Binding structures of tri‐N‐acetyl‐β‐glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

Lysozyme is a well‐studied enzyme that hydrolyzes the β‐(1,4)‐glycosidic linkage of N‐acetyl‐β‐glucosamine (NAG)_n oligomers. The active site of hen egg‐white lysozyme (HEWL) is believed to consist of six subsites, A‐F that can accommodate six sugar residues. We present studies exploring the use of polarizable force fields in conjunction with all‐atom molecular dynamics (MD) simulations to analyze binding structures of complexes of lysozyme and NAG trisaccharide, (NAG)₃. MD trajectories are applied to analyze structures and conformation of the complex as well as protein–ligand interactions, including the hydrogen‐bonding network in the binding pocket. Two binding modes (ABC and BCD) of (NAG)₃ are investigated independently based on a fixed‐charge model and a polarizable model. We also apply molecular mechanics with generalized born and surface area (MM‐GBSA) methods based on MD using both nonpolarizable and polarizable force fields to compute binding free energies. We also study the correlation between root‐mean‐squared deviation and binding free energies of the wildtype and W62Y mutant; we find that for this prototypical system, approaches using the MD trajectories coupled with implicit solvent models are equivalent for polarizable and fixed‐charge models. © 2012 Wiley Periodicals, Inc.     

Modification of polysulfone ultrafiltration membranes with UV irradiation and hydrophilicity increasing agents

Hydrophobic polysulfone UF membranes were modified with UV irradiation and hydrophilicity increasing agents. The modifications were tested with 0.5% whey-protein solution and 0.05% lysozyme solution at pH 6 and with 0.05% bovine serum albumin solution at various pH values. UV irradiation increased flux and the hydrophilicity of the membranes. The flux increases obtained varied with pH and modification agents used and could be more than 400% compared to unmodified conditions without any loss in retention. The best retentions were obtained at pH values, where both the protein and the membrane had the same charge, and a strong electrostatic repulsion was obtained. The pores enlarged to fixed sizes, which depended on the sizes of the proteins and the range of double layer forces between proteins and membranes at different states of charge density.     

A synthetic camel anti-lysozyme peptide antibody (peptibody) with flexible loop structure identified by high-resolution affinity mass spectrometry

We describe the synthesis and characterisation of the fully functional molecular recognition structure of a 26-amino acid residue peptide antibody, referred to as peptibody, designed from a monoclonal single-domain antibody fragment derived from a camel heavy-chain antibody. The CDR3 region (CDR = complementarity determining region) of the cAbLys3 camel antibody fragment, which binds to the active site of hen eggwhite lysozyme (HEL) and acts as a potent enzyme inhibitor by mimicking an oligosaccharide substrate, was prepared by solid-phase peptide synthesis. To obtain a closed loop-like structure resembling that in the crystal structure, N- and C-terminal cysteine residues were added to the linear peptide and oxidised to a cyclic disulfide-bridged peptide by using dimethylsulfoxide. A further, internal cysteine-12 residue was acetamidomethyl-protected to prevent possible oxidative byproducts. Affinity separation on a lysozyme microcolumn combined with MALDI-TOF mass spectrometry revealed that the peptide resumed high affinity to lysozyme only after deprotection of Cys-12, suggesting the importance of this paratope sequence for epitope recognition. The complex of lysozyme and active peptibody was characterised directly by conducting high-resolution ESI-FTICR mass spectrometry, which provided a molecular comparison of affinities for linear and cyclic peptibodies.     

脲和盐酸胍诱导溶菌酶去折叠的荧光相图法研究

用荧光相图法分别研究了脲和盐酸胍诱导卵清溶菌酶去抓叠的过程。当变性体 系中无还原剂2－巯基乙醇存在、脲浓度从0变化至4.0 mol/L（或盐酸胍浓度从0变 化至3.0 mol/L）时,溶菌酶从天然态转变为部分折叠中间态,当脲浓度从4.0 mol/L变化至8.0 mol/L（或盐酸胍浓度从3.0 mol/L变化至6.0 mol/L）时,溶菌 酶从中间态转变为去折叠态,此时该蛋白的变性过程符合“三态模型”。而当变性 体系中有该还原剂存在时,溶菌酶则由天然态直接转变为去折叠态,此时脲诱导该 蛋白去折叠的过程符合曲型的“二态模型”。实难结果表明荧光相图法可以检测蛋 白南去抓叠的中间态。     

Dynamical changes in hydration water accompanying lysozyme thermal denaturation

We study the dynamics of the first hydration shell of lysozyme to determine the role of hydration water that accompanies lysozyme thermal denaturation. We use nuclear magnetic resonance spectroscopy to investigate both the translational and rotational contributions. Data on proton self-diffusion and reorentational correlation time indicate that the kinetics of the lysozyme folding/unfolding process is controlled by the dynamics of the water molecules in the first hydration shell. When the hydration water dynamics change, because of the weakening of the hydrogen bond network, the three-dimensional structure of the lysozyme is lost and denaturation is triggered. Our data indicates that at temperatures above approximately 315 K, water behaves as a simple liquid and is no longer a good solvent.     

可用于色谱固定相的介孔氧化硅球材料的合成

采用非离子型嵌段高分子表面活性剂EO₂₀PO₃₀EO₂₀ (P65)为结构导向剂, 正硅酸乙酯为硅源, 在酸性介质中, 静置法制备了微米级介孔氧化硅球. 通过改变合成温度、反应时间或者无机盐KCl的加入量, 可以调节介孔氧化硅球的直径(9.0～17.6 μm); 加入1,3,5-三甲苯(TMB)或者调节水热温度, 可以调节介孔氧化硅球的孔径(2.3～4.8 nm). 采用X射线衍射(XRD)、N₂吸附-脱附、扫描电镜(SEM)、激光散射粒度分布和对溶菌酶的吸附等方法, 对介孔氧化硅球的结构、孔性质、形貌、吸附性质等进行了表征. 实验发现, 孔径较小的介孔氧化硅球(≤4.3 nm)对溶菌酶的吸附不明显(≤42 mg/g), 而孔径(4.8 nm)大于溶菌酶直径的材料对溶菌酶有较大的吸附量(192 mg/g), 说明孔径均匀可调的介孔氧化硅球材料可以很好地用作体积排阻色谱柱的固定相.     

Adhesion of protein crystals: Measurement of the detachment force

The degree of adhesion of protein crystals, heterogeneously nucleated and grown on different supports (e.g. glass plates and plates coated with poly‐L‐lysine, hexamethyl‐disilazane and silicon) is measured directly with a purposely‐developed technique. The sticking force crystal/support is determined by means of a flexible glass fibre, which bending is calibrated by means of series of weights. In this way an elastic constant, specific for each glass fiber is determined individually. Appropriate glass fibres with relative bending less than 10% (Hook's law) are used. The force which is necessary to be exerted, by means of a micro‐manipulator, in order to detach the crystal from the support is taken as a quantitative measure for the adhesion strength. Forces between 10 N cm^‐2 and 1 N cm^‐2 for differently oriented tetragonal hen‐egg‐white lysozyme and cubic ferritin crystals, and 0.1 N cm^‐2 for rhombohedral (porcine) insulin and orthorhombic trypsin crystals are measured. The tetragonal HEWL and rhombohedral insulin crystals show anisotropy of the adhesion strength. In contrast, the cubic ferritin crystals are isotropic also in this respect. For comparison purposes adhesion measurements are performed with NaCl and sugar crystals. An attempt is made to evaluate also the adhesion energy of the protein crystals. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

溶菌酶晶体生长前期溶液中聚集体研究

用动态光散射法研究了不同浓度NaCl对溶菌酶晶体生长前期溶液中聚集体状态的影响,并将这些溶液中的聚集体吸附到硅片表面,用原子力显微镜进行了观察.结果表明,在NaCl浓度为0～0.5 mol·L^-1时,随着NaCl浓度的升高,溶液中大的聚集体逐渐消失,直至基本上只存在几纳米大小的聚集体.测量了相应条件下溶液的Zeta电势值以说明NaCl与溶菌酶之间的相互作用的变化情况.本文从溶液中无序聚集体的角度出发提出了判断晶体能否生长的一个可能的标准,并对动态光散射与原子力显微镜的结果进行了对比和分析.     

聚乙烯醇与溶菌酶的相互作用及其对溶菌酶构象的影响

在生理条件下, 使用凝胶过滤色谱、荧光光谱法、差示扫描量热分析和傅里叶变换红外光谱法(FT-IR)研究了溶菌酶与聚乙烯醇(PVA)的相互作用. 结果表明PVA与溶菌酶结合形成复合物, 在它们的相互作用过程中, 溶菌酶酪氨酸的发射荧光部分被猝灭, 但是, 相互作用并没有改变酪氨酸的微环境; 差示扫描量热分析结果表明, 溶菌酶与PVA之间的相互作用没有破坏溶菌酶的高级结构; 进一步使用红外光谱法结合可增强分辨率的傅里叶去卷积技术和高斯曲线拟合技术共同用于对溶菌酶与PVA复合物冻干粉中溶菌酶酰胺I带的定量分析, 发现冻干粉溶菌酶分子中与分子间相互作用相关的β-折叠组分含量减少了, 但是, 用于衡量冻干状态蛋白质结构完整性的α-螺旋组分含量没有降低. 活性分析结果进一步确认, PVA与溶菌酶的相互作用没有破坏溶菌酶的三级结构.