分子间相互作用对蛋白质晶体生长的影响

采用原子力显微镜对溶菌酶和刀豆蛋白A的分子间相互作用力的情况进行了研究, 并用动态光散射研究了此二种分子间相互作用力有较大差异的蛋白质在晶体生长条件和非生长条件下, 溶液中的聚集体的状态(大小和分散度)随浓度和温度的变化情况. 实验结果表明, 范德华力强的刀豆蛋白A在成核前, 溶液中的聚集体不能很快转变为生长基元, 导致晶体生长时间长; 而范德华力弱的溶菌酶, 溶液中的聚集体可以很快转变成生长基元, 晶体生长时间也较短.     

Rotational and translational dynamics of lysozyme in water-glycerol solution

In this paper, we report a study of the effect of solvent viscosity on both translational and rotational dynamics of a simple model protein: the egg white lysozyme. For this, we investigated the dynamical properties of lysozyme in mixtures water–glycerol by means of parallel measurements of photon correlation spectroscopy (PCS) and dielectric spectroscopy at radiofrequencies (DS). In the framework of the Debye–Stokes–Einstein theory, the translational and rotational coefficients allow an estimation of hydrodynamic radius of the protein. A decoupling between translational and rotational dynamics, observed as a different estimation of hydrodynamic radius, is reported in the literature for some systems. In order to ascertain if this effect is present also in our sample, we performed PCS and DS measurements on lysozyme–water–glycerol solutions. The content of glycerol was in the range of 0–70% w/w, with a solvent viscosity from 0.9 to about 10 cpoise, and the protein concentration was up to 20 mg ml⁻¹. The average sizes of lysozyme, obtained by the two methods, are remarkably different at high protein concentrations. However, the values of hydrodynamic radius extrapolated to infinite dilution are coincident and independent of glycerol. These results indicate that the diffusive behavior of lysozyme in the water–glycerol mixture is coherent with the Debye–Stokes–Einstein hydrodynamic model.     

Chemical imaging of protein adsorption and crystallization on a wettability gradient surface

The use of self-assembled monolayers is an established method to study the effect of surface properties on proteins and other biological materials. The generation of a monolayer with a gradient of chemical properties allows for the study of multiple surface properties simultaneously in a high throughput manner. Typically, in order to detect the presence of proteins or biological material on a surface, the use of additional dyes or tags is required. Here we present a novel method of studying the effect of gradient surface properties on protein adsorption and crystallization in situ through the use of ATR-FTIR spectroscopic imaging, which removes the need for additional labeling. We describe the successful application of this technique to the measurement of the growth of a gradient monolayer of octyltrichlorosilane across the surface of a silicon ATR element. ATR-FTIR imaging was also used to study the adsorption of lysozyme, as a model protein, onto the modified surface. The sensitivity of measurements obtained with a focal plane array (FPA) detector were improved though the use of pixel averaging which allowed small absorption bands to be detected with minimal effect on the spatial resolution along the gradient. Study of the effect of surface hydrophobicity on both adsorption of lysozyme to the element and lysozyme crystallization revealed that more lysozyme adsorbed to the hydrophobic side of the ATR element and more lysozyme crystals formed in the same region. These findings strongly suggest a correlation exists between surface protein adsorption and protein crystallization. This method could be applied to the study of other proteins and whole cells.     

Solubility of lysozyme in the presence of aqueous chloride salts: common-ion effect and its role on solubility and crystal thermodynamics

Understanding protein solubility is important for a rational design of the conditions of protein crystallization. We report measurements of lysozyme solubility in aqueous solutions as a function of NaCl, KCl, and NH4Cl concentrations at 25 degrees C and pH 4.5. Our solubility results are directly compared to preferential-interaction coefficients of these ternary solutions determined in the same experimental conditions by ternary diffusion. This comparison has provided new important insight on the dependence of protein solubility on salt concentration. We remark that the dependence of the preferential-interaction coefficient as a function of salt concentration is substantially shaped by the common-ion effect. This effect plays a crucial role also on the observed behavior of lysozyme solubility. We find that the dependence of solubility on salt type and concentration strongly correlates with the corresponding dependence of the preferential-interaction coefficient. Examination of both preferential-interaction coefficients and second virial coefficients has allowed us to demonstrate that the solubility dependence on salt concentration is substantially affected by the corresponding change of protein chemical potential in the crystalline phase. We propose a simple model for the crystalline phase based on salt partitioning between solution and the hydrated protein crystal. A novel solubility equation is reported that quantitatively explains the observed experimental dependence of protein solubility on salt concentration.     

气相扩散法生长溶菌酶晶体的动态光散射研究

首次采用动态光散射研究了气相扩散法生长溶菌酶晶体.实验中采用了两种溶解溶菌酶的方法,所得实验结果是有区别的.这种区别表明了NaCl对溶菌酶分子间相互作用产生十分重要的影响.实验结果表明,晶体生长过程中,溶液中溶菌酶始终保持单分子与两分子聚集体的状态,这种状态是生长晶体的基础.     

Kinetics of Lysozyme Crystallization From Solution

Abstract

We suggest that the growth of molecular aggregates is the rate-controlling step in the crystallization of lysozyme from pH buffered aqueous solutions of strong electrolytes. We propose that the aggregation reaction passes through a charged transition state whose rate of formation is accelerated by Debye-Huckel screening and whose charge is stabilized by ion exchange with the solution. Applying the theory of the “primary kinetic salt effect”, we predict that the half-life for decay of the lysozyme concentration in solution in contact with a growing crystal should decrease linearly with the square root of the ionic strength. This prediction is confirmed experimentally in the case of lysozyme crystals precipitating at 4°C from pH buffered aqueous solutions of sodium chloride.     

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.     

Controlling Protein Crystal Nucleation by Droplet‐Based Microfluidics

Herein, we demonstrate the potential of droplet‐based microfluidics for controlling protein crystallization and generating single‐protein crystals. We estimated the critical droplet size for obtaining a single crystal within a microdroplet and investigated the crystallization of four model proteins to confirm the effect of protein molecular diffusion on crystallization. A single crystal was obtained in microdroplets smaller than the critical size by using droplet‐based microfluidics. In the case of thaumatin crystallization, a single thaumatin crystal was obtained in a 200 μm droplet even with high supersaturation. In the case of ferritin crystallization, the nucleation profile of ferritin crystals had a wider distribution than the nucleation profiles of lysozyme, thaumatin, and glucose isomerase crystallization. We found that the droplet‐based microfluidic approach was able to control the nucleation of a protein by providing control over the crystallization conditions and the droplet size, and that the diffusion of protein molecules is a significant factor in controlling the nucleation of protein crystals in droplet‐based microfluidics.     

Hydrogen bonding and the cryoprotective properties of glycerol/water mixtures

Molecular dynamics simulations and infrared spectroscopy were used to determine the hydrogen bond patterns of glycerol and its mixtures with water. The ability of glycerol/water mixtures to inhibit ice crystallization is linked to the concentration of glycerol and the hydrogen bonding patterns formed by these solutions. At low glycerol concentrations, sufficient amounts of bulk-like water exist, and at low temperature, these solutions demonstrate crystallization. As the glycerol concentration is increased, the bulk-like water pool is eventually depleted. Water in the first hydration shell becomes concentrated around the polar groups of glycerol, and the alkyl groups of glycerol self-associate. Glycerol-glycerol hydrogen bonds become the dominant interaction in the first hydration shell, and the percolation nature of the water network is disturbed. At glycerol concentrations beyond this point, glycerol/water mixtures remain glassy at low temperatures and the glycerol-water hydrogen bond favors a more linear arrangement. High glycerol concentration mixtures mimic the strong hydrogen bonding pattern seen in ice, yet crystallization does not occur. Hydrogen bond patterns are discussed in terms of hydrogen bond angle distributions and average hydrogen bond number. Shift in infrared frequency of related stretch and bend modes is also reviewed.     

Crystallization of tetrahedral patchy particles in silico

We investigate the competition between glass formation and crystallization of open tetrahedral structures for particles with tetrahedral patchy interactions. We analyze the outcome of such competition as a function of the potential parameters. Specifically, we focus on the separate roles played by the interaction range and the angular width of the patches, and show that open crystal structures (cubic and hexagonal diamond and their stacking hybrids) spontaneously form when the angular width is smaller than about 30°. Evaluating the temperature and density dependence of the chemical potential of the fluid and of the crystal phases, we find that adjusting the patch width affects the fluid and crystal in different ways. As a result of the different scaling, the driving force for spontaneous self-assembly rapidly grows as the fluid is undercooled for small-width patches, while it only grows slowly for large-width patches, in which case crystallization is pre-empted by dynamic arrest into a network glass.     

Synthesis of branched poly(butylene succinate): Structure properties relationship

A series of branched poly(butylene succinate) (PBS) were synthesized with several branching agents namely trimethylol propane (TMP), malic acid, trimesic acid, citric acid and glycerol propoxylate. The structure of the branched polymers was analyzed by SEC and ¹H-NMR. The effect of branching agent structure on crystallization was also investigated and played a significant role. Isothermal studies showed that glycerol propoxylate could act as a nucleating agent. By contrast high content of TMP disturbed the regularity of the chain and hindered the crystallization of PBS. From the non-isothermal kinetic study, it was found that glycerol propoxylate increased noticeably the crystallization rate due to the flexible structure of the branching agent. A secondary nucleation was observed with glycerol propoxylate attributed to the crystallization of amorphous fraction included between crystallites formed at the primary crystallization. Chain topology was obtained through rheological investigations and the synthesized polymers showed a typical behavior of a mixture of linear and randomly branched PBS. The incorporation of branches improved the processability of PBS for film blowing application and the modulus and the stress at break of the resulting film were significantly increased.     

Complex formation in mixtures of lysozyme-stabilized emulsions and human saliva

In this paper, we studied the interaction between human unstimulated saliva and lysozyme-stabilized oil-in-water emulsions (10 wt/wt% oil phase, 10 mM NaCl, pH 6.7), to reveal the driving force for flocculation of these emulsions. Confocal scanning laser microscopy (CSLM) showed formation of complexes between salivary proteins and lysozyme adsorbed at the oil-water interface and lysozyme in solution as well. To assess the electrostatic nature of the interaction in emulsion/saliva mixtures, laser-diffraction and rheological measurements were conducted in function of the ionic strength by adding NaCl to the mixture in the range between 0 and 168 mM. Increasing the ionic strength reduced the ability of saliva to induce emulsion flocculation as shown by the decreased floc size and the effect on the viscosity. Turbidity experiments with varying pH (3-7) and ionic strength also showed decreased complex formation in mixtures between saliva and lysozyme in solution upon NaCl addition up to 200 mM. Decreasing the pH increased the turbidity, in line with the increase of the positive net charge on the lysozyme molecule. We conclude that electrostatic attraction is the main driving force for complex formation between saliva components and lysozyme adsorbed at the oil droplets and in solution.     

Determination of preferential interaction parameters by multicomponent diffusion. applications to poly(ethylene glycol)-salt-water ternary mixtures

Poly(ethylene glycol) (PEG) is a hydrophilic nonionic polymer used in many biochemical and pharmaceutical applications. We report the four diffusion coefficients for the PEG-KCl-water ternary system at 25 degrees C using precision Rayleigh interferometry. Here, the molecular weight of PEG is 20 kg mol(-1), which is comparable to that of proteins. The four diffusion coefficients are examined and used to determine thermodynamic preferential interaction coefficients. We find that the PEG preferential hydration in the presence of KCl is 1 order of magnitude larger than that previously obtained under the same conditions for lysozyme, a protein of similar molecular weight. In correspondence, the coupled diffusion in the PEG case was greater than that observed in the lysozyme case. We attribute this difference to the greater exposure of polymer coils to the surrounding fluid compared to that of globular compact proteins. Moreover, we observe that the PEG preferential hydration significantly decreases as salt concentration increases and attribute this behavior to the polymer collapse. Finally, we have also employed the equilibrium isopiestic method to validate the accuracy of the preferential interaction coefficients extracted from the diffusion coefficients. This experimental comparison represents an important contribution to the relation between diffusion and equilibrium thermodynamics.     

Linear Poly(methyl glycerol) and Linear Polyglycerol as Potent Protein and Cell Resistant Alternatives to Poly(ethylene glycol)

The nonspecific interaction of proteins with surfaces in contact with biofluids leads to adverse problems and is prevented by a biocompatible surface coating. The current benchmark material among such coatings is poly(ethylene glycol) (PEG). Herein, we report on the synthesis of linear polyglycerol derivatives as promising alternatives to PEG. Therefore, gold surfaces as a model system are functionalized with a self‐assembled monolayer (SAM) by a two‐step anhydride coupling and a direct thiol immobilization of linear poly(methyl glycerol) and polyglycerol. Surface plasmon resonance (SPR) spectroscopy reveals both types of functionalized surfaces to be as resistant as PEG towards the adsorption of the test proteins fibrinogen, pepsin, albumin, and lysozyme. Moreover, linear polyglycerols adsorb even less proteins from human plasma than a PEG‐modified surface. Additional cell adhesion experiments on linear poly(methyl glycerol) and polyglycerol‐modified surfaces show comparable cell resistance as for a PEG‐modified surface. Also, in the case of long‐term stability, high cell resistance is observed for all samples in medium. Additional in vitro cell‐toxicity tests add to the argument that linear poly(methyl glycerol) and polyglycerol are strong candidates for promising alternatives to PEG, which can easily be modified for biocompatible functionalization of other surfaces.     

Probing protein stabilization by glycerol using electrospray mass spectrometry

This study shows that electrospray ionization mass spectrometry (ESI-MS), combined with a heated turbo ion-spray interface, allows monitoring protein stabilization by glycerol in solution. Measurements obtained with the two proteins lysozyme and cytochrome c are presented. The observed mass-to-charge (m/z) distributions reveal the stabilizing effect of the additive on the protein conformations against temperature and acid-induced unfolding, as well as against denaturation by acetonitrile. The data obtained with lysozyme allow detection of minor conformational changes upon glycerol addition to the native protein, and suggest that the protein structure in the presence of the additive is slightly compressed compared with its state in water. This result corroborates previous evidence obtained by nuclear magnetic resonance. It is also shown that analysis of the m/z distributions obtained by ESI-MS can lead to detection of partially folded and partially populated states in protein samples.     

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: theory and experiments

Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluid-solid transition and the gas-liquid coexistence curve (binodal) shift to lower temperatures and the gap between them increases. The experimentally observed trends are consistent with our theoretical predictions based on the thermodynamic perturbation theory and the Derjaguin-Landau-Verwey-Overbeek model for the lysozyme-lysozyme pair interactions. The values of the parameters describing the interactions, namely the refractive indices, dielectric constants, Hamaker constant and cut-off length, are extracted from literature or are experimentally determined by independent experiments, including static light scattering, to determine the second virial coefficient. We observe that both, glycerol and DMSO, render the potential more repulsive, while sodium chloride reduces the repulsion.     

Noncovalent polymerization of mesogens crystallizes lysozyme: correlation between nonamphiphilic lyotropic liquid crystal phase and protein crystal formation

Crystallization of proteins is important for fundamental studies and biopharmaceutical development but remains largely an empirical science. Here, we report the use of organic salts that can form a class of unusual nonamphiphilic lyotropic liquid crystals to crystallize the protein lysozyme. Certain nonamphiphilic organic molecules with fused aromatic rings and two charges can assemble into stable thread-like noncovalent polymers that may further form liquid crystal phases in water, traditionally termed chromonic liquid crystals. Using five of these mesogenic molecules as additives to induce protein crystallization, we discover that molecules that can form liquid crystal phases in water are highly effective at inducing the crystal formation of lysozyme, even at concentrations significantly lower than that required for forming liquid crystal phases. This result reveals an example of inducing protein crystallization by the molecular assembly of the additives, and is consistent with a new mechanism by which the strong hydration of an assembly process provides a gradual means to compete for the water molecules to enable solvated proteins to form crystals.     

The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals

We have studied the thermodynamic properties of hen egg white lysozyme crystals using a novel simulation method combining atomistic Monte Carlo simulation to calculate van der Waals interactions and the boundary element method to solve the Poisson-Boltzmann equation for the electrostatic interactions. For computational simplicity, we treat the protein as a rigid body, using the crystallographic coordinates of all non-hydrogen atoms of the protein to describe the detailed shape. NVT Monte Carlo simulations are carried out for tetragonal and orthorhombic crystals to obtain the van der Waals energy, incorporating an implicit solvation effect. For crystal phases, an optimally linearized Poisson-Boltzmann equation is used to include the effect of the Donnan equilibrium of the salt ions. The Helmholtz energy is obtained from expanded ensemble Monte Carlo simulations. By using the force field parameters that had previously been tuned for the solution properties, reasonable agreement with experiment is found for the crystallization energy of the tetragonal form. The prediction of the entropy is also reasonable with a slight underestimation suggesting the release of a few water molecules per protein during the crystallization. However, the predictions of the properties of the orthorhombic crystal are poor, probably due to differences in the solvation structure as indicated by experiments, and also as a result of the approximate force field used.     

Alginate Bioconjugate and Graphene Oxide in Multifunctional Hydrogels for Versatile Biomedical Applications

In this work, we combined electrically-conductive graphene oxide and a sodium alginate-caffeic acid conjugate, acting as a functional element, in an acrylate hydrogel network to obtain multifunctional materials designed to perform multiple tasks in biomedical research. The hybrid material was found to be well tolerated by human fibroblast lung cells (MRC-5) (viability higher than 94%) and able to modify its swelling properties upon application of an external electric field. Release experiments performed using lysozyme as the model drug, showed a pH and electro-responsive behavior, with higher release amounts and rated in physiological vs. acidic pH. Finally, the retainment of the antioxidant properties of caffeic acid upon conjugation and polymerization processes (Trolox equivalent antioxidant capacity values of 1.77 and 1.48, respectively) was used to quench the effect of hydrogen peroxide in a hydrogel-assisted lysozyme crystallization procedure.     

醇类低温保护剂对NaCl水溶液共晶的影响

为了研究低温保护剂对盐水溶液共晶的影响, 利用差示扫描量热法(DSC)对添加不同浓度的甘油、乙二醇、1, 2-丙二醇、1, 3-丙二醇和二甲基亚砜的NaCl 水溶液的共晶现象进行了研究. 发现NaCl 水溶液共晶是一个过冷随机过程,醇类和二甲基亚砜对之有抑制作用.保护剂浓度越高,共晶焓越小, 对共晶的抑制作用越大. 其中4种醇类保护剂的抑制能力从强到弱依次是甘油、乙二醇、1, 2-丙二醇和1, 3-丙二醇.其抑制能力的强弱主要由分子量/羟基数的比值决定, 其次受甲基影响. 二甲基亚砜抑制共晶的能力与乙二醇的接近. 研究发现升温过程中,三元溶液发生共晶体的玻璃化现象和反玻璃化现象.