Making and breaking peptide bonds: protein engineering using sortase

Sortases are a class of bacterial enzymes that possess transpeptidase activity. It is their ability to site-specifically break a peptide bond and then reform a new bond with an incoming nucleophile that makes sortase an attractive tool for protein engineering. This technique has been adopted for a range of applications, from chemistry-based to cell biology and technology. In this Minireview we provide a brief overview of the biology of sortase enzymes and current applications in protein engineering. We identify areas that lend themselves to further innovation and that suggest new applications.     

The use of a radiation inactivation method for characterization of the structure and catalytic properties of enzymes

The use of a radiation inactivation method for studies of the properties of enzymes of different classes is discussed. The possibilities of characterization of enzymes on the basis of the radiation-chemical parameters concerned are described.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No, 12, pp. 2828–2836, December, 1996.     

A proposed complementary pairing mode between single-stranded nucleic acids and β-stranded peptides: A possible pathway for generating complex biological molecules

A structure for a heterologous double-stranded molecule consisting of an oligoribonucleotide and a β-stranded oligopeptide, paired through complementary Watson-Crick-type hydrogen bonding, is proposed. The basis for such complementary pairings between oligoribonucleotides and oligopeptides is the close correspondence of the distances between the side-chains attached to the backbones of the two molecules. Both inter-nucleotide spacing and inter-amino acid side-chain spacing are approximately 3.4 Å. These kinds of interactions may have implications in protein-mediated-RNA splicing. Formation of a heterologous duplex through such a pairing mode could provide a simple coding mechanism for a reciprocal information transfer between oligonucleotides and oligopeptides. Because of its simplicity and versatility, allowing both specific and nonspecific coding, interactions via these kinds of pairing may have been relevant for prebiotic molecular evolution and for generating complex biological molecules.     

特异性识别半胱氨酸荧光探针的合成及细胞成像研究

基于光诱导电子转移(PET)机制,利用Cys亲核性较强,能够与探针分子发生亲核取代反应,使丙烯酰基离去,使探针分子体系内PET过程失效,合成了一种特异性识别半胱氨酸的荧光探针。当向探针溶液分别加入多种测试物时,除与Cys结构类似的Hcy和GSH会引起探针溶液微弱的荧光变化外,其他氨基酸均不会引起探针溶液荧光强度的变化,该探针对Cys具有良好的选择性和灵敏度,可在生理条件下检测Cys,并且区分Hcy和GSH。同时,该探针成功实现了细胞内Cys的荧光成像,为在生物学及医学中的实际应用建立了一种特异性识别Cys的分析方法。     

Isolation of New Polyketide Synthase Gene Fragments and a Partial Gene Cluster from East China Sea and Function Analysis of a New Acyltransfrase

Using the consensus-degenerate hybrid oligonucleotide primer polymerase chain reaction method, 26 new ketoacyl synthase (KS) fragments were isolated from a marine sediment sample in the East China Sea (ECS) and analyzed by construction of a phylogenetic tree. With a digoxigenin-labeled KS gene fragment used as a probe, a partial polyketide synthase (PKS) gene cluster was isolated and identified by hybridization screening of a marine sediment sample metagenome fosmid library constructed for this study. A new acyltransferase (AT) gene was cloned from the PKS gene cluster and heterogeneously expressed as a protein fused to maltose-binding protein (MBP). Ultraviolet spectrophotometry was used to study the binding of the MBP–AT fusion protein and single AT domain to substrates using MBP and bovine serum albumin as control proteins. Binding constants (Ka, per micromolar) were calculated and used to analyze the substrate specificity of the acyltransferase. We concluded that there are many unrevealed new PKS gene clusters in marine sediments in the ECS. The acyltransferase is presumably an acetyltransferase from a new PKS gene cluster.     

基于氨基酸位置特异性的蛋白质Loop区结构预测改进方法

蛋白质loop区的结构预测是理解蛋白质功能的重要一环,而长loop区的结构预测至今还是生物信息学中的难题.目前己经出现了多种loop结构的算法,其中LEAP是预测精度最高的算法之一,但它在长loop区初始主链构象采样上仍有较大的改进余地.本文中我们将蛋白质二级结构预测算法SPINE X与LEAP算法结合起来,构建了新的主链扭转角分布图(拉氏图),在主链初始构象采样中引入氨基酸在蛋白序列中的位置特异性信息,使得初始构象的采样更具针对性,对取自CASP10单链蛋白的loop测试集的分析表明,对长度为10,11,12个氨基酸的长loop区,改进后算法都比原始LEAP算法的预测精度有显著提升.这种引入氨基酸位置特异性从而提高预测精度的思路有望进一步推广至loop结构预测的其他算法.     

Structure-function relationships of a catalytically efficient β-<Emphasis Type="SmallCaps">D</Emphasis>-xylosidase

β-d-Xylosidase from Selenomonas ruminantium is revealed as the best catalyst known (k _cat, k _cat/K _m) for promoting hydrolysis of 1,4-β-d-xylooligosaccharides. ¹H nuclear magnetic resonance experiments indicate the family 43 glycoside hydrolase acts through an inversion mechanism on substrates 4-nitrophenyl-β-d-xylopyranoside (4NPX) and 1,4-β-d-xylobiose (X2). Progress curves of 4-nitrophenyl-β-d-xylobioside, xylotetraose and xylohexaose reactions indicate that one residue from the nonreducing end of substrate is cleaved per catalytic cycle without processivity. Values of k _cat and k _cat/K _m decrease for xylooligosaccharides longer than X2, illustrating the importance to catalysis of subsites −1 and +1 and the lack there of subsite +2. Homology models of the enzyme active site with docked substrates show that subsites bey ond−1 are blocked by protein and subsites bey ond +1 are not formed; they suggest that D14 and E186 serve catalysis as general base and general acid, respectively. Individual mutations, D14A and E186A, erode k _cat and k _cat/K _m by <10³ and to asimilar extent for substrates 4NPX and 4-nitrophenyl-α-l-arabinofuranoside (4NPA), indicating that the two substrates share the same active site. With 4NPX and 4NPA, pH governs k _cat/K _m with pK _a values of 5.0 and 7.0 assigned to D14 and E186, respectively. k _cat (4NPX) has a pK _a value of 7.0 and k _cat (4NPA) is pH independent above pH 4.0, suggesting that the catalytically inactive, “dianionic” enzyme form (D14-E187-) binds 4NPX but not 4NPA. The mention of firm names or trade products does not imply that they are end orsed or recommended by the US Department of Agriculture over other firms or similar products not mentioned.     

Preparation of a multi-hapten antigen and broad specificity polyclonal antibodies for a multiple pesticide immunoassay

A multi-determinant artificial antigen was prepared by haptens of four pesticides (chlorpyrifos, triazophos, carbofuran and parathion methyl) conjugating to the carrier protein BSA in turn. Male New Zealand white rabbits were immunized with this multi-determinant immunogen to produce the polyclonal antibodies (PAbs), which can recognize the four pesticides. The PAbs displayed high level for each relative hapten-OVA conjugate, with the favorable titers of 4.49 × 10⁴, 8.98 × 10⁴, 2.24 × 10⁴ and 1.86 × 10⁴, for CHBu-OVA, THHe-OVA, BFNB-OVA and MP5-OVA, respectively. Characterization studies of the PcAbs showed that it has high affinity and specificity to the four relative pesticides. An indirect competitive ELISA was developed for multi-residue determination. The I₅₀ value for the four pesticides was 0.290, 0.065, 0.582 and 2.824 μg mL⁻¹, with the detection limit (I₁₀) of 0.022, 0.005, 0.015 and 0.115 μg mL⁻¹ for carbofuran, triazophos, chlorpyrifos and parathion methyl, respectively. The linear rang was 0.016-2.000, 0.005-0.500, 0.010-2.000 and 0.063-5.000 μg mL⁻¹, respectively, for carbofuran, triazophos, chlorpyrifos and parathion methyl. Results indicated that, this study provided a new strategy to develop immunoassays through artificial antigen design for pesticides multi-residue determination.     

A highly specific immunoassay for microcystin-LR detection based on a monoclonal antibody

Microcystins (MC) are cyanobacterial hepatotoxins responsible for animal-poisoning and human health incidents. Immunoassays provide a sensitive and fast means to detect these toxins, but cross-reactivity (CR) characteristic of different antibodies was variable. Here, we have produced and characterized a monoclonal antibody (Clone MC8C10) with highly specificity against the most frequent and most toxic variant of microcystins, MC-LR. MC8C10 is more specific against MC-LR among the reported antibodies before. The immunogen was synthesized from the modified MC-LR and bovine serum albumin (BSA). An indirect competitive enzyme-linked immunosorbent assay (ic-ELISA) with MC8C10 was established to detect the MCs in waters, which showed highly specificity with MC-LR, and have a detection limit for MC-LR 0.1 μg L⁻¹, the 50% inhibition concentration (IC₅₀) for MC-LR was 1.8 ± 0.1 μg L⁻¹ and the quantitative detection range was from 0.3 to 10 μg L⁻¹. The [4-arginine] microcystins and the nodularin-R showed lower cross-reactivates (CR < 10%), and other MCs such as MC-LF and MC-LW are not recognized (CR < 10⁻⁴). The analysis results of real water samples with ic-ELISA showed that all the coefficients of variation were less than 15%, and the recovery was (100.3 ± 5.9)%. So the highly specific ic-ELISA will commendably suit for sensitive analysis for MC-LR in surface water as well as drinking water.