纤维素酶的底物专一性

天然纤维素的有效酶解取决于外切葡聚糖纤维二糖水解酶（ＣＢＨ）和内切葡聚糖水解酶（ＥＧ）的协同作用。ＥＧ随机水解纤维素无定形区分子链内的β－１,４－糖苷键;ＣＢＨ则由分子链的还原性末端水解出纤维二糖。这种底物专一性差别的原因在于ＣＢＨ呈“桶状”的活性部痊表面存在２个“ｌｏｏｐ”结构,只能容许纤维素分子链的末端伸入到活性裂隙中。ＥＧ无“ｌｏｏｐ”结构在存在,对底物是充分可及的。ＥＧ催化结构域中底物结合     

Inactivation of Leuconostoc Mesenteroids NRRL B-512F Dextransucrase by Specific Modification of Lysine Residues with Pyridoxal-5′-Phosphate

Abstract

Dextransucrase from Leuconostoc mesentwoides NRRL B-512F was inactivated by pyridoxal-5′-phosphate (PLP). The inactivation was reversible in as much as the loss of enzyme activity was completely reversed by prolonged dialysis. PLP-modified dextransucrase after reduction with sodium borohydride showed a characteristic fluorescence emission maximum at 397 nm when excited at 325 nm. The stoichiometric results indicated that four lysine residues are modified by PLP under the experimental conditions. These results established for the first time that lysine residues are essential for the activity of dextransucrase.     

Conversion of the Extracellular Dextransucrase Isoenzymes from Leuconostoc mesenteroides NRRL B-1299

Effect of oxygen tension on l-lysine, l-threonine and l-isoleucine accumulation was investigated. Sufficient supply of oxygen to satisfy the cell’s oxygen demand was essential for the maximum production in each fermentation. The dissolved oxygen level must be controlled at greater than 0.01 atm in every fermentation, and the optimum redox potentials of culture media were above ?170 mV in l-lysine and l-threonine and above ?180 mV in l-isoleucine fermentations. The maximum concentrations of the products were 45.5 mg/ml for l-lysine, 10.3 mg/ml for l-threonine and 15.1 mg/ml for l-isoleucine. The degree of the inhibition due to oxygen limitation was slight in the fermentative production of l-lysine, l-threonine and l-isoleucine, whose biosynthesis is initiated with l-aspartic acid, in contrast to the accumulation of l-proline, l-glutamine and l-arginine, which is biosynthesized by way of l-glutamic acid.     

Relationships Between the Catechol Substrate Binding Site and Amphetamine, Cocaine, and Mazindol Binding Sites in a Kinetic Model of the Striatal Transporter of Dopamine In Vitro

Abstract: Experiments were conducted to determine how (−)-cocaine and S (+)-amphetamine binding sites relate to each other and to the catechol substrate site on the striatal dopamine transporter (sDAT). In controls, m -tyramine and S (+)-amphetamine caused release of dopamine from intracellular stores at concentrations ≥12-fold those observed to inhibit inwardly directed sDAT activity for dopamine. In preparations from animals pretreated with reserpine, m -tyramine and S (+)-amphetamine caused release of preloaded dopamine at concentrations similar to those that inhibit inwardly directed sDAT activity. S (+)-Amphetamine and m -tyramine inhibited sDAT activity for dopamine by competing for a common binding site with dopamine and each other, suggesting that phenethylamines are substrate analogues at the plasmalemmal sDAT. (−)-Cocaine inhibited sDAT at a site separate from that for substrate analogues. This site is mutually interactive with the substrate site ( K _int = 583 n M ). Mazindol competitively inhibited sDAT at the substrate analogue binding site. The results with (−)-cocaine suggest that the (−)-cocaine binding site on sDAT is distinct from that of hydroxyphenethylamine substrates, reinforcing the notion that an antagonist for (−)-cocaine binding may be developed to block (−)-cocaine binding with minimal effects on dopamine transporter activity. However, a strategy of how to antagonize drugs of abuse acting as substrate analogues is still elusive.     

FTMove: A Web Server for Detection and Analysis of Cryptic and Allosteric Binding Sites by Mapping Multiple Protein Structures

Protein mapping distributes many copies of different molecular probes on the surface of a target protein in order to determine binding hot spots, regions that are highly preferable for ligand binding. While mapping of X-ray structures by the FTMap server is inherently static, this limitation can be overcome by the simultaneous analysis of multiple structures of the protein. FTMove is an automated web server that implements this approach. From the input of a target protein, by PDB code, the server identifies all structures of the protein available in the PDB, runs mapping on them, and combines the results to form binding hot spots and binding sites. The user may also upload their own protein structures, bypassing the PDB search for similar structures. Output of the server consists of the consensus binding sites and the individual mapping results for each structure - including the number of probes located in each binding site, for each structure. This level of detail allows the users to investigate how the strength of a binding site relates to the protein conformation, other binding sites, and the presence of ligands or mutations. In addition, the structures are clustered on the basis of their binding properties. The use of FTMove is demonstrated by application to 22 proteins with known allosteric binding sites; the orthosteric and allosteric binding sites were identified in all but one case, and the sites were typically ranked among the top five. The FTMove server is publicly available at https://ftmove.bu.edu.     

The Formation of Glucose 1,6-Diphosphate from Fructose 1,6-Diphosphate by Yeast Phosphoglucomutase

It was found that fructose 1,6-diphosphate, the main intermediate of glycolysis, was able to act as a coenzyme of yeast phosphoglucomutase reaction. The mechanism of the coenzymatic activity of fructose 1,6-diphosphate was studied. It was indicated in the fructose 1,6-diphosphate dependent reaction that glucose 1,6-diphosphate was formed by the phosphate-transfer of fructose 1,6-diphosphate to glucose 1-phosphate in the first step, and in the second step the conversion of glucose 1-phosphate to glucose 6-phosphate, the original mutase reaction, occurred in the presence of glucose 1,6-diphosphate. The kinetic constants in the reaction of the first step were determined from the time courses of the fructose 1,6-diphosphate dependent reaction.     

Comparison of family 12 glycoside hydrolases and recruited substitutions important for thermal stability

As part of a program to discover improved glycoside hydrolase family 12 (GH 12) endoglucanases, we have studied the biochemical diversity of several GH 12 homologs. The H. schweinitzii Cel12A enzyme differs from the T. reesei Cel12A enzyme by only 14 amino acids (93% sequence identity), but is much less thermally stable. The bacterial Cel12A enzyme from S. sp. 11AG8 shares only 28% sequence identity to the T. reesei enzyme, and is much more thermally stable. Each of the 14 sequence differences from H. schweinitzii Cel12A were introduced in T. reesei Cel12A to determine the effect of these amino acid substitutions on enzyme stability. Several of the T. reesei Cel12A variants were found to have increased stability, and the differences in apparent midpoint of thermal denaturation (T(m)) ranged from a 2.5 degrees C increase to a 4.0 degrees C decrease. The least stable recruitment from H. schweinitzii Cel12A was A35S. Consequently, the A35V substitution was recruited from the more stable S. sp. 11AG8 Cel12A and this T. reesei Cel12A variant was found to have a T(m) 7.7 degrees C higher than wild type. Thus, the buried residue at position 35 was shown to be of critical importance for thermal stability in this structural family. There was a ninefold range in the specific activities of the Cel12 homologs on o-NPC. The most and least stable T. reesei Cel12A variants, A35V and A35S, respectively, were fully active. Because of their thermal tolerance, S. sp. 11AG8 Cel12A and T. reesei Cel12A variant A35V showed a continual increase in activity over the temperature range of 25 degrees C to 60 degrees C, whereas the less stable enzymes T. reesei Cel12A wild type and the destabilized A35S variant, and H. schweinitzii Cel12A showed a decrease in activity at the highest temperatures. The crystal structures of the H. schweinitzii, S. sp. 11AG8, and T. reesei A35V Cel12A enzymes have been determined and compared with the wild-type T. reesei Cel12A enzyme. All of the structures have similar Calpha traces, but provide detailed insight into the nature of the stability differences. These results are an example of the power of homolog recruitment as a method for identifying residues important for stability.     

Simultaneous saccharification and fermentation of amorphous cellulose to ethanol by recombinant Klebsiella oxytoca SZ21 without supplemental cellulase

A derivative of Klebsiella oxytoca M5A1 containing chromosomally integrated genes for ethanol production from Zymomonas mobilis (pdc, adhB) and endoglucanase genes from Erwinia chrysanthemi (celY, celZ) produced over 20 000 U endoglucanase l^–1 activity during fermentation. In combination with the native ability to metabolize cellobiose and cellotriose, this strain was able to ferment amorphous cellulose to ethanol (58–76% of theoretical yield) without the addition of cellulase enzymes from other organisms.     

Arabidopsis AtADF1 is Functionally Affected by Mutations on Actin Binding Sites

The plant actin depolymerizing factor (ADF) binds to both monomeric and filamentous actin, and is directly involved in the depolymerization of actin filaments. To better understand the actin binding sites of the Arabidopsis thaliana L. AtADF1, we generated mutants of AtADF1 and investigated their functions in vitro and in vivo. Analysis of mutants harboring amino acid substitutions revealed that charged residues (Arg98 and Lys100) located at the α‐helix 3 and forming an actin binding site together with the N‐terminus are essential for both G‐ and F‐actin binding. The basic residues on the β‐strand 5 (K82/A) and the α‐helix 4 (R135/A, R137/A) form another actin binding site that is important for F‐actin binding. Using transient expression of CFP‐tagged AtADF1 mutant proteins in onion (Allium cepa) peel epidermal cells and transgenic Arabidopsis thaliana L. plants overexpressing these mutants, we analyzed how these mutant proteins regulate actin organization and affect seedling growth. Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional, unless the affinity for actin monomers is also affected. The G‐actin binding activity of the ADF plays an essential role in actin binding, depolymerization of actin polymers, and therefore in the control of actin organization.     

Inhibition of Bacteriophage ϕX174 Replicaiive-form DNA Replication by Rifampicin

?X174 DNA synthesis as well as phage production was inhibited by rifampicin when added in early phase of infection. Rifampicin did not inhibit the formation of parental duplex replicative-form, RF, and it inhibited the synthesis of progeny RF under conditions where protein synthesis was not necessary to be synthesized continuously. In addition, replication of parental RF into progeny RF was inhibited by rifampicin under conditions where a high concentration of chloramphenicol did not affect the replication. Consequently, it could be concluded that RNA synthesis other than that required for protein synthesis was necessary for both the initiation and continuation of RF replication.     

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information

Proteases are enzymes that cleave and hydrolyse the peptide bonds between two specific amino acid residues of target substrate proteins. Protease-controlled proteolysis plays a key role in the degradation and recycling of proteins, which is essential for various physiological processes.Thus, solving the substrate identification problem will have important implications for the precise understanding of functions and physiological roles of proteases, as well as for therapeutic target identification and pharmaceutical applicability. Consequently, there is a great demand for bioinformatics methods that can predict novel substrate cleavage events with high accuracy by utilizing both sequence and structural information. In this study, we present Procleave, a novel bioinformatics approach for predicting protease-specific substrates and specific cleavage sites by taking into account both their sequence and 3D structural information. Structural features of known cleavage sites were represented by discrete values using a LOWESS data-smoothing optimization method,which turned out to be critical for the performance of Procleave. The optimal approximations of all structural parameter values were encoded in a conditional random field(CRF) computational framework, alongside sequence and chemical group-based features. Here, we demonstrate the outstanding performance of Procleave through extensive benchmarking and independent tests. Procleave is capable of correctly identifying most cleavage sites in the case study. Importantly, when applied to the human structural proteome encompassing 17,628 protein structures, Procleave suggests a number of potential novel target substrates and their corresponding cleavage sites of different proteases.Procleave is implemented as a webserver and is freely accessible at http://procleave.erc.monash.edu/.     

绿豆上胚轴中油菜素甾酮的结合特性

绿豆上胚轴中油菜素甾酮的结合特性徐如涓，何宇炯，王玉琴，赵敏橘（中国科学院上海植物生理研究所，上海２０００３２）关键词：油菜素甾酮，绿豆，上胚轴，结合位点近十年来的研究表明，由体类化合物广泛存在于植物体内，（Ｗｅｗｉｔｔ等１９８０，横田孝雄１９８７）...     

转录因子结合位点的计算预测方法研究进展

转录因子结合位点的计算预测是研究基因转录调控的重要环节,但现有算法的预测特异性偏低.在深入分析转录因子结合位点生物特征的基础上,对当前基于保守模体和基于比较基因组学的两类计算预测方法进行了综述,指出了方法各自的优点和不足,并探讨了可能的改进方向.     

Isolation of Taka-amylase A Peptides Required for Substrate Binding

An α-amylase from Aspergillus oryzae, Taka-amylase A (TAA), was cleaved into peptide fragments by an acid protease. Inactivation of TAA was greatly retarded by the addition of α-cyclodextrin or Ca²⁺. TAA peptide fragments were separated into two groups having no and high affinity to the substrate, soluble starch. This separation was done by the forced affinity chromatography method by a column of epichlorohydrin cross-linked soluble starch gel. Three peptides were isolated from the high-affinity fragments, purified by the ODS-120T column, and their amino acids were sequenced. Peptides I, II, and III originated from α2-helix, α3-helix, and β2-sheet, respectively, and all of these were located in the (β/α)₈ barrel of the main domain of TAA molecule. A stereo graphic view showed that Peptides I–III were at the cleft near the catalytic site. Occurrence of a Trp residue in all three peptides strongly suggested that Trp was very important in the binding of TAA to the substrate, soluble starch.     

MiyabenolC和KobophenolA与雌激素受体的结合位点

iyabenolC (MiyC)和kobophenolA (KobA)是两种新型的植物雌激素。为了探讨MiyC和KobA与雌激素受体 (ER)的结合部位 ,运用计算机辅助分子模拟构建它们与ER结合的空间模型 ,找出结合位点 ,设计ER的两个突变体M1ER(ERM517AG52 1D)和M2ER(ERE353GR394 G) ;运用PCR技术将ER与MiyC或KobA的结合位点进行突变 ;运用报告基因检测实验 ,检测MiyC和KobA对突变的ER是否具有激活功能。结果显示MiyC激活M1ER使之促下游基因转录的作用下降 ,KobA对M1ER无激活作用 ;MiyC和KobA对M2ER无激活作用。以上结果显示MiyC和KobA与ER的结合位点可能为ER的Glu353 、Arg394 、Met517和Gly52 1。     

Legionella pneumophila secretes an endoglucanase that belongs to the family-5 of glycosyl hydrolases and is dependent upon type II secretion

Examination of cell-free culture supernatants revealed that Legionella pneumophila strains secrete an endoglucanase activity. Legionella pneumophila lspF mutants were deficient for this activity, indicating that the endoglucanase is secreted by the bacterium's type II protein secretion (T2S) system. Inactivation of celA , encoding a member of the family-5 of glycosyl hydrolases, abolished the endoglucanase activity in L. pneumophila culture supernatants. The cloned celA gene conferred activity upon recombinant Escherichia coli . Thus, CelA is the major secreted endoglucanase of L. pneumophila . Mutants inactivated for celA grew normally in protozoa and macrophage, indicating that CelA is not required for the intracellular phase of L. pneumophila . The CelA endoglucanase is one of at least 25 proteins secreted by the type II system of L. pneumophil a and the 17th type of enzyme effector associated with this pathway. Only a subset of the other Legionella species tested expressed secreted endoglucanase activity, suggesting that the T2S output differs among the different legionellae. Overall, this study represents the first documentation of an endoglucanase (EC 3.2.1.4) being produced by a strain of Legionella .     

化学突变具有底物结合部位的单克隆抗体制备含硒抗体酶

开发了一种制备抗体酶的新方法。用二硝基氯苯（ＤＮＣＢ）专一地与谷胱甘肽（ＧＳＨ）的巯基反应,合成出半抗原ＧＳＨ－Ｓ－ＤＮＰ。用戊二醛将半抗原偶联到牛血清白蛋白（ＢＳＡ）上,制成全抗原。再用标准的单抗制备法获得具有ＧＳＨ结合部位的单抗（４Ａ４ＩｇＧ）。用苯甲基磺酞氟（ＰＭＳＦ）和Ｈ２Ｓｅ相继处理该单抗,则将单拉结合部位上的丝氨酸（Ｓｅｒ）突变成硒代半胱氨酸（ＳｅＣｙｓ,因而在单抗结合部位上引入了谷胱甘肽过氧化物酶（ＧＰＸ）的催化基团。突变后的单抗具有ＧＰＸ活性,其活力已达到天然ＧＰＸ的数量级水平。动力学行为也与天然ＧＰＸ类似。这种新的含硒抗体酶有优于ＧＰＸ的一些特点。