NMR-STUDIES ON THE COORDINATION OF RARE-EARTHS WITH GLYCYL-DL-VALINE AND THE CONFORMATION OF THEIR COMPLEX IN AQUEOUS-SOLUTION

In this paper lanthanide-induced shifts have been measured for C-13 and H-1 nuclei of glycyl-DL-valine in the presence of three lanthanide cations (La3+, Ho3+ and Yb3+) in aqueous solution. The stability constants of the coordination compounds of rare earths (Ho, Yb) with glycyl-DL-valine have been calculated. The coordination of rare earths with the ligand has been discussed. The simulation for conformation of lanthanide coordination compounds with glycyl-DL-valine shows that the ligand is coordinated to lanthanide ion through oxygen atoms of carboxyl group and the bond length of Ln-O is 0.226 nm. In the coordination compounds glycyl-DL-valine is in extended state with minimal steric hindrance.

CONFORMATION OF PHENYL RINGS IN THE HELICAL CHAIN POLYMER POLY(TRIPHENYLMETHYL METHACRYLATE)

The conformation of phenyl rings in the side groups of the helical chain polymer poly(tripenyl-methyl methacrylate) (1) in solution was studied by spectroscopic methods. According to the Raman spectrum the phenyl rings of 1 and triphenylmethyl methacrylate in solution have the same depolarization ratio at 1002 cm-1. The electronic spectra (ultraviolet and fluorescence) of 1 are similar to those of model substances, except for the "red shift" of the spectra of about 5 nm. It was concluded that the phenyl rings can rotate around the phenyl-C bond.

Numerical Analysis on Intermittent Flow in a Longitudinal Section of Bingham Fluid along a Slope

The transition process of intermittent flow in a longitudinal section of Bingham fluid from initial distribution to fully developed state was numerically investigated in this paper. The influences of slope dimensionless runoff Q* and viscosity μ0* on the dimensionless surge speed U* were also presented in a wide range of parameters. By one typical example, the intermittent flow possessed wave characteristics and showed a supercritical flow conformation for a fully developed flow. The distributions of gravity and bed drag along the flow path and the velocity distribution of flow field were also analyzed.

Forced Dissociation of Selectin-ligand Complexes Using Steered Molecular Dynamics Simulation

Selectin-ligand interactions are crucial to such biological processes as inflammatory cascade or tumor metastasis. How transient formation and dissociation of selectin-ligand bonds in blood flow are coupled to molecular conformation at atomic level, however, has not been well understood. In this study, steered molecular dynamics (SMD) simulations were used to elucidate the intramolecular and intermolecular conformational evolutions involved in forced dissociation of three selectin-ligand systems: the construct consisting of P-selectin lectin (Lec) and epidermal growth factor (EGF)-like domains (P-LE) interacting with synthesized sulfoglycopeptide or SGP-3, P-LE with sialyl Lewis X (sLeX), and E-LE with sLeX. SMD simulations were based on newly built-up force field parameters including carbohydrate units and sulfated tyrosine(s) using an analogy approach. The simulations demonstrated that the complex dissociation was coupled to the molecular extension. While the intramolecular unraveling in P-LESGP-3 system mainly resulted from the destroy of the two anti-parallel sheets of EGF domain and the breakage of hydrogen-bond cluster at the Lec-EGF interface, the intermolecular dissociation was mainly determined by separation of fucose (FUC) from Ca2+ ion in all three systems. Conformational changes during forced dissociations depended on pulling velocities and forces, as well as on how the force was applied. This work provides an insight into better understanding of conformational changes and adhesive functionality of selectin-ligand interactions under external forces.

Simulated pathogenic conformational switch regions matched well with the biochemical findings

Pathogenic conformational conversion is a general causation of many disease, such as transmissible spon- giform encephalopathy (TSE) caused by misfolding of prion, sickle cell anemia, and etc. In such structural changes, misfolding occurs in regions important for the stability of native structure firstly. This destabi- lizes the normal conformation and leads to subsequent errors in folding pathway. Sites involved in the first stage can be deemed switch regions of the protein, and are vital for conformational conversion. Namely it could be a switch of disease at residue level. Here we report an algorithm that can identify such sites computationally with an accuracy of 93%, by calculating the probability of the native structure of a short segment jumping to a mistake one. Knowledge of such switch sites could be used to target clinical therapy, study physiological and pathologic mechanism of protein, and etc.

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

Detection of constitutive heterodimerization of the integrin Mac-1 subunits by fluorescence resonance energy transfer in living cells

Macrophage differentiation antigen associated with complement three receptor function (Mac-1) belongs to beta(2) subfamily of integrins that mediate important cell-cell and cell-extracellular matrix interactions. Biochemical studies have indicated that Mac-1 is a constitutive heterodimer in vitro. Here, we detected the heterodimerization of Mac-1 subunits in living cells by means of two fluorescence resonance energy transfer (FRET) techniques (fluorescence microscopy and fluorescence spectroscopy) and our results demonstrated that there is constitutive heterodimerization of the Mac-1 subunits and this constitutive heterodimerization of the Mac-1 subunits is cell-type independent. Through FRET imaging, we found that heterodimers of Mac-1 mainly localized in plasma membrane, perinuclear, and Golgi area in living cells. Furthermore, through analysis of the estimated physical distances between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) fused to Mac-1 subunits, we suggested that the conformation of Mac-1 subunits is not affected by the fusion of CFP or YFP and inferred that Mac-1 subunits take different conformation when expressed in Chinese hamster ovary (CHO) and human embryonic kidney (HEK) 293T cells, respectively. (c) 2006 Elsevier Inc. All rights reserved.

中国簇毛黄耆亚属的分类修订和系统位置初探

摘要 "簇毛黄耆亚属隶属于豆科黄耆属，主要分布在青藏高原和横断山区，大多数种类都是狭域分布的。由于缺乏野外工作，标本不够丰富，模式标本不易收集齐全等原因，相当一部分种类的划分尚不能令人满意，应予以修订。除此之外，这个亚属的范围及其系统位置也存在一定的争议，还有待于深入的研究。本文对我国簇毛黄耆亚属的种类进行了分类修订，通过形态学和分子系统学两方面的研究，重新界定了该亚属的范围，并对其系统位置进行了探讨。 1. 分类修订 通过查阅文献，标本室研究与野外观察相结合，对簇毛黄耆亚属形态性状的变异式进行了分析，特别调查了性状在居群中的变异幅度。发现茎和花的长短以及果实的形态等是可靠的分类性状。另外，茎和小叶的被毛状况，小叶和小苞片的形状以及花的颜色等对于亚属下种类的划分也有重要的意义。 本文将7种植物从簇毛黄耆亚属中分出，9种处理为异名，确认中国簇毛黄耆亚属植物有23种。多尼尔黄耆是中国分布新记录种，亚东黄耆和单花黄耆都是该种的异名。狭叶黄耆、芒齿黄耆和丽江黄耆是弯齿黄耆的异名，这些种类中存在的分类困难得到了澄清。本文给出了每一个种的形态描述和标本信息以及亚属内的分种检索表。 2. 微形态学 观察了簇毛黄耆亚属植物花柱的发育过程，发现通常使用的术语“柱头具毛”没有准确地描述其中一部分簇毛黄耆的特征。这些植物的毛只是长在花柱的顶端，柱头是光滑无毛的。除毛被直立且向上指外，其它与花粉刷（pollen brush）相关的特征，在这些植物中也出现。所以，这些簇毛黄耆的花柱及其毛被也应该叫做花粉刷。在山羊豆族中，花粉刷正是区分鱼鳔槐亚族的关键特征。因此，这一构造支持将一部分簇毛黄耆从黄耆属（黄耆亚族）中分出，作为一个属放入鱼鳔槐亚族当中。 3. 叶表皮研究 在光学显微镜下观察了代表簇毛黄耆亚属4个组的11种植物的叶表皮。发现所观察种类都具有两种气孔类型，以无规则型为主，放射状细胞型数量很少。 表皮细胞根据细胞轮廊和垂周壁的情况，可以分为三种类型：一是表皮细胞不规则形，垂周壁波状纹或深波状纹，代表为扁荚组植物;二是表皮细胞为多边形，狭长形为主，垂周壁平直，略有浅波状纹，袋果组植物属于这种类型;三是表皮细胞为多边形，垂周壁平直，属于这种类型的有膨果组和背扁组植物。表皮细胞形状对于亚属范围的确定以及亚属下组的划分有一定的意义。 4. 分子系统学 测定了簇毛黄耆亚属植物的ITS序列，并从Genbank中下载了48个种的ITS序列，包括了黄耆属及其临近12个属的代表。以锦鸡儿属（Caragana）为外类群，进行简约性分析，构建簇毛黄耆亚属与其临近类群的系统发育树状图。结果显示，扁荚组与亚属其余类群在系统树上处于不同的分支，亲缘关系较远，表明包括扁荚组的簇毛黄耆亚属不是一个单系类群;膨果组，背扁组和袋果组的代表作为一个单系类群能得到ITS序列的支持，但它们与鱼鳔槐亚族关系更近。这种分支方式能够得到形态证据的支持，说明一部分簇毛黄耆的确与鱼鳔槐亚族有更近的关系，这些种类的分类位置值得重新考虑。"

魔芋葡甘聚糖结构及其应用研究

本文以葡甘聚糖为试材，运用分子模拟同仪器分析相结合的手段，预测了葡甘聚糖分子链的高级结构，分析了无机分子对其结构、性能的影响，探讨了葡甘聚糖与卡拉胶微观作用机理。 主要研究内容与结果如下： 1. 葡甘聚糖单链高级结构的预测 利用Hyperchem7.0、VM2.0分子结构计算软件采用分子动力学和分子力学的方法，以真空中葡甘聚糖单链为研究模型，研究了聚合度、取代基对动态构象的影响及影响链构象的作用力。首次提出了KGM链的动态模型，得到了以下结果：聚合度影响其链形态和稳定性，对于高聚合度的魔芋葡甘聚糖来说，其链呈现无规卷曲状态且稳定性下降，在整个动态运动过程中KGM链脱乙酰基前后都呈现无规卷曲状态，而且其伸展和卷曲的变化是周期性的，表现出了很好的柔性，说明乙酰基不是影响其链形态的主要因素，二面角能和静电作用是真空中影响单链构象的主要的键合作用力和非键合作用力，但是乙酰基对氢键作用的影响较大。 2. 无机分子对葡甘聚糖溶液体系结构性能影响的研究 利用Hyperchem7.0分子结构计算软件，采用分子动力学及红外光谱、核磁共振等技术，对无机分子对葡甘聚糖体系的影响进行分析，很好的解释了性能变化的结构原因，结合以往的研究及参考文献得出以下结论：KGM在碱性条件下由于化学作用乙酰基的脱除分子间氢键作用的加强提高了凝胶强度，分子间氢键的主要作用位点是葡萄糖 的O(6)与甘露糖的O(2)之间;硼与KGM形成的分子内和分子间配合作用及分子间作用力氢键的增强是KGM特性粘度和致密性提高的主要原因，分子间型配位反应发生在葡萄糖和甘露糖两个糖环之间的几率最大;加入尿素后，表现为宏观性能的下降，葡甘聚糖氢键网络被破坏，氢键的作用位点由甘露糖的O(2)、O（3）变为O(4)，葡萄糖的O（3）、O(6)变为O（1）、O（2）。 3. 葡甘聚糖与卡拉胶共混作用的研究 利用Hyperchem7.0分子结构计算软件运用分子动力学方法、DSC、红外光谱技术，研究了葡甘聚糖与卡拉胶的微观结构及作用过程，揭示了性能变化的结构原因和分子之间的作用位点。得出了以下结论：葡甘聚糖同卡拉胶共混后通过分子间氢键作用形成了强度高、弹性好的热可逆凝胶。其凝胶强度与单一胶相比较，凝胶特性得到了很大的改善。通过红外光谱可以发现形成复合溶胶后化学基团没有发生本质上的改变，但是氢键缔合作用增强;通过DSC分析可以发现仅出现1个吸热峰，两种生物大分子达到了相容的结果，经过分子动力学模拟表明，与单一体系比较，葡甘聚糖与卡拉胶共混时稳定性提高，分子间氢键作用力明显增强，主要的作用位点是葡甘聚糖的上甘露糖的O(2)、O(4)、O(6)、乙酰基位置及卡拉胶上糖环上的 O(6)、硫酸基。

Molecular dynamics research of G249 and S249 substitutions of p53 protein.

,The molecular dynamics research of the core domain of p53 protein crystal structure shows that besides the stability in biochemistry this domain also shows a high stability in molecular mechanics. Based on that work, the residue R249 was substituted with amino acids Gly and Ser respectively, and molecular dynamics researches were performed separately. The results show that these substitutions cause a relax tendency between loop2 and 3 domains, leading to an alteration of the whole conformation of p53 core domain and ruining its stability. The results visually explains the mechanism of p53 changes in immunological and biochemical reactions, which are caused by 249 residue substitutions from 3-D structure variations.

Novel cathelicidin-derived antimicrobial peptides from Equus asinus

In the present study, EA-CATH1 and EA-CATH2 were identified from a constructed lung cDNA library of donkey (Equus asinus) as members of cathelicidin-derived antimicrobial peptides, using a nested PCR-based cloning strategy. Composed of 25 and 26 residues, respectively, EA-CATH1 and EA-CATH2 are smaller than most other cathelicidins and have no sequence homology to other cathelicidins identified to date. Chemically synthesized EA-CATH1 exerted potent antimicrobial activity against most of the 32 strains of bacteria and fungi tested, especially the clinically isolated drug-resistant strains, and minimal inhibitory concentration values against Gram-positive bacteria were mostly in the range of 0.3-2.4 mu g center dot mL-1. EA-CATH1 showed an extraordinary serum stability and no haemolytic activity against human erythrocytes in a dose up to 20 mu g center dot mL-1. CD spectra showed that EA-CATH1 mainly adopts an alpha-helical conformation in a 50% trifluoroethanol/water solution, but a random coil in aqueous solution. Scanning electron microscope observations of Staphylococcus aureus (ATCC2592) treated with EA-CATH1 demonstrated that EA-CATH could cause rapid disruption of the bacterial membrane, and in turn lead to cell lysis. This might explain the much faster killing kinetics of EA-CATH1 than conventional antibiotics revealed by killing kinetics data. In the presence of CaCl2, EA-CATH1 exerted haemagglutination activity, which might potentiate an inhibition against the bacterial polyprotein interaction with the host erythrocyte surface, thereby possibly restricting bacterial colonization and spread.