Molecular Dynamics Simulation of Ester‐Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure

The three‐dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester‐linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester‐linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains.     

Elucidation of Metal‐Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing RhIII Ions as the Model Surfaces

Metal‐ion accumulation on protein surfaces is a crucial step in the initiation of small‐metal clusters and the formation of inorganic materials in nature. This event is expected to control the nucleation, growth, and position of the materials. There remain many unknowns, as to how proteins affect the initial process at the atomic level, although multistep assembly processes of the materials formation by both native and model systems have been clarified at the macroscopic level. Herein the cooperative effects of amino acids and hydrogen bonds promoting metal accumulation reactions are clarified by using porous hen egg white lysozyme (HEWL) crystals containing Rh^III ions, as model protein surfaces for the reactions. The experimental results reveal noteworthy implications for initiation of metal accumulation, which involve highly cooperative dynamics of amino acids and hydrogen bonds: i) Disruption of hydrogen bonds can induce conformational changes of amino‐acid residues to capture Rh^III ions. ii) Water molecules pre‐organized by hydrogen bonds can stabilize Rh^III coordination as aqua ligands. iii) Water molecules participating in hydrogen bonds with amino‐acid residues can be replaced by Rh^III ions to form polynuclear structures with the residues. iv) Rh^III aqua complexes are retained on amino‐acid residues through stabilizing hydrogen bonds even at low pH (≈2). These metal–protein interactions including hydrogen bonds may promote native metal accumulation reactions and also may be useful in the preparation of new inorganic materials that incorporate proteins.     

Inhibitory effect of safranal and crocin,two principle compounds of <Emphasis Type="Italic">Crocus sativus</Emphasis>, on fibrillation of lysozyme

A key feature in more than twenty amyloid-related diseases is the aggregation of intra-and/or extracellular misfolded proteins as amyloid fibrils. Therefore, preventing or reversing amyloid aggregation by using of small molecules is considered as useful approaches to the treatment of these diseases. We have evaluated the ability of safranal and crocin, to inhibit amyloid self-assembly of hen egg white lysozyme (HEWL), as an in vitro model system. Structural properties of HEWL in the presence of these compounds were investigated individually using thioflavin T, anilinonaphthalene-8-sulfonic acid fluorescence assays, far-UV circular dichroism and scanning electron microscopy as well as docking method. Our results showed that incubation of HEWL with either crocin or safranal at various concentrations leads a significant inhibition in the rate of amyloid formation. Docking analysis revealed crocin and safranal interact with the central hydrophobic region of lysozyme through van der Waals interaction. Hydroxyl group in crocin through hydrogen bonds connected to the several hydrophilic amino acids of lysozyme, while in safranal there are just one aldehyde group that through hydrogen bonds connected to aspartic acid in lysozyme. It can be concluded that both hydrophobic and hydrophilic groups contribute to lower lysozyme fibril accumulation.     

Denaturation of hen egg white lysozyme in electromagnetic fields: a molecular dynamics study

Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25-0.5 V Arms-1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500 K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.     

Hen egg white fractionation by ion-exchange chromatography

Major hen egg white proteins have been widely studied for their functional properties but these studies still are unable to explain, alone, all of the biological properties of hen egg white. Hence, it is still interesting to produce pure and non-altered proteins to improve our knowledge on the biological properties of hen egg white. Presently, identification and characterization of both bioactive peptides and minor proteins from hen egg white is essential work for progressing in the understanding of hen egg white biological properties. With this objective in mind, a new process for a complete "mucin free" hen egg white fractionation based on ion exchange chromatography is proposed. "Mucin free" egg white is fractionated into six different fractions. Four of them are high-recovery yield purified fractions of lysozyme, ovotransferrin, ovalbumin and flavoprotein. The two other fractions are enriched in recently detected minor proteins in hen egg white.     

磷酰化对丙氨酸与溶菌酶相互作用的影响

在电喷雾离子阱质谱图中发现丙氨酸不能和溶菌酶形成二聚体, 而磷酰化丙氨酸(DIPP-Ala)能和溶菌酶形成二聚体. 进一步研究发现丙氨酸及其他氨基酸磷酰化后, 自身形成二聚能力大大增强. 在Silicon Graplics图形工作站上采用SYBYL 6.8软件, 利用Tripos力场和分子力学方法研究了DIPP-Ala最低能量构象, 并用分子对接(DOCK)研究了二聚体的形成. 结果说明磷氧双键的存在增强了分子间的相互作用.     

Photo-CIDNP reveals differences in compaction of non-native states of lysozyme

Photo-CIDNP effects interpreted for individual residues are used for the structural characterization of non-native ensembles of proteins, which is described in this paper. Two-dimensional photo-CIDNP experiments are compared to conventional HSQC spectra to elucidate the relative solvent exposure of the six tryptophan residues in non-native states of hen egg white lysozyme. The differential solvent accessibility of the tryptophan residues in non-native lysozyme coincides with the dynamical properties of these residues monitored for both backbone and side chain NH sides obtained from analysis of transverse relaxation measurements. These data can be interpreted in the context of the hydrophobic clustering around the tryptophan residues and is supported by the application of this method to the cluster breaking W62G mutant of lysozyme.     

用蛋白电泳和高效凝胶排阻色谱法分析还原脲变性蛋白溶菌酶稀释复性过程的集聚体

本文利用蛋白电泳和高效凝胶排阻层析法分析了还原脲变性蛋白溶菌酶稀释复性过程中的集聚体。当用复性液稀释复性还原脲变性蛋白溶菌酶时,会迅速产生可观量的沉淀。沉淀和上清液的不连续十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)和高效凝胶排阻层析分析结果表明,还原脲变性蛋白溶菌酶在稀释复性过程中除了能够复性成天然态蛋白溶菌酶分子外,还会形成可溶的蛋白溶菌酶分子二聚体和三聚体,二聚体和三聚体主要是靠分子间二硫键的错配连接而成的;可溶的蛋白溶菌酶分子二聚体之间通过非共价键相互作用而形成集聚体沉淀,而可溶的三聚体溶菌酶分子则仍处于复性液上清液中。     

The Lysozyme Inhibitor Thionine Acetate Is Also an Inhibitor of the Soluble Lytic Transglycosylase Slt35 from Escherichia coli

Lytic transglycosylases such as Slt35 from E. coli are enzymes involved in bacterial cell wall remodelling and recycling, which represent potential targets for novel antibacterial agents. Here, we investigated a series of known glycosidase inhibitors for their ability to inhibit Slt35. While glycosidase inhibitors such as 1-deoxynojirimycin, castanospermine, thiamet G and miglitol had no effect, the phenothiazinium dye thionine acetate was found to be a weak inhibitor. IC₅₀ values and binding constants for thionine acetate were similar for Slt35 and the hen egg white lysozyme. Molecular docking simulations suggest that thionine binds to the active site of both Slt35 and lysozyme, although it does not make direct interactions with the side-chain of the catalytic Asp and Glu residues as might be expected based on other inhibitors. Thionine acetate also increased the potency of the beta-lactam antibiotic ampicillin against a laboratory strain of E. coli.     

Elucidation of Binding Mechanism of Photodynamic Therapeutic Agent Toluidine Blue O with Chicken Egg White Lysozyme by Spectroscopic and Molecular Dynamics Studies

The nature of binding mechanism of toluidine blue O (TBO) with chicken egg white lysozyme was studied comprehensively by various spectroscopic and computational methods. Both steady state and time‐resolved fluorescence studies unambiguously point to the prevalence of static quenching mechanism in lysozyme–TBO system. Thermodynamic parameters revealed that the association of TBO with lysozyme was a spontaneous process in which hydrophobic and hydrogen bond interactions played a pivotal role in the binding process. The secondary and tertiary conformational changes of lysozyme in the presence of TBO were unraveled using absorption, Fourier transform infrared spectroscopy (FT‐IR) and circular dichroism (CD) techniques. Molecular docking studies of lysozyme–TBO system substantiated the findings of site marker experiment and revealed TBO adjacent to Trp‐63 and Trp‐108 residues of lysozyme. Molecular dynamics (MD) simulation studies of lysozyme–TBO system indicate a stable and effective complexation of TBO with lysozyme. It is hoped that the results presented here will enable further understanding of TBO toxicity.     

Porous Protein Crystals as Catalytic Vessels for Organometallic Complexes

Porous protein crystals, which are protein assemblies in the solid state, have been engineered to form catalytic vessels by the incorporation of organometallic complexes. Ruthenium complexes in cross‐linked porous hen egg white lysozyme (HEWL) crystals catalyzed the enantioselective hydrogen‐transfer reduction of acetophenone derivatives. The crystals accelerated the catalytic reaction and gave different enantiomers based on the crystal form (tetragonal or orthorhombic). This method represents a new approach for the construction of bioinorganic catalysts from protein crystals.     

An integrated process for purification of lysozyme, ovalbumin, and ovomucoid from hen egg white

This article describes an integrated process for simultaneous purification of lysozyme, ovalbumin, and ovomucoid from hen egg white. The crude egg white extract was passed through a cation exchanger Streamline trade mark SP and the bound lysozyme was eluted with 5% ammonium carbonate, pH 9.0, containing 1 M NaCl after elution of avidin. This partially purified lysozyme was further purified 639-fold on dye-linked cellulose beads. Ovalbumin and ovomucoid did not bind to Streamline SP. Ovalbumin could be precipitated from this unbound fraction by 5% trichloroacetic acid, and ovomucoid was removed from the supernatant by precipitation with ethanol. The yields of lysozyme, ovomucoid, and ovalbumin were 77, 94, and 98%, respectively. All the purified proteins showed single bands on sodium dodecyl sulfate polyacrylamide gel electrophoresis. All the steps are easily scalable, and the process described here can be used for large-scale simultaneous purification of these proteins in the pure form.     

Enzyme-catalyzed direct three-component aza-Diels-Alder reaction using hen egg white lysozyme

The direct three-component aza-Diels-Alder reaction of aromatic aldehyde, aromatic amine, and 2-cyclohexen-1-one was catalyzed by hen egg white lysozyme for the first time. Under the optimized conditions investigated in this paper, the enzyme-catalyzed aza-Diels-Alder reaction gave yields up to 98% and stereoselectivity of endo/exo ratios up to 90:10.     

盐酸胍诱导的变性卵清溶菌酶分子重折叠过程及其各稳定构象态的分布和过渡

采用变性和非变性电泳、 高效凝胶排阻色谱、 内源荧光发射光谱和荧光相图以及生物活性测定等方法, 研究了盐酸胍诱导的变性卵清溶菌酶分子的重折叠过程及此过程中卵清溶菌酶分子各稳定构象态的分布和过渡. 结果表明, 当复性液中盐酸胍浓度分别约为5.0和2.4 mol/L时, 变性卵清溶菌酶分子的重折叠过程各存在1个稳定折叠中间态, 重折叠过程符合"四态模型". 在卵清溶菌酶分子四态重折叠过程基础上, 结合盐酸胍与卵清溶菌酶分子之间的缔合-解离平衡, 给出了一个定量描述变性剂诱导的蛋白质分子复性过程中蛋白质分子复性率随溶液中变性剂浓度变化的方程. 该方程包含2个特征折叠参数, 一个是蛋白质分子从一个稳定构象态过渡到另一个稳定构象态的热力学过渡平衡常数k; 另一个是在此过程中平均每个蛋白质分子所结合的变性剂分子数目m. 通过这2个特征折叠参数能够定量描述盐酸胍诱导的变性卵清溶菌酶完全去折叠态、 折叠中间态和天然态分子随复性液中盐酸胍浓度变化的分布和过渡情况.     

Hydroxy-Porphyrin as an Effective,Endogenous Molecular Clamp during Early Stages of Amyloid Fibrillization

Amyloid fibril formation of proteins is of great concern in neurodegenerative disease and can be detrimental to the storage and stability of biologics. Recent evidence suggests that insulin fibril formation reduces the efficacy of type II diabetes management and may lead to several complications. To develop anti-amyloidogenic compounds of endogenous origin, we have utilized the hydrogen bond anchoring, π stacking ability of porphyrin, and investigated its role on the inhibition of insulin amyloid formation. We report that hydroxylation and metal removal from the heme moiety yields an excellent inhibitor of insulin fibril formation. Thioflavin T, tyrosine fluorescence, Circular Dichorism (CD) spectroscopy, Field emission scanning electron microscopy (FESEM) and molecular dynamics (MD) simulation studies suggest that hematoporphyrin (HP) having hydrogen bonding ability on both sides is a superior inhibitor compared to hemin and protoporphyrin (PP). Experiments with hen egg white lysozyme (HEWL) amyloid fibril formation also validated the efficacy of endogenous porphyrin based small molecules. Our results will help to decipher a general therapeutic strategy to counter amyloidogenesis.     

非还原脲变性蛋白溶菌酶稀释复性过程中集聚现象的研究

用十二烷基硫酸钠-聚丙烯酰胺凝胶电泳、阴极聚丙烯酰胺凝胶电泳和高效凝胶排阻色谱法, 研究了非还原脲变性蛋白溶菌酶在稀释复性过程中的集聚现象. 实验发现, 在整个稀释复性过程中, 没有蛋白溶菌酶集聚体沉淀产生. 当最终复性液中蛋白溶菌酶浓度小于4.0 mg/mL时, 复性过程中不会形成蛋白溶菌酶分子集聚体; 当最终复性液中蛋白溶菌酶浓度介于4.0～8.0 mg/mL时, 复性过程中会形成由非共价相互作用所引起的蛋白溶菌酶二分子和三分子集聚体; 而当最终复性液中蛋白溶菌酶浓度大于8.0 mg/mL时, 复性过程中除了会形成二分子和三分子蛋白溶菌酶集聚体外, 还会形成四分子蛋白溶菌酶集聚体. 在此基础上, 结合文献, 对非还原脲变性蛋白溶菌酶的稀释复性过程进行了描述.     

Concentration-Dependent Influence of Silver Nanoparticles on Amyloid Fibrillation Kinetics of Hen Egg-White Lysozyme

Understanding the influence of nanoparticles on the formation of protein amyloid fibrillation is crucial to extend their application in related biological diagnosis and nanomedicines. In this work, Raman spectroscopy was used to probe the amyloid fibrillation of hen egg-white lysozyme in the presence of silver nanoparticles (AgNPs) at different concentrations, combined with atomic force microscopy and thioflavin T (ThT) fluorescence assays. Four representative Raman indicators were utilized to monitor transformation of the protein tertiary and secondary structures at the molecular level: the Trp doublet bands at 1340 and 1360 cm^-1, the disulfide stretching vibrational peak at 507 cm^-1, the N-C$\alpha$-C stretching vibration at 933 cm^-1, and the amide Ⅰ band. All experimental results confirmed the concentration-dependent influence of AgNPs on the hen egg-white lysozyme amyloid fibrillation kinetics. In the presence of AgNPs at low concentration (17 μg/mL), electrostatic interaction of the nanoparticles stabilizes disulfide bonds, and protects the Trp residues from exposure to hydrophilic environment, thus leading to formation of amorphous aggregates rather than fibrils. However, with the action of AgNPs at high concentration (1700 μg/mL), the native disulfide bonds of hen egg-white lysozyme are broken to form Ag-S bonds owing to the competition of electrostatic interaction from a great deal of nanoparticles. As for providing functional surfaces for protein to interact with, AgNPs play a bridge role in direct transformation from $\alpha$-helices to organized $\beta$-sheets. The present investigation sheds light on the controversial effects of AgNPs on the kinetics of hen egg-white lysozyme amyloid fibrillation.     

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.     

ESI mass spectrometry and X-ray diffraction studies of adducts between anticancer platinum drugs and hen egg white lysozyme

The interactions of cisplatin and its analogues, transplatin, carboplatin and oxaliplatin, with hen egg white lysozyme were analysed through ESI mass spectrometry, and the resulting metallodrug-protein adducts identified; the X-ray crystal structure of the cisplatin lysozyme derivative, solved at 1.9 A resolution, reveals selective platination of imidazole Nepsilon of His15.     

溶液中金属盐对溶菌酶高级结构的影响

探索蛋白质结构稳定性及其淀粉样纤维化的环境条件具有重要意义.本文采用了荧光光谱法研究溶液中的金属盐对鸡卵清溶菌酶内源荧光和淀粉样纤维化的影响.结果表明,金属盐能够增加溶菌酶的热稳定性,减小淬灭剂对内源荧光的作用,对溶菌酶的高级结构具有一定的稳定作用.另一方面,在长时间热胁迫的情况下,金属盐可促进溶菌酶分子的聚集而纤维化.金属盐的这种双重作用分别与其阳离子和阴离子的性质有关.