Exploration of GH94 Sequence Space for Enzyme Discovery Reveals a Novel Glucosylgalactose Phosphorylase Specificity

The substantial increase in DNA sequencing efforts has led to a rapid expansion of available sequences in glycoside hydrolase families. The ever-increasing sequence space presents considerable opportunities for the search for enzymes with novel functionalities. In this work, the sequence-function space of glycoside hydrolase family 94 (GH94) was explored in detail, using a combined approach of phylogenetic analysis and sequence similarity networks. The identification and experimental screening of unknown clusters led to the discovery of an enzyme from the soil bacterium Paenibacillus polymyxa that acts as a 4-O-β-d -glucosyl-d -galactose phosphorylase (GGalP), a specificity that has not been reported to date. Detailed characterization of GGalP revealed that its kinetic parameters were consistent with those of other known phosphorylases. Furthermore, the enzyme could be used for production of the rare disaccharides 4-O-β-d -glucosyl-d -galactose and 4-O-β-d -glucosyl-l -arabinose. Our current work highlights the power of rational sequence space exploration in the search for novel enzyme specificities, as well as the potential of phosphorylases for rare disaccharide synthesis.     

Synthesis and Anti‐herpetic Activity of Phosphoramidate ProTides

Among the many prodrug approaches aimed at delivering nucleoside monophosphates into cells, the phosphoramidate ProTide approach is one that has shown success, which has made it possible for some of the phosphoramidates to enter into clinical trials. Herein, we report the synthesis and antiviral activity of a series of phosphoramidate ProTides designed to bypass the thymidine kinase (TK) dependence of the parent nucleoside analogues. Phosphoramidate derivatives of (E)‐5‐(2‐bromovinyl)‐2′‐deoxyuridine (BVDU) that contain L ‐alanine or pivaloyloxymethyl iminodiacetate (IDA‐POM) exhibit anti‐HSV‐1 and anti‐VZV activity in cell cultures, but they largely lost antiviral potency against TK‐deficient virus strains. Among deazapurine nucleosides and their phosphoramidate derivatives, the 7‐deazaadenine containing nucleosides and their phosphoramidate triester derivatives showed weak antiviral activity against VZV. Apparently, intracellular nucleotide delivery with these phosphoramidates is partly successful. However, none of the compound prodrugs showed superior activity to their parent drugs.     

Discovery of an Acyclic Nucleoside Phosphonate that Inhibits Mycobacterium tuberculosis ThyX Based on the Binding Mode of a 5‐Alkynyl Substrate Analogue

The urgent need for new antibiotics poses a challenge to target un(der)exploited vital cellular processes. Thymidylate biosynthesis is one such process due to its crucial role in DNA replication and repair. Thymidylate synthases (TS) catalyze a crucial step in the biosynthesis of thymidine 5‐triphosphate (TTP), an elementary building block required for DNA synthesis and repair. To date, TS inhibitors have only been successfully applied in anticancer therapy due to their lack of specificity for antimicrobial versus human enzymes. However, the discovery of a new family of TS enzymes (ThyX) in a range of pathogenic bacteria that is structurally and biochemically different from the “classic” TS (ThyA) has opened the possibility to develop selective ThyX inhibitors as potent antimicrobial drugs. Here, the interaction of the known inhibitor 5‐(3‐octanamidoprop‐1yn‐1yl)‐2′‐deoxyuridine‐5′‐monophosphate ( 1 ) with Mycobacterium tuberculosis ThyX enzyme is explored using molecular modeling starting from published crystal structures, with further confirmation through NMR experiments. While the deoxyuridylate (dUMP) moiety of compound 1 occupies the cavity of the natural substrate in ThyX, the rest of the ligand (the “5‐alkynyl tail”) extends to the outside of the enzyme between two of its four subunits. The hydrophobic pocket that accommodates the alkyl part of the tail is formed by displacement of Tyr 44.C, Tyr 108.A and Lys 165.A. Changes to the resonance of the Lys 165 NH₃ group upon ligand binding were monitored in a titration experiment by 2D HISQC NMR. Guided by the results of the modeling and NMR studies, and inspired by the success of acyclic antiviral nucleosides, compounds where a 5‐alkynyl uracyl moiety is coupled to an acyclic nucleoside phosphonate (ANP) were synthesized and evaluated. Of the compounds evaluated, sodium (6‐(5‐(3‐octanamidoprop‐1‐yn‐1‐yl)‐2,4‐dioxo‐3,4‐dihydropyrimidin‐1(2H)‐yl)hexyl)phosphonate ( 3 e ) exhibited 43 % of inhibitory effect on ThyX at 50 μM . While only modest activity was achieved, this is the first example of an ANP inhibiting ThyX, and these results can be used to further guide structural modifications to this class to develop more potent compounds with potential application as antibacterial agents acting through a novel mechanism of action.     

Synthesis and properties of aminopropyl nucleic acids

Oligonucleotides that contain up to three aminopropyl nucleoside analogues have been synthesized. Dimers of aminopropyl adenine and thymidine were prepared and used as building blocks by applying phosphoramidite chemistry. Both R and S isomers of the aminopropyl nucleosides were used. This incorporation led to a reduction of thermal stability of double-stranded DNA. Furthermore, the (R)-adenine analogue, which yielded (S)-APNA, can be considered as a candidate for universal base pairing.     

Local porosity analysis of pore structure in cement paste

Three-dimensional (3-D) local porosity theory (LPT) was originally proposed by Hilfer and recently used for the analysis of pore space geometry in model sandstone. LPT pursues to define the probability density functions of porosity and porosity connectivity. In doing so, heterogeneity differences in various sandstone samples were assessed. However, fundamental issues as to the stochastic concept of geometric heterogeneity are ignored in Hilfer's LPT theory. This paper focuses on proper sampling procedures that should be based on stochastic approaches to multistage sampling and geometric heterogeneity. Standard LPT analysis provides a 3-D microscopic modeling approach to materials. Traditional experimental techniques yield two-dimensional (2-D) section images, however. Therefore, this paper replaces the method for assessing material data in standard LPT theory to a more practical one, based on stereological, 3-D interpretation of quantitative image analysis data. The developed methodology is used to characterize the pore structure in hardened cement paste with various water/cement ratios (w/c) at different hydration stages.     

Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis

Sucrose phosphorylase is a promising biocatalyst for the glycosylation of a wide variety of acceptor molecules, but its low thermostability is a serious drawback for industrial applications. In this work, the stability of the enzyme from Bifidobacterium adolescentis has been significantly improved by a combination of smart and rational mutagenesis. The former consists of substituting the most flexible residues with amino acids that occur more frequently at the corresponding positions in related sequences, while the latter is based on a careful inspection of the enzyme's crystal structure to promote electrostatic interactions. In this way, a variant enzyme could be created that contains six mutations and whose half-life at the industrially relevant temperature of 60 °C has more than doubled compared with the wild-type enzyme. An increased stability in the presence of organic co-solvents could also be observed, although these effects were most noticeable at low temperatures.     

Iminodipropionic acid as the leaving group for DNA polymerization by HIV-1 reverse transcriptase

Previous studies have demonstrated that some selected amino monoacids and amino diacids can function as leaving groups in the polymerase‐catalyzed incorporation of deoxynucleotides into DNA. Among these, the iminodiacetic acid phosphoramidate of deoxyadenosine monophosphate (IDA‐dAMP) represents an interesting example, as it could overcome some of the problems observed when using L ‐aspartic acid as the leaving group, that is, poor chain elongation. We have now synthesized and evaluated a series of IDA‐dAMP analogues that bear either an extended aliphatic chain in the amino acid function, or a phosphonic acid moiety (substituting for the carboxylic acid function). Among these compounds, the nucleotide with an iminodipropionic acid leaving group (IDP‐dAMP) was identified as the best substrate; the excellent single incorporation (91 % conversion to a P+1 strand at 50 μM ) was at a substrate concentration ten times lower than that used for IDA‐dAMP). This nucleotide also presented improved kinetics and elongation capability compared to IDA‐dAMP. The analogues with T, G, and C base moieties were also investigated for their incorporation ability with HIV‐1 RT. The incorporation efficiency was found to decrease in the order A>T>G>C. The properties of the iminodipropionic acid as the leaving group surpass those of previously evaluated leaving groups; this acid will be a prime candidate for in vivo testing.     

State multiplicity in CSTR-separator-recycle polymerisation systems

This article continues earlier work (Comput. Chem. Eng. 24 (2000) 209) concerning the design and control of isothermal reactor-separator-recycle systems. The multiplicity behaviour of six reaction systems of increasing complexity, from one-reactant, first-order reaction to chain-growth polymerisation, is investigated. Below a critical value of the plant Damkohler number, Da<Da^cr, the only steady state involves infinite flow rates. Feasible steady states become possible if the critical value is exceeded, Da>Da^cr. For one-reaction systems, one stable steady state is born at a transcritical bifurcation. For consecutive-reaction systems, including polymerisation, a fold bifurcation can lead to two feasible steady states. Moreover, the transcritical bifurcation is destroyed when two reactants are involved. If the gel-effect is included, a maximum of four steady states are possible. When multiple steady states exist, the achievable conversion is constrained by the instability of the low-conversion branch. This has practical importance for polymerisation systems when the radicals’ quasi-steady state assumption is not valid or the gel effect is significant.     

Diffusion-reaction modelling of DNA hybridization kinetics on biochips

An analytical expression for the rate of DNA hybridization on the surface of DNA biochips is established for the case of a finite 1-D diffusion space. The expression allows to account for the diffusion-limited supply of unreacted probe DNA and was obtained by solving the continuous 1-D reaction-diffusion mass balance using a Finite Fourier Transform technique. The extrapolation of the presently considered 1-D case to the full 3-D case is outlined as well. By bringing the obtained result into concurrence with the results of a stochastic random walk study, the kinetic constant k of the continuous reaction-diffusion model could be expressed as a function of the basic physico-chemical parameters (persistence length and jump frequency of the Brownian motion, collision frequency, binding probability) of the individual molecules. With the availability of an analytical expression describing the full time course of the 1-D hybridization process, and by using the Damköhler number Da=kh/D_mol, the different reaction- and diffusion-limited regimes occurring during the course of a hybridization process can now be described in general, dimensionless terms, allowing to establish some very simple rules for the design of DNA biochips and flow-through biosensors.     

水泥基复合材料集料与浆体界面研究综述(一):实验技术

关于界面研究,概括起来主要可以从以下5个方面考虑：(1)界面研究的相关技术手段;(2)界面微观结构特征的研究;(3)界面微观结构的形成及劣化机理;(4)影响界面微观结构因素的研究;(5)界面过渡区的性能对材料宏观性能(包括：力学性能和耐久性)影响的研究。对这些问题的研究是为了回答以下2个问题：(1)各种层次的界面过渡区到底在多大程度上影响着整个材料的力学性能和耐久性;(2)通过改善界面来达到改善水泥基复合材料的性能这一措施是否可行。由于界面研究的技术手段与方法随着其它相关技术与设备的引入而不断取得新的进展,促进了水泥基复合材料集料与浆体界面相关研究也不断取得新的成果。关于界面研究的新实验技术和方法,从如下4个方面进行了描述：(1)与界面过渡区微观结构表征相关的实验技术;(2)与界面过渡区力学性能(包括：粘结强度、刚度和断裂力学性能)相关的技术和方法;(3)与界面过渡区传输性能相关的技术和方法;(4)与界面过渡区收缩性能相关的技术和方法。