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.     

Surface Adsorption and Photo-Reactivity of Sulfonylurea Herbicides

Photodegradation of two sulfonylurea herbicides, triasulfuron and thifensulfuron-methyl adsorbed on Preveza or Nea Malgara soils (Greece) was studied in outdoor and laboratory experiments. Herbicides on adsorbed phase and kept in the dark were characterised by a high reactivity, giving depletion curves that can be all described by a first order equation. In the irradiation experiments the kinetic behaviour of photodegradation was complex and characterised by a double step photoreaction. After a first period varying from 8 to 24 h the rate of reaction was reduced to 7-31% of the initial rate. The kinetic constant related to the degradation of triasulfuron practically showed the same values of those obtained for thifensulfuron-methyl. The half-lives obtained on Nea Malgara soil were generally higher than those obtained using Preveza soil. The observed behaviour is explained considering the photochemical properties of the herbicides, and the organic matter content of the soils.     

溶菌酶在裸金电极和疏基乙酸或正十二疏烷基醇修饰电极上的吸附

电化学石英晶体阻抗系统;疏基乙酸;溶菌酶在裸金电极和疏基乙酸或正十二疏烷基醇修饰电极上的吸附     

Study of Growth Mechanism of Lysozyme Crystal by Batch Crystallization Method

Space environment is regarded as the perfect environment for the production of higher quality protein crystals since the sedimentation movement and convective flow due to the gravity is negligible under the microgravity condition of space environment. A n…     

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.     

大肠杆菌在直流电场刺激作用下的生长机理研究

以钛网电极和铂网电极对培养瓶中大肠杆菌生长过程进行加电刺激,考察其在直流电场作用下的生长情况,并结合盐桥、循环伏安扫描、恒电流等技术对电场作用机理进行研究。结果表明,在电流密度为0.2275mA/cm2时,直流电场能有效促进大肠杆菌的生长,且随着电流密度的增大,菌体的生长速度逐步加快;当使用盐桥屏蔽电极反应产物时,单纯的离子电流对细胞的生长没有显著影响,水的阴极电解产物是促进微生物生长的主要因素。通过对析氢活性不同的铂网电极与钛网电极加相同电流密度0.0455mA/cm2的电场后,起促进生长作用的主要是阴极电解产物吸附氢和氢气,其中对摇瓶培养的细菌氢气的促进作用显著。     

复合氧化物LaMn1-xFexO3(x=0-1)的XPS研究

用XPS方法研究了具有ABO3结构的LaMn1-xFexO3（x＝0－1）氧化物的氧化还原性能、表面组成和吸附氧种．样品经还原和再氧化处理后，Mn2p和Fe2p结合能的变化对Fe和Mn之间发生的氧化还原提供了明显的证据．可表示如下：Me4＋＋Fe（3－δ）→Mn（4－δ）＋＋Fe3＋通过计算机用三种氧物种（OⅠ，OⅡ和OⅢ）对O1s峰进行拟合，确定了每种氧物种的状态．同时，以氧物种含量随还原、再氧化的变化，确定了发生在表面上的氧化还原反应同OⅠ和OⅡ吸附氧物种有关．在此基础上，对吸附位与氧之间的电子转移过程进行了讨论．     

Surface interrogation mode of scanning electrochemical microscopy for oxidation study of adsorbed CO generated from serine on platinum

We report a new method for detection and oxidation of adsorbed carbon monoxide(CO_（ads）) generated from serine on a polycrystalline platinum ultramicroelectrode（UME） by bromine（Br₂） using in situ surface interrogation（SI） mode of scanning electrochemical microscopy（SECM）.In the SI mode,tip and substrate are both Pt UMEs,and CO_（ads） on Pt substrate,generated from serine,can be oxidized by the tip-generated Br₂ giving a positive response.Dosing CO_（ads） from serine instead of purging CO gas expands the newly introduced reaction of Br₂ with CO_（ads） and further enhances the hope to get rid of CO_（ads） on Pt for fuel cells.     

Adsorbate-substrate interaction between chlorodifluoromethane and titanium dioxide: Infrared spectroscopy and density functional theory studies

Infrared spectra of chlorodifluoromethane (CHClF₂) adsorbed on titanium dioxide (TiO₂) at room temperature have been investigated for the first time. From the comparison between the adsorption characteristics and the gas-phase spectra it can be deduced that the molecule interacts with the surface Lewis acid site (Ti⁴⁺) mainly through the Cl atom even if also the adsorption with one F atom is also observed. Moreover, the spectra show the presence of H-bonds between the CH group and the surface Lewis basic site (OH⁻ or O²⁻). In order to obtain more information on the molecule orientation and the variation of the structural parameters, a DFT-B3LYP study has been carried out considering the anatase (1 0 1) surface and evaluating the adsorption energetics in terms of interaction, distortion and binding energies. The obtained geometries confirm that both the acid-base interactions through Cl or F atoms are possible and suggest the formation of one H-bond between the CH group of the molecule and the Lewis basic site of the surface. The calculated vibrational frequencies of the adsorbed molecule have been found to be in reasonable agreement with the experimental data.     

等转化率法分析溶菌酶在添加剂影响下的热变性行为

利用差示扫描量热法(DSC)研究了溶菌酶在不同浓度的添加剂(蔗糖、葡萄糖、果糖、甘露醇)和不同浓度的磷酸盐缓冲液影响下的热变性过程,并用等转化率法对该过程进行了分析.变性温度Tm随扫描速率和添加剂浓度的增加而提高,随磷酸盐缓冲液浓度的增加而降低.磷酸盐加速了溶菌酶的变性过程,降低了溶菌酶的热稳定性,而添加剂则增强了溶菌酶的热稳定性.在添加剂存在的条件下,溶菌酶变性过程部分为聚集不可逆过程,部分则可逆.等转化率法表明溶菌酶在所有条件下,其表观活化能在不同的转化率下并未保持不变,而是随转化率增大而减小,说明了一个简单的反应机理并不能用来描述溶菌酶的变性过程,其过程并不是标准两态可逆过程,而是一个涉及多种蛋白质状态的复杂过程.