Preparation of oriented β‐form poly(L‐lactic acid) by solid‐state extrusion

Melt‐crystallized, low molecular weight poly(L ‐lactic acid) (PLLA) consisting of α crystals was uniaxially drawn by solid‐state extrusion at an extrusion temperature (T_ext) of 130–170 °C. A series of extrusion‐drawn samples were prepared at an optimum T_ext value of 170 °C, slightly below the melting temperature (T_m) of α crystals (～180 °C). The drawn products were characterized by deformation flow profiles, differential scanning calorimetry (DSC) melting thermograms, wide‐angle X‐ray scattering (WAXD), and small‐angle X‐ray scattering as a function of the extrusion draw ratio (EDR). The deformation mode in the solid‐state extrusion of semicrystalline PLLA was more variable and complex than that in the extensional deformation expected in tensile drawing, which generally gave a mixture of α and β crystals. The deformation profile was extensional at a low EDR and transformed to a parabolic shear pattern at a higher EDR. At a given EDR, the central portion of an extrudate showed extensional deformation and the shear component became progressively more significant, moving from the center to the surface region. The WAXD intensities of the (0010)_α and (003)_β reflections on the meridian as well as the DSC melting thermograms showed that the crystal transformation from the initial α form to the oriented β form proceeded rapidly with increasing EDR at an EDR greater than 4. Furthermore, WAXD showed that the crystal transformation proceeded slightly more rapidly at the sheath region than at the core region. This fact, combined with the deformation profiles (shear at the sheath and extensional at the core), indicated that the crystal transformation was promoted by shear deformation under a high pressure rather than by extensional deformation. Thus, a highly oriented rod consisting of only β crystals was obtained by solid‐state extrusion of melt‐crystallized, low molecular weight PLLA slightly below T_m. The structure and properties of the α‐ and β‐form crystals were also studied. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 95–104, 2002     

Specific empirical free energy function for automated docking of carbohydrates to proteins

We present an automated docking protocol specifically optimized to predict the structure and affinity of a protein-carbohydrate complex. A scoring function was developed based on a training set of 30 protein-carbohydrate complexes of known structure and affinity. Combinations of several models for hydrogen bonding, torsional entropy loss, and solvation were tested for their ability to fit the training set data, and the best model was used with AutoDock. The electrostatic empirical coefficient is larger than in a previously obtained model using a training set comprised of various types of protein-ligand complexes, indicating that electrostatic interactions play a more important role in determining the affinity between a carbohydrate and a protein. The differences in the relative weighting of the empirical coefficients in the model yields predicted free energies for the training set with a standard error of 1.403 kcal/mol. The new scoring function was tested on 17 Aspergillus niger glucoamylase inhibitors for which binding energies had been determined experimentally. Free energies of complex formation were predicted with a residual standard error of 1.101 kcal/mol. The new scoring function therefore provides a robust method for predicting free energies of formation and optimal conformations of carbohydrate-protein complexes.     

α-glucosidase inhibitory,antioxidant activity,and GC/MS analysis of Descurainia sophia methanolic extract: In vitro,in vivo,and in silico studies

Due to the presence of various phenolic compounds in D.sophia, this plant may have an inhibitory effect on α-Glc and ultimately diabetes control. Therefore, this work aims to scrutinize total phenolic, flavonoid contents, antioxidant capacity, and α-Glc inhibitory activity in aerial parts of methanolic D.sophia extract. The methanolic flower extracts were selected from among aerial parts for the experimental study of anti-diabetic effects by α-Glc inhibitory assays. The flower extracts were also studied by GC/MS to detect the compounds. The total phenolic and flavonoid contents were 21.38 ± 0.93 GAE/g and 96.2 ± 0.20 QE/g, respectively. The IC₅₀ value of flower extract for α-Glc inhibition with mixed (Competitive/non-competitive) mode was found to be 20.34 ± 0.11 mg/ml. Furthermore, in-vivo studies showed that the blood glucose level reduced after consumption of flower extract compared to the control group. Twenty-one compounds were identified by GC/MS technique. These compounds were assessed for high docking scores against α-Glc in silico. Docking score calculations exhibited that the DES-α-Glc complex had a significantly higher binding energy (-6.13 Kcal/mol) than other compounds. The DES-α-Glc complex which displayed a higher docking energy value than the ACR was subjected to MDs studies. The findings of this study suggest that the flower extract of D.sophia can be used as a suitable additive in syrups or foods with anti-diabetic capacity.     

The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase

This paper describes the application of PRO_–LEADS to the flexible docking of ligands into crystallographically derived enzyme structures that are assumed to be rigid. PRO_–LEADS uses a Tabu search methodology to perform the flexible search and an empirically derived estimate of the binding affinity to drive the docking process. The paper tests the extent to which the assumption of a rigid enzyme compromises the accuracy of the results. All-pairs docking experiments are performed for three enzymes (thrombin, thermolysin and influenza virus neuraminidase) based on six or more ligand-enzyme crystal structures for each enzyme. In 76% of the cases, PRO_–LEADS can successfully identify the correct ligand conformation as the lowest energy configuration when the enzyme structure is derived from that ligand's crystal structure, but the methodology only docks 49% of the cases successfully when the ligand is docked against enzyme crystal structures derived from other ligands. Small movements in the enzyme structure lead to an under-prediction in the energy of the correct binding mode by up to 14 kJ/mol and in some cases this under-prediction can lead to the native mode not being recognised as the lowest energy solution. The type of movements responsible for mis-docking are: the movement of sidechains as a result of changes in C position; the movement of sidechains without changes in C position; the movement of flexible portions of main chains to facilitate the formation of hydrogen bonds; and the movement of metal atoms bound to the enzyme active site. The work illustrates that the assumption of a rigid active site can lead to errors in identification of the correct binding mode and the assessment of binding affinity, even for enzymes which show relatively small shift in atomic positions from one ligand to the next. A good docking code, such as PRO_–LEADS, can usually dock successfully if there is induced fit in relatively rigid enzymes but there remains the need to develop improved strategies for dealing with enzyme flexibility. The work implies that treatments of enzyme flexibility which focus only on sidechain rotations will not deal with the critical shifts responsible for mis-docking of ligands in thrombin, thermolysin and neuraminidase. The paper demonstrates the utility of all pairs docking experiments as a method of assessing the effectiveness of docking methodologies in dealing with enzyme flexibility.     

Extrudate swell and flow analysis of polystyrene melt flowing in an electro‐magnetized die in a single screw extruder

An electro‐magnetized capillary die via a parallel co‐extrusion technique was used to study the changes in the overall and radial extrudate swell ratio of polystyrene (PS) melt flowing in a single screw extruder. The effects of magnetic flux density, wall shear rate (screw rotating speed) and die temperature were studied. The results suggested that, in the case of non‐magnetic die the average overall swell ratio of the melt ranged from 1.25 to 1.55. The swelling ratio increased with increasing wall shear rate up to 8.5 sec^?1 and then decreased at 17.1 sec^?1. Increasing die temperature caused a reduction of extrudate swell ratio. The changes in extrudate swell ratio can be explained using the simultaneously measured velocity profiles during the flow in the die, and the swell ratio decreased with increasing radial position. Melt contraction of the melt layer near the die wall was observed. The die temperature was found to have no effect on the change of the radial extrudate swell profiles. When an electro‐magnetized die was used, the average overall swell ratio was found to increase with increasing magnetic flux density to a maximum value and then decreased at higher flux densities. The magnetic flux density of the maximum swell was changed by the wall shear rate. It was associated with a balance of elastic and magnetic energies during the flow. The magnetic energy was thought to have a pronounced effect on the swell ratio at low shear rate and low die temperature. Considering the radial position, the highest swell ratio occurred at the duct center, in the range 2.4–3.3. There was no extrudate contraction of the melt layer near the die wall. Copyright © 2005 John Wiley & Sons, Ltd.     

基于分子对接的苯丙素甙（PPGs）类化合物的虚拟筛选和合理设计

采用虚拟化合物生成法对抗肿瘤的苯丙素甙(PPGs)类化合物进行了配体受体对 接研究。以三种不同的骨架结构为基础分别生成了五十个虚拟苯丙素甙(PPGs)类化 合物，并将它们与端粒DNA受体进行分子对接，分析已知结构的对接结果，通过虚 拟筛选的方法得到了一批与受体相互作用能较高并且复合物能量较低的新的有潜力 的活性化合物。该方法可以弥补分子对接研究中，只能计算药物与受体的相互作用 ，无法有效设计新化合物的不足。这种方法在基于结构的药物分子设计中具有重要 的意义。     

Mechanisms behind concentration profiles illustrated by charge and concentration distributions around ions in double layers

The mechanisms behind the behaviour of concentration and charge density profiles in diffuse electric double layers are investigated quantitatively for 1:1 and 2:2 electrolytes. This is done by analysing various contributions to the mean force that acts on each ion. The forces are obtained from the calculated ionic charge and concentration distributions around individual ions at various positions in the double layer. These distributions are presented graphically which allows an immediate visual illustration of the mechanisms in action. Some features studied are charge inversion in double layers for divalent aqueous electrolytes, overcompensation of surface charge due to large amounts of physisorbed counterions, ion size effects in the double layer structure and various mechanisms that cause deviations from the predictions of the Poisson–Boltzmann approximation. A major objective of the paper is to present the results in a visual form and explain aspects of modern double layer theory in a simple manner.     

Water‐Soluble Molecular Capsules: Self‐Assembly and Binding Properties

The self‐assembly and characterization of water‐soluble calix[4]arene‐based molecular capsules ( 1?2 ) is reported. The assemblies are the result of ionic interactions between negatively charged calix[4]arenes 1 a and 1 b , functionalized at the upper rim with amino acid moieties, and a positively charged tetraamidiniumcalix[4]arene 2 . The formation of the molecular capsules is studied by ¹H NMR spectroscopy, ESI mass spectrometry (ESI‐MS), and isothermal titration calorimetry (ITC). A molecular docking protocol was used to identify potential guest molecules for the self‐assembled capsule 1 a?2 . Experimental guest encapsulation studies indicate that capsule 1 a?2 is an effective host for both charged (N‐methylquinuclidinium cation) and neutral molecules (6‐amino‐2‐methylquinoline) in water.     

A Simulation on the Complexation of Cyclodextrins with Phospholipid Headgroups

The inclusion complexes of α-, β- and γ-cyclodextrin (CD) with three isolated phospholipid (PI – phosphatidylinositol; PS – phosphatidylserine; and PE – phosphatidylethanolamine) headgroups were studied using a flexible docking algorithm FDOCK based on molecular mechanics (CFF91 force filed). In the three phospholipid headgroups, PI headgroup exhibits the strongest affinity for CD, and the affinity of PS headgroup is greater than that of PE headgroup. By investigating the energy distribution and the complex structure in the inclusion procedure, it can be found that the van der Waals force is the main driving force responsible for the complexation. For the α-CD complex of PI headgroup, more than one inclusion complex should coexist due to the steric hindrance, which is reasonably consistent with the experimental results. Furthermore, analyses of the complex of PS and PE headgroup with α-CD also show that two or three possible complexes may appear in the inclusion process, and the complex structure with full inclusion is of the lowest energy and should be the most stable structure in the mixture. For β-␣and γ-CD, the energies of the most stable complexes structures for the three phospholipids headgroups were also discussed.