Characterization of an Isozyme of β-Glucosidase from Sweet Almond

A sweet almond β-glucosidase (EC 3.2.1.21) isozyme was purified from commercial crude product. The process of purification consisted of a Protein-Pak Q anion exchange chromatography following by a Superdex 75 HR gel filtration separation. The purified enzyme is a monomeric glycoprotein with molecular weight of 58 kDa and pI=4.55 which is distinguished from reported isozymes. The enzyme has apH optimum in the range of 5.2-5.6 when p-nitrophenyl-β-D-glycopyranosides are used as substrate and is stable up to 50 °C at that pH range. The purified protein also exhibits profound β-galactosidase and σ-L-arabinosidase activity. The study of substrate specificity revealed that lacking of hydroxymethyl group at C-5 of glycosides resulted in higher affinity for substrate binding to enzyme, whereas the chemical step of hydrolysis (k_cst) was prevented significantly. The pH activity profile displayed a bell-shaped curve for all measured p-nitrophenyl-β-D-glycopyranosides with apparent pK₁ and pK₂ values of 4.4-4.7 and 6.2-6.4, respectively. This isozyme was strongly inhibited by δ-gluconolactone (K_i = 160 μM) and 4-phenylimidazole (K_i = 17.8 μM) reversibly at pH 6.2. Among the tested glycoses, the binding affinity of N-acetyl-β-D-glucosamine to the enzyme (K_l = 52 mM) was 6 times stronger than that of glucose and its epimers.     

Molecularly Imprinted Polymers with Bi-functional Monomers of Polymerizable Cyclodextrin Derivatives and 2-（Diethylamino）ethyl Methacrylate for Recognition of Norfloxacin in Aqueous Media

Molecular imprinting technique is one of the most promising methodologies for synthesizing artificial receptors and has already demonstrated their potential for the separation and analytical application1-6. In the case of molecularly imprinted polymers pr…     

The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.     

组织工程相关生物材料表面工程的研究进展

生物材料用作人工细胞外基质(ECM ) 在组织工程中占据重要位置。本文在分析细胞2生物材料表面相互作用的基础上, 从生物材料中的水、材料表面的形态、材料表面的特异性识别及生物材料诱发愈合等方面探讨了生物材料的复杂性。生物材料对细胞的影响是一个双向、动态过程, 起着调节细胞增殖和凋亡平衡的作用。基于生物材料对细胞生长的影响, 本文提出了生物材料表面生物仿生化以提高细胞亲和力,糖链团簇、糖脂质及材料表面蛋白质修饰以提高细胞特异性识别, 材料表面的自组装修饰以改善表面形态等观点。     

Substrate specificity of the human proteasome

BACKGROUND: Regulated proteolysis by the proteasome is crucial for a broad array of cellular processes, from control of the cell cycle to production of antigens. RESULTS: The rules governing the N-terminal primary and extended substrate specificity of the human 20S proteasome in the presence or absence of 11S proteasome activators (REGalpha/beta and REGgamma) have been elaborated using activity-based proteomic library tools. CONCLUSIONS: The 11S proteasome activators are shown to be important for both increasing the activity of the 20S proteasome and for altering its cleavage pattern and substrate specificity. These data also establish that the extended substrate specificity is an important factor for proteasomal cleavage. The specificities observed have features in common with major histocompatibility complex (MHC) class I ligands and can be used to improve the prediction of MHC class I restricted cytotoxic T-cell responses.     

胆酸印迹聚合物的制备及在含水介质中的结合性能

为了在含水介质中进行有效印迹,本研究中以双甲基丙烯酰-β-环糊精（BMA-β-CD）和2-(二乙基胺基)乙基甲基丙烯酸酯(DEAEM)为功能单体制备了胆酸印迹聚合物MIP1,并用平衡结合实验研究了MIP1在含水介质中对模板分子的识别能力。结果表明,MIP1比单独以BMA-β-CD或DEAEM为功能单体制备的印迹聚合物MIP2和MIP3,显示出对模板分子更好的选择性结合能力。MIP1的特异性吸附量ΔCP为38.81μmol/g,印迹因子IF为2.46。研究表明,在含水介质中,利用模板分子与功能单体之间的疏水作用和离子作用是提高印迹聚合物分子识别能力的关键。研究还表明,在识别过程中,疏水作用在驱动分子进入印迹孔穴时起重要作用。     

Comparative Study of Substrate- and Stereospecificity of Penicillin G Amidases from Different Sources and Hybrid Isoenzymes

Summary.  Four natural pencillin G amidase variants from different sources and two genetically constructed hybrid enzymes were produced and purified to homogeneity. The specificity constants of one enzyme (E. coli) were found to differ six orders of magnitude for hydrolytic transformations within a wide range of substrates. The substrate specificity of the homologous penicillin amidases was found to differ less than one order of magnitude for hydrolysis of the most specific and up to two orders of magnitude for the less specific substrates. The -substrate specificity in hydrolytic and transfer reactions (studied mainly with the E. coli enzyme) varied more than three orders of magnitude for the different substrates. The penicillin amidases were found to be R-specific in the S ₁-binding site and S-specific in the -binding site. The S ₁-stereoselectivity differs less than one order of magnitude for the different variants. The -stereoselectivity is more pronounced, increases with nucleophile specificity, and was found to differ up to three orders of magnitude in transfer reactions for the enzyme from E. coli. The observed variation of enatioselectivity for different penicillin amidases and one substrate can also be achieved by changes in temperature. Comparison of substrate- and stereospecificity of penicillin amidases from different sources and hybrid isoenzymes suggests that similar changes can be expected for enzyme variants derived by rational protein design or directed evolution. Received December 20, 1999. Accepted (revised) February 4, 2000     

Substrate specificity of <Emphasis Type="Italic">Streptomyces</Emphasis> transglutaminases

Transglutaminase (TGase) is a multifunctional enzyme vital for many physiologic processes, such as cell differentiation, tissue regeneration, and plant pathogenicity. The acyl transfer function of the enzyme can activate primary amines and, consequently, attach them onto a peptidyl glutamine, a reaction important for various in vivo and in vitro protein crosslinking and modification processes. To understand better the structure-function relationship of the enzyme and to develop it further as an industrial biocatalyst, we studied TGase secreted by several Streptomyces species and Phytophthora cactorum. We purified the enzyme from S. lydicus, S. platensis, S. nigrescens, S. cinnamoneus, and S. hachijoensis. The pH and temperature profiles of S. lydicus, S. platensis, and S. nigrescens TGases were determined. The specificity of S. lydicus TGase toward its acyl-accepting amine substrates was characterized. Correlation of the electronic and steric features of the substrates with their reactivity supported the mechanism previously proposed for Streptomyces mobaraensis TGase.     

Site specificity of OH α-H abstraction reaction for a β-hairpin peptide: an ab initio study

A β-hairpin peptide (PDB ID 1UAO) was modeled to explore the backbone oxidation of a protein by an OH radical to abstract one α-H atom with ab initio calculation at the B3LYB/6-31G(d) without any constraint. Three glycine residues located at three different sites in 1UAO were used to examine the possible site specificity of this backbone oxidation. The pre- and post-reactive complexes along with their associated transition states were located and verified by the intrinsic reaction coordinate method. The reaction profile of these α-H abstraction reactions was constructed. The effects of the aqueous solution were estimated by the conductor-like polarizable continuum model (CPCM) model. Rate constants were calculated with transition state theory. The reaction rate of the OH α-H abstraction varies among these three different sites. The differences among these three sites were rationalized in terms of the molecular and electronic structures of the reactive complexes along the reaction pathway. The explicit solvation effect was estimated through the similar abstraction of a zwitterionic glycine with the combination of microsolvation and a CPCM model. Our results indicate that the α-H abstraction at certain sites requires explicit salvation to obtain accurate results. A replica exchange molecular dynamics simulation was performed to demonstrate the structural change due to this type of abstraction.