A Photoswitchable Trivalent Cluster Mannoside to Probe the Effects of Ligand Orientation in Bacterial Adhesion

We have recently demonstrated, by employing azobenzene glycosides, that bacterial adhesion to surfaces can be switched through reversible reorientation of the carbohydrate ligands. To investigate this phenomenon further, we have turned here to more complex—that is, multivalent—azobenzene glycoclusters. We report on the synthesis of a photosensitive trivalent cluster mannoside conjugated to an azobenzene hinge at the focal point. Molecular dynamics studies suggested that this cluster mannoside, despite the conformational flexibility of the azobenzene-glycocluster linkage, offers the potential for reversibly changing the glycocluster's orientation on a surface. Next, the photoswitchable glycocluster was attached to human cells, and adhesion assays with type 1 fimbriated Escherichia coli bacteria were performed. They showed marked differences in bacterial adhesion, dependent on the light-induced reorientation of the glycocluster moiety. These results further underline the importance of orientational effects in carbohydrate recognition and likewise the value of photoswitchable glycoconjugates for their study.     

链转移剂2-巯基乙醇对AM/AA共聚反应的影响

以AM和AA为原料，过硫酸铵和亚硫酸氢钠氧化还原体系为引发剂，在链转移剂的作用下，采用水溶液聚合的工艺路线，合成了低相对分子质量的AM／AA共聚物。比较了不同链转移剂的作用效果；研究了2-巯基乙醇作为链转移剂对聚合过程和共聚物相对分子质量的影响。结果表明：在共聚物相对分子质量较低时，可以较大幅度提高聚合单体的浓度，聚合能平稳进行。     

Graft Copolymerization of Chitosan with Butyl Acrylate and Application of the Copolymers to Cotton Fabric

Graft polymerization of butyl acrylate (BuA) onto chitosan using potassium persulfate (KPS) as initiator was studied under different conditions. The grafting percentage (G%) and the grafting efficiency (GE%) increase by increasing KPS concentration up to 40 mmol/L then decrease thereafter. Another trend was observed with BuA concentration where G% increases significantly as BuA concentration increases within the range studied, i.e., 10%–100%, based on weight of chitosan sample (ows), meanwhile GE% exhibits a maximum at BuA concentration of 50% ows. Temperature acts in favor of grafting up to 65°C where maxima for both G% and GE% could be achieved. The grafting reaction is characterized by an initial fast rate during the first 60 minutes then levels off thereafter. Poly (BuA)-chitosan graft copolymers were applied to cotton fabric in presence and absence of low formaldehyde cross-linking agent. Introduction of the copolymer and the cross-linking agent to cotton fabric enhances the performance of the latter to a great extent provided that the copolymer and the cross-linking agent are applied in two subsequent steps. Fabric performance was assessed through monitoring, nitrogen content, crease recovery angle, tensile strength and elongation at break.     

聚合条件对P（AN-co—IA）分子质量分布影响的研究

采用凝胶色谱（GPC）法测定了丙烯腈与衣康酸共聚物P（AN—co—IA）的重均分子质量和数均分子质量,并通过已知聚丙烯腈的重均分子质量数据和数均分子质量数据对所测的分子质量进行校正,进一步计算得到共聚物的多分散系数。同时研究了引发剂用量、单体浓度、聚合温度、聚合时间对P（AN—co—IA）分子质量分布的影响。研究结果表明,P（AN-co-IA）分子质量分布随引发剂用量的增大、聚合单体浓度的增加而变宽,与聚合反应温度、聚合反应时间无明显的变化趋势。     

How to Extend the Use of Grid‐Based Interaction Energy Maps from Chemistry to Biotopics

Many computational tools routinely used in chemistry could successfully be applied to the biosciences since protein–protein and protein–ligand interactions are governed by the laws of chemistry. This paper shows that it is possible to extend the use of existing computational tools from their traditional application field (e.g. chemistry) to culturally‐related research areas by the implementation of simple but well‐designed utilities. In particular, a computational strategy obtained by combining GRID (the program originally designed by Peter Goodford, and now distributed by Molecular Discovery Ltd.) and BIOCUBE4mf (an application freely available at www.casmedchem.unito.it ) was used to a) characterize the surface properties of the cavity of the Bacillus anthracis protective antigen heptameric prepore; b) suggest how to design mutagenesis experiments; c) quantitatively show the selectivity of the KvAP channel for K⁺ over Na⁺ ions and d) rationalize the pharmacokinetic behavior of 1,4‐DHP third‐generation drugs.     

Veratridine Can Bind to a Site at the Mouth of the Channel Pore at Human Cardiac Sodium Channel NaV1.5

The cardiac sodium ion channel (Na_V1.5) is a protein with four domains (DI-DIV), each with six transmembrane segments. Its opening and subsequent inactivation results in the brief rapid influx of Na⁺ ions resulting in the depolarization of cardiomyocytes. The neurotoxin veratridine (VTD) inhibits Na_V1.5 inactivation resulting in longer channel opening times, and potentially fatal action potential prolongation. VTD is predicted to bind at the channel pore, but alternative binding sites have not been ruled out. To determine the binding site of VTD on Na_V1.5, we perform docking calculations and high-throughput electrophysiology experiments in the present study. The docking calculations identified two distinct binding regions. The first site was in the pore, close to the binding site of Na_V1.4 and Na_V1.5 blocking drugs in experimental structures. The second site was at the “mouth” of the pore at the cytosolic side, partly solvent-exposed. Mutations at this site (L409, E417, and I1466) had large effects on VTD binding, while residues deeper in the pore had no effect, consistent with VTD binding at the mouth site. Overall, our results suggest a VTD binding site close to the cytoplasmic mouth of the channel pore. Binding at this alternative site might indicate an allosteric inactivation mechanism for VTD at Na_V1.5.     

Multidimensional high‐temperature liquid chromatography: A new technique to characterize the chemical heterogeneity of Ziegler‐Natta‐based bimodal HDPE

High temperature two‐dimensional liquid chromatography (HT 2D‐LC) was recently introduced as a new technique to analyze the heterogeneities with regard to composition and molar mass present in model blends of polyolefins and various olefin copolymers. The method uses graphite as stationary phase and solvent gradients of 1‐decanol → 1,2,4‐trichlorobenzene as mobile phase for the compositional separation. With the aim to maximize the chromatographic resolution, the influence of the separation's temperature in the first dimension was evaluated: approaching the θ‐temperature of polyethylene (PE) in 1‐decanol selectively enhances the retention of higher molar mass PE standards while that of the lower molar mass ones is hardly affected. A bimodal ethylene/1‐butene copolymer and its temperature rising elution fraction (TREF) fractions were separated by HT 2D‐LC. For the first time, both axes of the contour plot were calibrated with regard to chemical composition and molar mass, respectively. Prefractionation of the bulk sample by TREF enhances the detectability of separated components of the 2D separation. The influence of the separation temperature, that is, working around the θ‐temperature of PE in 1‐decanol, can be used to enhance the chromatographic resolution of the 2D chromatography. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

Effects of 1,2‐butadiene on the anionic copolymerization of styrene and 1,3‐butadiene in the presence of polar additives

1,2‐Butadiene is shown to be a chain terminating/transferring agent in butyllithium‐initiated diene polymerization. The influence of 1,2‐butadiene on the anionic copolymerization of 1,3‐butadiene and styrene is investigated using n‐butyllithium as initiator and tetrahydrofuran or N,N,N′,N′‐tetramethylethylenediamine as polar additive. A decrease of copolymerization rate is observed on the addition of 1,2‐butadiene. On introducing 1,2‐butadiene, the number average molecular weight (M_n ) decreases and the molecular weight distribution broadens. The vinyl content of copolymer increases slightly with an increase of 1,2‐butadiene. During the copolymerization, 1,2‐butadiene in the presence of a high ratio of polar additives to n‐butyllithium greatly decreases the copolymerization rate, resulting in a lower value of M_n and a narrower molecular weight distribution than that found for a low ratio of polar additives to n‐butyllithium. This evolution can be explained by the base‐catalyzed isomerization of 1,2‐butadiene to form 1‐butylene in the presence of polar additives. With an increasing amount of 1,2‐butadiene, the vulcanized rubber exhibits an increased rolling resistance and a reduced wet skid resistance owing to the decrease of coupling efficiency. These results further indicate the activity of alkynyllithium derivatives produced by the reaction of alkyllithium and 1‐butyne is less than that of the alkyllithium. Copyright © 2007 Society of Chemical Industry     

Molecular dynamics simulations of molecularly imprinted polymer approaches to the preparation of selective materials to remove norfloxacin

A novel molecularly imprinted polymer (MIP) designed by molecular dynamics (MD) simulations was successfully prepared with norfloxacin as a template molecule, methyl acrylic acid as a functional monomer, and ethylene glycol dimethacrylate as a crosslinker. According to the theoretical prediction and experimental preparation methods, three kinds of molecular imprinting materials were designed and synthesized with MD simulations and molecular imprinting technology. The best ratio of the template to the functional monomer to the crosslinker was 1:8:40 in these studies. The experimental results illustrate that the MD simulations were credible in compounding the components of the MIPs. The structure of the prepared polymers were characterized with various methods. To analyze the adsorption performances, many kinds of static adsorption tests, including kinetic, isotherm, and selectivity tests, were used. The results indicate that the novel adsorbents conformed to the pseudo–second‐order kinetic equation and followed the Langmuir isotherm model. The adsorption amounts of MIP2 at a ratio of 1:8:40 were about 29.35 mg/g at 298 K_. The selective adsorption and reusable performance of norfloxacin were excellent. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 132, 42817.     

Unusually strong positive cooperativity in binding of peptides to latent membrane protein-1 DNA fragments of the Epstein-Barr viral gene

The DNA-binding preferences of two oligopeptide amides, (His-Pro-Arg-Lys)(3)NH(2) (HR-12) and (Ser-Pro-Arg-Lys)(3)NH(2) (SP-12), have been examined by quantitative DNase I footprinting studies. Two different DNA fragments were investigated: a pair of 5'-(32)P-labeled duplexes from pBR322 with one or other of the complementary strands labeled and a corresponding pair of 5'-(32)P-labeled duplexes representing fragments of the latent membrane protein (LMP-1) gene from a pathogenic Epstein-Barr virus variant derived from nasopharyngeal carcinoma. The major objective was to examine molecular recognition and cooperative features associated with sequence-selective binding of synthetic peptides to the LMP-1 fragments. At various binding sites on the pBR322 fragments, Hill coefficients (n(H)) ranging from 1.9-2.2 were observed; these results indicate modest positive cooperativity between binding sites for both peptides. By contrast, unusually high values of n(H), ranging from 4.0-9.3, were observed at various binding sites on the LMP-1 fragments. Allosteric models can be constructed to interpret the observed cooperative interactions between different DNA recognition sites in the LMP-1 gene upon binding of the peptide ligands. It is noteworthy that these models feature a novel network of cooperativity interconnecting multiple DNA allosteric sites. The evidence of sequence selectivity and strong cooperativity discovered in this work may prove to be a general feature of peptide interactions with some nucleic acids.     

Benzodioxane-Benzamides as Antibacterial Agents: Computational and SAR Studies to Evaluate the Influence of the 7-Substitution in FtsZ Interaction

FtsZ is a crucial prokaryotic protein involved in bacterial cell replication. It recently arose as a promising target in the search for antimicrobial agents able to fight antimicrobial resistance. In this work, going on with our structure-activity relationship (SAR) study, we developed variously 7-substituted 1,4-benzodioxane compounds, linked to the 2,6-difluorobenzamide by a methylenoxy bridge. Compounds exhibit promising antibacterial activities not only against multidrug-resistant Staphylococcus aureus, but also on mutated Escherichia coli strains, thus enlarging their spectrum of action toward Gram-negative bacteria as well. Computational studies elucidated, through a validated FtsZ binding protocol, the structural features of new promising derivatives as FtsZ inhibitors.     

Effects of the SAPO-11 synthetic process on dehydration of ethanol to ethylene

The effects of the synthetic condition of SAPO-11 molecular sieves on ethanol dehydration to ethylene were studied. Product-compositions, ethanol conversion, and selectivity to ethylene of synthesized and commercial SAPO-11 molecular sieves were compared. Results are as follows: the optimal synthetic conditions for SAPO-11 molecular sieves are adding pseudoboehmite before orthophoshporic, using di-n- propylamine as the template, having a mass fraction of 40% colloidal silica as the silica source and the starting gel obtained, and running at 200°C for 48 h. From the patterns of NH₃-TPD, the amount of acid synthesized by SAPO-11 molecular sieves is less than that by commercial SAPO-11 molecular sieves, and has a stronger weak acid. Also, ethanol conversion and selectivity to ethylene reached 99% at 280°C on synthesized SAPO-11, lower by 20°C compared to commercial SAPO-11. For two SAPO-11 molecular sieves, the by-products in the gas phase are mainly ethane, propane, propene, isobutane, n-butane, propadiene, butylene and some higher hydrocarbons. The by-products in the liquid phase are ethyl ether and acetaldehyde.     

From Molecular Recognition to the “Vehicles” of Evolutionary Complexity: An Informational Approach

Countless informational proposals and models have explored the singular characteristics of biological systems: from the initial choice of information terms in the early days of molecular biology to the current bioinformatic avalanche in this “omic” era. However, this was conducted, most often, within partial, specialized scopes or just metaphorically. In this paper, we attempt a consistent informational discourse, initially based on the molecular recognition paradigm, which addresses the main stages of biological organization in a new way. It considers the interconnection between signaling systems and information flows, between informational architectures and biomolecular codes, between controlled cell cycles and multicellular complexity. It also addresses, in a new way, a central issue: how new evolutionary paths are opened by the cumulated action of multiple variation engines or mutational ‘vehicles’ evolved for the genomic exploration of DNA sequence space. Rather than discussing the possible replacement, extension, or maintenance of traditional neo-Darwinian tenets, a genuine informational approach to evolutionary phenomena is advocated, in which systemic variation in the informational architectures may induce differential survival (self-construction, self-maintenance, and reproduction) of biological agents within their open ended environment.     

Structure‐Based Design of Potent Small‐Molecule Binders to the S‐Component of the ECF Transporter for Thiamine

Energy‐coupling factor (ECF) transporters are membrane‐protein complexes that mediate vitamin uptake in prokaryotes. They bind the substrate through the action of a specific integral membrane subunit (S‐component) and power transport by hydrolysis of ATP in the three‐subunit ECF module. Here, we have studied the binding of thiamine derivatives to ThiT, a thiamine‐specific S‐component. We designed and synthesized derivatives of thiamine that bind to ThiT with high affinity; this allowed us to evaluate the contribution of the functional groups to the binding affinity. We determined six crystal structures of ThiT in complex with our derivatives. The structure of the substrate‐binding site in ThiT remains almost unchanged despite substantial differences in affinity. This work indicates that the structural organization of the binding site is robust and suggests that substrate release, which is required for transport, requires additional changes in conformation in ThiT that might be imposed by the ECF module.     

Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

Anchor residues, which are deeply buried upon binding, play an important role in protein-protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs) which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17-Asn29, abbreviated as p53N) which are involved in binding with two different targets (MDM2 and Taz2), and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex). We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs).     

ABCBA Pentablock Copolymers Consisting of Poly(l‐lactide) (PLLA: A), Poly(d‐lactide) (PDLA: B), and Poly(butylene succinate) (PBS: C): Effects of Semicrystalline PBS Segments on the Stereo‐Crystallinity and Properties

A new stereo pentablock copolymer consisting of poly(l ‐lactide) (PLLA: A), poly‐d ‐lactide (PDLA: B), and poly(butylene succinate) (PBS: C) is synthesized by two‐step ring‐opening polymerization of d ‐ and l ‐lactides in the presence of bis‐hydroxyl‐terminated PBS prepolymer that has been prepared by the ordinary polycondensation. The pentablock copolymers (PLLA‐PDLA‐PBS‐PDLA‐PLLA) as well as the triblock copolymers (PLLA‐PBS‐PLLA) obtained as the intermediates show different properties depending on the polymer compositions. In the pentablock copolymers, the direct connection of the PLLA and PDLA blocks allows easy formation of the stereocomplex crystals, while the introduction of the semicrystalline PBS block is effective not only for changing the crystallization kinetics but also for imparting an elastomeric property.

     

Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies

Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC₅₀ = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91).     

Investigations of the Binding of [Pt2(DTBPA)Cl2](II) and [Pt2(TPXA)Cl2](II) to DNA via Various Cross-Linking Modes

We have constructed models for a series of platinum-DNA adducts that represent the binding of two agents, [Pt₂(DTBPA)Cl₂](II) and [Pt₂(TPXA)Cl₂](II), to DNA via inter- and intra-strand cross-linking, and carried out molecular dynamics simulations and DNA conformational dynamics calculations. The effects of trans- and cis-configurations of the centers of these di-nuclear platinum agents, and of different bridging linkers, have been investigated on the conformational distortions of platinum-DNA adducts formed via inter- and intra-strand cross-links. The results demonstrate that the DNA conformational distortions for the various platinum-DNA adducts with differing cross-linking modes are greatly influenced by the difference between the platinum-platinum distance for the platinum agent and the platinum-bound N7–N7 distance for the DNA molecule, and by the flexibility of the bridging linkers in the platinum agent. However, the effects of trans/cis-configurations of the platinum-centers on the DNA conformational distortions in the platinum-DNA adducts depend on the inter- and intra-strand cross-linking modes. In addition, we discuss the relevance of DNA base motions, including opening, shift and roll, to the changes in the parameters of the DNA major and minor grooves caused by binding of the platinum agent.     

Effects of the Protonation State of Titratable Residues and the Presence of Water Molecules on Nocodazole Binding to β‐Tubulin

Regulation of microtubule assembly by antimitotic agents is a potential therapeutic strategy for the treatment of cancer, parasite infections, and neurodegenerative diseases. One of these agents is nocodazole (NZ), which inhibits microtubule polymerization by binding to β‐tubulin. NZ was recently co‐crystallized in Gallus gallus tubulin, providing new information about the features of interaction for ligand recognition and stability. In this work, we used state‐of‐the‐art computational approaches to evaluate the protonation effects of titratable residues and the presence of water molecules in the binding of NZ. Analysis of protonation states showed that residue E198 has the largest modification in its pK_a value. The resulting E198 pK_a value, calculated with pH‐REMD methodology (pK_a=6.21), was higher than the isolated E amino acid (pK_a=4.25), thus being more likely to be found in its protonated state at the binding site. Moreover, we identified an interaction between a water molecule and C239 and G235 as essential for NZ binding. Our results suggest that the protonation state of E198 and the structural water molecules play key roles in the binding of NZ to β‐tubulin.