THE STRUCTURAL BASIS OF THE POOR FIBRIN SPECIFICITY OF UROKINASE(Ⅰ)——KNOWLEDGE-BASED PREDICTION OF KRINGLE STRUCTURES OF UROKINASE AND ITS RELATED PROTEINS

The Kringle-1 structure of plasminogen (PGK-1), the Kringle-2 structure of tissue plasminogen activator (PAK-2) and the Kringle structure of prourokinase (UKK) has been modeled on the basis of the three-dimensional structure of Kringle-1 of prothrombin (PTK-1) at 2.8 resolution. The predicted three-dimensional structure of these Kringles shows that the binding site of PGK-1 is characterized by an apparent dipolar site, the polar parts of which are separated by a hydrophobic region. PAK-2 possesses the anionic center but has not a cationic binding center which might be provided by a guanidinium group from Arg-69 located adjacent to the Arg-71 position. UKK possesses neither the anionic binding center nor the cationic center which are probably the main reason for the poor fibrin specificity of urokinase.     

Modeling and simulation of free radical polymerization of styrene under semibatch reactor conditions

The first part of this approach is concerned with the elaboration of a radical polymerization model of styrenne, based on a kinetic diagram that includes chemical and thermal initiation, propagation, termination by recombination and chain transfer to the monomer. Furthermore, volume contraction during polymerization is considered, as well as the gel and glass effects. The mathematical formalism that describes the model in terms of moments is explored in detail. The model was then used to predict the changes in monomer conversion and molecular weight after intermediate addition of initiator and monomer. The results of this operation are dependent on the conditions of the reaction mass, quantity, and moment of substance addition. Therefore, the simulations were performed at different times with respect to the gel effect; before, during and after this phenomenon, and also with respect to different temperatures and initiators. Increasing the initiator concentration before the gel effect leads to an earlier appearance of the phenomenon and to a decrease in molecular weight. The ratio reveals a polydispersity index smaller for the intermediate addition of initiator. No significant changes take place during or after the gel effect. If along with the initiator, unreacted monomver (used to dissolve the initiator) enters the reactor, a small dip in conversion is observed. The general conclusion of this paper reveals the intermediate addition of initiator as a method to control polymer properties and to prevent the “dead-end” polymerization of styrene.     

Molecular modeling of cytochrome P450 3A4

The three-dimensional structure of human cytochrome P450 3A4 was modeled based on crystallographic coordinates of four bacterial P450s: P450 BM-3, P450cam, P450terp, and P450eryF. The P450 3A4 sequence was aligned to those of the known proteins using a structure-based alignment of P450 BM-3, P450cam, P450terp, and P450eryF. The coordinates of the model were then calculated using a consensus strategy, and the final structure was optimized in the presence of water. The P450 3A4 model resembles P450 BM-3 the most, but the B helix is similar to that of P450eryF, which leads to an enlarged active site when compared with P450 BM-3, P450cam, and P450terp. The 3A4 residues equivalent to known substrate contact residues of the bacterial proteins and key residues of rat P450 2B1 are located in the active site or the substrate access channel. Docking of progesterone into the P450 3A4 model demonstrated that the substrate bound in a 6-orientation can interact with a number of active site residues, such as 114, 119, 301, 304, 305, 309, 370, 373, and 479, through hydrophobic interactions. The active site of the enzyme can also accommodate erythromycin, which, in addition to the residues listed for progesterone, also contacts residues 101, 104, 105, 214, 215, 217, 218, 374, and 478. The majority of 3A4 residues which interact with progesterone and/or erythromycin possess their equivalents in key residues of P450 2B enzymes, except for residues 297, 480 and 482, which do not contact either substrate in P450 3A4. The results from docking of progesterone and erythromycin into the enzyme model make it possible to pinpoint residues which may be important for 3A4 function and to target them for site-directed mutagenesis.     

Thermal degradation of poly(vinyl chloride)

This paper presents an initial attempt at describing poly(vinyl chloride) (PVC) thermal degradation through a semi-detailed and lumped kinetic model. A mechanism of 40 species and pseudocomponents (molecules and radicals) involved in about 250 reactions permits quite a good reproduction of the main characteristics of PVC degradation and volatilization. The presence of the two step mechanism—the first step of which corresponds to dehydrochlorination and the second to the tar release and residue char formation—are correctly predicted both in quantitative terms and in the temperature ranges. The model was validated by comparison with several thermo gravimetric analyses, both dynamic at different heating rates, and isothermal. When compared with the typical one step global apparent degradation models, the approach proposed here spans quite large operative ranges, especially when it comes to predicting product distributions. The initial results of these product predictions, even though quite preliminary, are encouraging and confirm the validity of the model.     

Development of new lubricating grease formulations using recycled LDPE as rheology modifier additive

The recovery of plastic waste but also its applicability in product development may be an incentive to industry, since the use of such plastics represents a cheaper source of raw material. The aim of the present paper is to study the feasibility of recycling polyolefins as additives to improve the rheological properties of lithium 12-hydroxystearate lubricating greases. The effects that both soap and recycled low-density polyethylene (LDPE) concentration exert on the rheology of lithium lubricating greases and its relationship with grease microstructure are discussed in this work. In this way, different lubricating grease formulations were manufactured by modifying the concentration of lithium 12-hydroxystearate and content of recycled LDPE, according to a RSM statistical design. These lubricating greases were rheologically characterized through small-amplitude oscillatory shear (SAOS) and viscous flow measurements. In addition to these, scanning electronic microscopy (SEM) observations and mechanical stability tests were also carried out. Recycled LDPE was found to be an effective additive to modify grease rheology, acting as filler in the soap entangled microstructure. The values of both apparent viscosity and viscoelastic functions in the linear viscoelastic region increase with soap and recycled polymer concentrations. However, the addition of recycled LDPE distort the microstructural network of these greases resulting greases with less relative elastic characteristics and poorer mechanical properties as LDPE content increases.     

Study of a Catalytic Mechanism in Additive Differential Pulse Techniques

The new electrochemical double pulse technique, known as additive differential normal pulse voltammetry (ADNPV) when there is no restriction on the duration of both pulses, and additive differential pulse voltammetry (ADPV) when t₂?t₁, has been applied to a pseudo‐first‐order catalytic mechanism. The expressions obtained here are applicable to planar and spherical electrodes, of any radius. This is of great interest since the size of the electrode plays an important role in the preponderating of diffusive and kinetics processes. The signal obtained with this technique presents the same morphological characteristics as the triple pulse technique, double differential pulse voltammetry (DDPV) and is more advantageous than DDPV and than the double pulse one, differential pulse voltammetry (DPV).     

On Physically Unacceptable Numerical Solutions Yielding Strong Chaotic Signals

Physically unacceptable chaotic numerical solutions of nonlinear circuits and systems are discussed in this paper. First, as an introduction, a simple example of a wrong choice of a numerical solver to deal with a second-order linear ordinary differential equation is presented. Then, the main result follows with the analysis of an ill-designed numerical approach to solve and analyze a particular nonlinear memristive circuit. The obtained trajectory of the numerical solution is unphysical (not acceptable), as it violates the presence of an invariant plane in the continuous systems. Such a poor outcome is then turned around, as we look at the unphysical numerical solution as a source of strong chaotic sequences. The 0–1 test for chaos and bifurcation diagrams are applied to prove that the unacceptable (from the continuous system point of view) numerical solutions are, in fact, useful chaotic sequences with possible applications in cryptography and the secure transmission of data.     

Microscale Thermophoresis and Molecular Modelling to Explore the Chelating Drug Transportation in the Milk to Infant

The microscale thermophoresis (MST) technique was utilized to investigate lactoferrin–drug interaction with the iron chelator, deferiprone, using label-free system. MST depends on the intrinsic fluorescence of one interacting partner. The results indicated a significant interaction between lactoferrin and deferiprone. The estimated binding constant for the lactoferrin–deferiprone interaction was 8.9 × 10⁻⁶ ± 1.6, SD, which is to be reported for the first time. Such significant binding between lactoferrin and deferiprone may indicate the potentiation of the drug secretion into a lactating mother’s milk. The technique showed a fast and simple approach to study protein–drug interaction while avoiding complicated labeling procedures. Moreover, the binding behavior of deferiprone within the binding sites of lactoferrin was investigated through molecular docking which reflected that deferiprone mediates strong hydrogen bonding with ARG121 and ASP297 in pocket 1 and forms H-bond and ionic interaction with ASN640 and ASP395, respectively, in pocket 2 of lactoferrin. Meanwhile, iron ions provide ionic interaction with deferiprone in both of the pockets. The molecular dynamic simulation further confirmed that the binding of deferiprone with lactoferrin brings conformational changes in lactoferrin that is more energetically stable. It also confirmed that deferiprone causes positive correlation motion in the interacting residues of both pockets, with strong negative correlation motion in the loop regions, and thus changes the dynamics of lactoferrin. The MM-GBSA based binding free energy calculation revealed that deferiprone exhibits ∆G TOTAL of −63,163 kcal/mol in pocket 1 and −63,073 kcal/mol in pocket 2 with complex receptor–ligand difference in pocket 1 and pocket 2 of −117.38 kcal/mol and −111.54 kcal/mol, respectively, which in turn suggests that deferiprone binds more strongly in the pocket 1. The free energy landscape of the lactoferrin–deferiprone complex also showed that this complex remains in a high energy state that confirms the strong binding of deferiprone with the lactoferrin. The current research concluded that iron-chelating drugs (deferiprone) can be transported from the mother to the infant in the milk because of the strong attachment with the lactoferrin active pockets.     

Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach

Aptamers, the nucleic acid analogs of antibodies, bind to their target molecules with remarkable specificity and sensitivity, making them promising diagnostic and therapeutic tools. The systematic evolution of ligands by exponential enrichment (SELEX) is time-consuming and expensive. However, regardless of those issues, it is the most used in vitro method for selecting aptamers. Therefore, recent studies have used computational approaches to reduce the time and cost associated with the synthesis and selection of aptamers. In an effort to present the potential of computational techniques in aptamer selection, a simple sequence-based method was used to design a 69-nucleotide long aptamer (mod_09) with a relatively stable structure (with a minimum free energy of −32.2 kcal/mol) and investigate its binding properties to the tyrosine kinase domain of the NT-3 growth factor receptor, for the first time, by employing computational modeling and docking tools.     

耦合FE/WB法在声分析中的应用

简要描叙FE法(finite element method)和WB法(wave based method)的理论背景以及耦合FE/WB法的数学基础.耦合FE/WB法利用两者的优势——FE法的广泛应用和WB法的高收敛特性,将FE模型中较大且几何简单的部分采用WB法代替.耦合模型具有相对较少的自由度.对于较高的频率还可以进行细分得到更高的计算精度,并利用模态缩减法进一步减少自由度数.数值算例结果表明,该耦合方法有潜力覆盖中频段的声分析.