady‐State Anisotropy

The photophysical properties of three dendrimers containing a p‐terphenyl core with appended sulfonimide branches of different size and n‐octyl chains have been investigated in dichloromethane solution. In the dendrimer absorption spectra contributions from both the branches and the core are clearly identified. The fluorescence spectra show only the characteristic fluorescence of the terphenyl unit. Energy transfer from the appended chromophoric groups to the core does not occur. In the dendrimers, the terphenyl core exhibits a very high fluorescence quantum yield (ca. 0.75) and a short emission lifetime (0.8 ns). These properties allowed investigations of the fluorescence depolarization caused by rotation of the dendrimers. The dendrimers show a very high steady‐state anisotropy in dichloromethane solution at room temperature (0.24 for the largest one), compared to that of the parent terphenyl under the same experimental conditions (<0.01) and in rigid matrix (0.33). Both the n‐octyl chains and the sulfonimide branches play important roles to slow down the molecular rotation.     

固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征

基于分子动力学模拟方法比较了超嗜热菌FlgM 蛋白在常温(293 K)和生理温度(358 K)下的结构特征.基于GROMACS软件包, 采用OPLS-AA分子力场和TIP3P水模型, 对超嗜热菌FlgM 蛋白在293 和358 K进行了2组独立的长时间分子动力学模拟, 每组体系模拟时间为1500 ns. 主要分析了两种温度下超嗜热菌FlgM蛋白的二级结构特征、整体构象变化及半无序化区域和结构化区域的构象特征. 研究结果表明: 在常温下, N端具有一定程度的螺旋成分, 但在生理温度下, 超嗜热菌FlgM 蛋白的结构变得松散, 螺旋结构减少, 构象稳定性减弱, H1 螺旋散开, FlgM 蛋白构象灵活性增强, 不稳定程度增加. 这些不同温度的结构变化说明: 半无序化区域(N端)在非结合状态下有一定的螺旋结构, 但该段螺旋的稳定性随温度升高而降低. 超嗜热菌FlgM蛋白会通过增加结构的无序程度使结构更加灵活, 以适应高温, 从而使该类固有无序蛋白更好地行使其功能, 如提高同其他成分的结合速率等.     

Role of Temperature in Controlling Performance of Photorefractive Organic Glasses

We present a detailed temperature‐dependence study of dielectric, birefringent, conductive, and photorefractive (PR) properties of high‐performance low‐molecular weight organic glasses that contain 2‐dicyanomethylene‐3‐cyano‐2,5‐dihydrofuran (DCDHF) derivatives. DCDHF organic glasses sensitized with C₆₀ exhibit high two‐beam coupling gain coefficients in the red‐wavelength region. However, in the best performing DCDHF glasses at room temperature the PR dynamics are limited by slow molecular reorientation in the electric field. While orientational and, therefore, PR speed can be significantly improved by increasing the temperature above the glass‐transition temperature of the material, the steady‐state performance may worsen. Comprehensive study of the temperature dependence of various processes, which contribute to the PR effect in DCDHF glasses, clarifies the limiting factors and allows for optimization of the overall PR performance.     

Double Histidine Based EPR Measurements at Physiological Temperatures Permit Site-Specific Elucidation of Hidden Dynamics in Enzymes

Protein dynamics is at the heart of all cellular processes. Here, we utilize the dHis-Cu^IINTA label to obtain site-specific information on dynamics for both an α-helix and β-sheet site of GB1, the immunoglobulin binding domain of protein G. Spectral features found in our CW-EPR measurements were consistent with the overall rigid nature of GB1 and with predictions from molecular dynamics simulations. Using this information, we show the potential of this approach to elucidate the role of dynamics in substrate binding of a functionally necessary α-helix in human glutathione transferase A1-1 (hGSTA1-1). We observe two dynamical modes for the helix. The addition of the inhibitor GS-Met and GS-Hex resulted in hGSTA1-1 to favor the more rigid active state conformation, while the faster mode potentially aids the search for substrates. Together the results illustrate the remarkable potential of the dHis-based labelling approach to measure site-specific dynamics using room temperature lineshape analysis.