Cluster analysis of water molecules in alanine racemase and their putative structural role

Conservation of water molecules was identified by a cluster analysis of seven crystal structures of alanine racemase from Bacillus stearothermophilus. A total of 47 clusters of consensus water sites were determined and found to be highly localized, as indicated by their low mobilities. These clusters are located in the region of the active sites as well as at the interface between the N-terminal domain (the alpha/beta-barrel) of the first monomer and the C-terminal domain of the second monomer. The clusters located at the dimer interface form extensive hydrogen-bonding networks linked to the protein backbone. These water-mediated hydrogen bonds, and also all hydrogen-bonding interactions at the dimer interface, were monitored during a 2 ns molecular dynamics simulation and showed that when the inhibitor propionate was bound to the enzyme, some of these interactions were disrupted. The data we present here indicate that the consensus water sites identified at the interface between the two monomers of alanine racemase may play a structural role, which is to maintain and stabilize the alanine racemase dimer. A second role might be to supply the active site continuously with water molecules in order to allow rapid equilibration of active site protons with the solvent.     

大口径内槽给排水管件模具

内环槽管性在给排水管网系统中具有施工方便、密封性高、伸缩区长、塑性较好的优点，但制件给模具带来了很多新的技术问题。介绍了模具环槽处内缩型芯的组合结构及抽芯运动原理，并总结了实际生产中，模具制造工艺及注射产品时应注意的问题。     

Recognition by nonaromatic and stereochemical subunit-containing polyamides of the four Watson-Crick base pairs in the DNA minor groove

In order to develop an optimal subunit as a T‐recognition element in hairpin polyamides, 15 novel chirality‐modified polyamides containing (R)‐α,β‐diaminopropionic acid (^Rβ), (S)‐α,β‐diaminopropionic acid (^Sβ), (1R,3S)‐3‐aminocyclopentanecarboxylic acid (^RSCp), (1S,3R)‐3‐amino‐cyclopentanecarboxylic acid (^RSCp), (1R,3R)‐3‐aminocyclopentanecarboxylic acid (^RRCp) and (1S,3S)‐3‐amino‐cyclopentanecarboxylic acid (^SSCp) residues were synthesized. Their binding characteristics to DNA sequences 5′‐TGC N CAT‐3′/3′‐ACG N′ GTA‐5′ ( N?N′ =A ? T, T ? A, G ? C and C ? G) were systemically studied by surface plasmon resonance (SPR) and molecular simulation (MSim) techniques. SPR showed that polyamide 4 , AcIm‐^Sβ‐ImPy‐γ‐ImPy‐β‐Py‐βDp (β/^Sβ pair), bound to a DNA sequence containing a core binding site of 5′‐TGC A CAT‐3′ with a dissociation equilibrium constant (K_D) of 4.5×10^?8 m. This was a tenfold improvement in specificity over 5′‐TGCTCAT‐3′ (K_D=4.5×10^?7 M ). MSim studies supported the SPR results. More importantly, for the first time, we found that chiral 3‐aminocyclopentanecarboxylic acids in polyamides can be employed as base readers with only a small decrease in binding affinity to DNA. In particular, SPR showed that polyamide 9 (^RRCp/β pair) had a 15‐fold binding preference for 5′‐TGCTCAT‐3′ over 5′‐TGCACAT‐3′. A large difference in standard free energy change for A ? T over T ? A was determined (ΔΔG^o=5.9 kJ mol^?1), as was a twofold decrease in interaction energy by MSim. Moreover, a 1:1 stoichiometry ( 9 to 5′‐TGC T CAT‐3′/3′‐ACG A GTA‐5′) was shown by MSim to be optimal for the chiral five‐membered cycle to fit the minor groove. Collectively, the study suggests that the (S)‐α‐amino‐β‐aminopropionic acid and (1R,3R)‐3‐aminocyclopentanecarboxylic acid can serve as a T‐recognition element, and the stereochemistry and the nature of these subunits significantly influence binding properties in these recognition events. Subunit (1R,3R)‐3‐aminocyclopentanecarboxylic acid broadens our scope to design novel polyamides.     

Surface modifications of molecularly imprinted polymers for improved template recognition in water media

New Restricted Access Materials—Molecularly Imprinted Polymers (RAM-MIP) were synthesized by using caffeine (CAFF), methacrylic acid (MAA), divinyl benzene (DVB) and glycidil methacrylate (GMA) as model template, functional monomer, crosslinking agent and pro-hydrophilic co-monomer, respectively. Furthermore, a screening of the ratio of functional monomer to template was performed. After the preliminary characterizations of conventional MIP prepared in absence of GMA, different GMA amounts were inserted in the pre-polymerization feeds and different reactions conditions were tested for GMA epoxide ring opening. In particular, perchloric acid, ammonia, lactic acid, glycine and triethylene glycol were chosen for this purpose. In perchloric acid and ammonia cases, a further modification was performed by phosphorylation and methylation procedures, respectively. Imprinting efficiency of all the obtained materials was evaluated by binding experiments using caffeine and its analogue theophylline both in organic and in water media. The increased hydrophilic characteristics of RAM polymers by water absorption measurement and protein binding experiments were performed.     

Systematic placement of structural water molecules for improved scoring of protein-ligand interactions

Structural water molecules are found in many protein-ligand complexes. They are known to be vital in mediating hydrogen-bonding interactions and, in some cases, key for facilitating tight binding. It is thus very important to consider water molecules when attempting to model protein-ligand interactions for cognate ligand identification, virtual screening and drug design. While the rigid treatment of water molecules present in structures is feasible, the more relevant task of treating all possible positions and orientations of water molecules with each possible ligand pose is computationally daunting. Current methods in molecular docking provide partial treatment for such water molecules, with modest success. Here we describe a new method employing dead-end elimination to place water molecules within a binding site, bridging interactions between protein and ligand. Dead-end elimination permits a thorough, though still incomplete, treatment of water placement. The results show that this method is able to place water molecules correctly within known complexes and to create physically reasonable hydrogen bonds. The approach has also been incorporated within an inverse molecular design approach, to model a variety of compounds in the process of de novo ligand design. The inclusion of structural water molecules, combined with ranking based on the electrostatic contribution to binding affinity, improves a number of otherwise poor energetic predictions.     

水分子对HKUST-1甲烷吸附性能的影响

以三水合硝酸铜和均苯三甲酸为反应物、N,N’-二甲基甲酰胺为溶剂,采用溶剂热法合成金属有机骨架材料HKUST-1。将HKUST-1浸渍于等体积去离子水中,考察浸渍时间对其理化性能的影响,并通过XRD、SEM、BET和高压气体吸附表征研究了水分子对HKUST-1吸附甲烷性能的影响。结果表明,水分子易于吸附在HKUST-1中不饱和金属活性位点且对其骨架结构产生影响,浸渍72 h后,HKUST-1的BET比表面积和孔容分别从1 478.8 m2·g~(-1)和0.700 cm3·g~(-1)降至53.6 m~2·g~(-1)和0.005 cm3·g~(-1),在298 K和3.5 MPa条件下,甲烷吸附量从203.91 cm3·g~(-1)降至13.74 cm3·g~(-1)。但24 h浸渍后的HKUST-1骨架中生成一定数量的介孔,有利于较大的气体或液体分子吸附存储,值得深入研究。     

Diffusion coefficient and equilibrium solubility of water molecules in biodegradable polymers

The diffusion coefficient and solubility of water molecules were measured in polyglycolide (PGA), poly(L ‐lactide) (PLLA), poly[(R)‐3‐hydroxybutyrate] (PHB), poly(ϵ‐caprolactone) (PCL), and Skygreen^R (SG). The diffusion coefficient and equilibrium solubility decreased in the order SG > PCL > PLLA > PHB > PGA and PGA > SG > PLLA > PHB > PCL, respectively. The diffusion coefficient and solubility of water at low sorption temperature in PHB varied according to the initial crystallinity of the matrix polymer even though crystallization of PHB molecules took place during the sorption experiment. In contrast, the amorphous PLLA and the crystalline PLLA showed an almost identical diffusion coefficient and solubility of water, in spite of the fact that the amorphous PLLA remained practically amorphous during the whole sorption procedure. A strong correlation existed between the water solubility and the surface tension or contact angle of the polymer matrix. The water diffusivity in PGA was almost 2 orders of magnitude lower while water was more soluble in PGA with a lower heat of sorption than that corresponding to the other more hydrophobic polymers, indicating that the transport of water molecules in PGA followed the solution–diffusion model. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 1716–1722, 2000     

The role of desalination in water reuse

If reuse of water is being considered in an area where seawater desalination will be used to produce the basic water source, overall water resource development costs should be considered before selection of the basic desalination process. In cases where the system's wastewater is treated and used for artificial ground-water recharge and recovery, there are inherent benefits in utilizing a thermal rather than a membrane process to produce the basic water source from seawater.     

Zeta potential of Nafion molecules in isopropanol‐water mixture solvent

Structure of Nafion in isopropanol/water mixture solvent has been investigated using zeta potential. It was found that zeta potential of Nafion strongly depends on the concentration. When the concentration of Nafion varied from 0.5 to 1 wt %, zeta potential increased significantly from about 0 to ?12 mV, corresponding to the change of structure of Nafion molecules from true solution to dispersion of aggregates. While the concentration is above 5 wt %, micelle‐like structure of Nafion aggregates was proposed. The dependence of zeta potential of Nafion on pH value at concentration of 5 wt % shows a nonmonotonic function and isoelectric point of Nafion‐Na of 8.0 was observed. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

A distribution kinetics model for chromatography of block-like molecules

We develop the theory for chromatographic separation of isomers such as polycyclic aromatic hydrocarbons, polychlorinated biphenyls, dioxins, steroids, and carotenoids based on shape-selective mechanisms for either exclusion or adsorption. Block-like solute transport and retention on oriented stationary phases are modeled by a dispersed-flow chromatographic equation combined with simultaneous exclusion partitioning and shaped-based adsorption. Molecules to be separated are considered distributed continuously with respect to the shape and sorption parameters. The population balance equations of distribution kinetics provide the governing differential equations that are solved for the temporal moments of the concentration in a chromatographic column. By including dispersive mass transport effects, the model allows estimation of peak variance and HETP and is thus an improvement over theories that focus solely on retention time. The model predictions are compared with experimental data from the literature for gas chromatography.     

A distillation method for water in soaps

Conclusion The use of anhydrous barium chloride for an anti-foaming agent in the distillation method for determining the amount of water in soap, is superior to sodium acetate in respect to speed, ease of handling the test, and finally in respect to leaving more cleanable apparatus. It offers another advantage in that anhydrous BaCl₂ is more easily prepared than is anhydrous sodium acetate.     

A supramolecular optic sensor for selective recognition AMP

Cu-coordinated complex based on 7-membered amide cycle has been designed and synthesized. And its binding ability with nucleotides (AMP, adenosine 5′-monophosphate; ADP, adenosine 5′-diphosphate; ATP, adenosine 5′-triphosphate) has been studied by UV–vis spectrum. Results indicate that the receptor shows the highest binding ability with AMP among studied nucleotides and can selectively and strongly bind nucleotides at neutral medium. The receptor can be used as optical sensor for the detection of AMP.     

Interspecific recognition among termites of the genusReticulitermes: Evidence for a role for the cuticular hydrocarbons

Two species of termites,Reticulitermes (lucifugus) grassei andR. (l.) banyulensis, show a high degree of aggressivity toward each other. The epicuticular signature, recognized by contact, can be extracted using organic solvents, and the removal of the signature abolished all types of aggressive behavior. The signature can be transferred to lures, where it triggers interspecies aggression. It was found to be mainly present in the apolar fraction of the cuticular extracts, which contained only hydrocarbons, are determined by GC/MS techniques. Chemical recognition contributes towards isolation of the two species belonging to theR. lucifugus complex.