非天然氨基酸突变的小鼠RANKL蛋白原核表达及抗血清制备

目的:研究非天然氨基酸突变的小鼠RANKL(m RANKL)蛋白的原核表达,并以表达的蛋白制备抗m RANKL蛋白的抗血清。方法:从小鼠的骨髓中提取总RNA,经PCR扩增m RANKL的胞外段,逆转录合成目的 DNA片段。将目的基因中编码第234位酪氨酸的密码子(TAT)突变成可编码非天然氨基酸p-硝基苯丙氨酸(p NO2Phe)的琥珀密码子(TAG),构建p ET28a-p NO2Phe234m RANKL重组表达载体,与p EVOL质粒共转化至表达菌E.coli BL-21(DE3),诱导表达并纯化。以纯化的蛋白免疫小鼠,制备小鼠抗m RANKL抗血清。采用ELISA测定抗血清效价,用Western Blot测定其特异性。结果:RT-PCR扩增出750bp的RANKL基因,并成功构建了p ET28a-p NO2Phe234m RANKL重组表达载体;p-硝基苯丙氨酸突变的m RANKL蛋白获得成功表达和纯化;以纯化的蛋白免疫小鼠,获得抗m RANKL抗血清,ELISA检测效价为1:6400,Western Blot结果显示该抗血清既可与p-硝基苯丙氨酸突变的m RANKL结合,也可与野生型m RANKL结合。结论:原核表达并纯化了p-硝基苯丙氨酸突变的m RANKL,制备了小鼠抗m RANKL的抗血清,为进一步研究阻断RANKL-RANK通路的新方法奠定了基础。     

Single-Molecule Imaging of a Fluorescent Unnatural Amino Acid Incorporated Into Nicotinic Receptors

We report on the first, to our knowledge, successful detection of a fluorescent unnatural amino acid (fUAA), Lys(BODIPYFL), incorporated into a membrane protein (the muscle nicotinic acetylcholine receptor, nAChR) in a living cell. Xenopus oocytes were injected with a frameshift-suppressor tRNA, amino-acylated with Lys(BODIPYFL) and nAChR (α/β19′GGGU/γ/δ) mRNAs. We measured fluorescence from oocytes expressing nAChR β19′Lys(BODIPYFL), using time-resolved total internal reflection fluorescence microscopy. Under conditions of relatively low receptor density (<0.1 receptors/μm²), we observed puncta with diffraction-limited profiles that were consistent with the point-spread function of our microscope. Furthermore, diffraction-limited puncta displayed step decreases in fluorescence intensity, consistent with single-molecule photobleaching. The puncta densities agreed with macroscopic ACh-induced current densities, showing that the fUAA was incorporated, and that receptors were functional. Dose-response relations for the nAChR β19′Lys(BODIPYFL) receptors were similar to those for wild-type receptors. We also studied nAChR β19′Lys(BODIPYFL) receptors labeled with α-bungarotoxin monoconjugated with Alexa488 (αBtxAlexa488). The nAChR has two αBtx binding sites, and puncta containing the Lys(BODIPYFL) labeled with αBtxAlexa488 yielded the expected three discrete photobleaching steps. We also performed positive control experiments with a nAChR containing enhanced green fluorescent protein in the γ-subunit M3-M4 loop, which confirmed our nAChR β19′Lys(BODIPYFL) measurements. Thus, we report on the cell-based single-molecule detection of nAChR β19′Lys(BODIPYFL).     

High-Yield,Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation

Synthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacterium Escherichia coli, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-l-tyrosine incorporation system in E. coli. A translational switch was turned on after addition of 3-iodo-l-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.     

Amino Acid Catabolism and Malic Enzyme in Differentiating Dictyostelium discoideum

Amino acids produced from protein degradation are the major energy source for differentiation and aging in Dictyostelium discoideum. Considering the reactions involved in the conversion of amino acids from an average protein into tricarboxylic acid cycle intermediates, a route from a cycle intermediate (probably malate) to acetyl coenzyme A is required for the complete utilization of amino acids. Citrate was isolated from cells pulse-labeled with (14)C-labeled amino acids and was cleaved with citrate lyase. When cells were pulse-labeled with [U-(14)C]-glutamate the specific radioactivity of the acetate and oxaloacetate portions of citrate were consistent with the conclusion that one-third of the carbon flowing through the tricarboxylic acid cycle is removed for the synthesis of acetyl coenzyme A. The data were also consistent with the patterns of carbon flux required to maintain steady-state levels of cycle intermediates in cells catabolizing amino acids. It is suggested that the malic enzyme (EC 1.1.1.40) catalyzes the synthesis of acetyl coenzyme A from malate and is responsible for the observed citrate labeling pattern. In cell extracts the activity of this enzyme increased markedly with the onset of differentiation. The properties of partially purified (40-fold) malic enzyme isolated at culmination indicated that the enzyme was allosteric and was positively affected by aspartate and glutamate. Thus, amino acid production from protein degradation would stimulate a reaction essential for the efficient utilization of these amino acids for energy.     

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

The MACiE database contains 223 distinct step-wise enzyme reaction mechanisms and holds representatives from each EC sub-subclass where there is a crystal structure and sufficient evidence in the literature to support a mechanism. Each catalytic step of every reaction sequence in MACiE is fully annotated so that it includes the function of the catalytic residues involved in the reaction and the mechanism by which substrates are transformed into products. Using MACiE as a knowledge base, we have seen that the top 10 most catalytic residues are histidine, aspartate, glutamate, lysine, cysteine, arginine, serine, threonine, tyrosine and tryptophan. Of these only seven (cysteine, histidine, aspartate, lysine, serine, threonine and tyrosine) dominate catalysis and provide essentially five functional roles that are essential. Stabilisation is the most common and essential role for all classes of enzyme, followed by general acid/base (proton acceptor and proton donor) functionality, with nucleophilic addition following closely behind (nucleophile and nucleofuge). We investigated the occurrence of these residues in MACiE and the Catalytic Site Atlas and found that, as expected, certain residue types are associated with each functional role, with some residue types able to perform diverse roles. In addition, it was seen that different EC classes of enzyme have a tendency to employ different residues for catalysis. Further, we show that whilst the differences between EC classes in catalytic residue composition are not immediately obvious from the general classes of Ingold mechanisms, there is some weak correlation between the mechanisms involved in a given EC class and the functions that the catalytic amino acid residues are performing. The analysis presented here provides a valuable insight into the functional roles of catalytic amino acid residues, which may have applications in many aspects of enzymology, from the design of novel enzymes to the prediction and validation of enzyme reaction mechanisms.     

Why Threonine Is an Essential Amino Acid in Mammals and Birds: Studies at the Enzyme Level

The only pathway for the synthesis of essential amino acids in vertebrates is reversible transamination of their keto analogs with glutamic acid. At the same time, it is commonly accepted that such essential amino acids as lysine and threonine are not involved in transamination and, therefore, cannot be synthesized from their keto analogs. However, using radio-labeled isotopes, synthesis of threonine was demonstrated in rat liver and in a reaction mixture containing chicken liver threonine dehydrogenase. In the review, we discuss why threonine is an essential amino acid in mammals and birds based on the pathways of threonine biosynthesis in these two classes of vertebrates.     

吊瓜籽中氨基酸质量分数的测定

样品吊瓜籽经酸水解处理,应用氨基酸分析仪进行分析,结果表明,吊瓜籽含所有常规17种氨基酸,质量分数高达23.28%,其中谷氨酸(G lu)和精氨酸(Agr)质量分数达4.39%和3.88%。     

The Amino Acid Sequence of Ribitol Dehydrogenase-F, a Mutant Enzyme with Improved Xylitol Dehydrogenase Activity

A mutant ribitol dehydrogenase (RDH-F) was purified from Klebsiella aerogenes strain F which evolved from the wild-type strain A under selective pressure to improve growth on xylitol, a poor substrate used as sole carbon source. The ratio of activities on xylitol (500 mM) and ribitol (50 mM) was 0.154 for RDH-F compared to 0.033 for the wild-type (RDH-A) enzyme. The complete amino acid sequence of RDH-F showed the mutations. Q60 for E60 and V215 for L215 in the single polypeptide chain of 249 amino acid residues. Structural modeling based on homologies with two other microbial dehydrogenases suggests that E60 Q60 is a neutral mutation, since it lies in a region far from the catalytic site and should not cause structural perturbations. In contrast, L215 V215 lies in variable region II and would shift a loop that interacts with the NADH cofactor. Another improved ribitol dehydrogenase, RDH-D, contains an A196 P196 mutation that would disrupt a surface -helix in region II. Hence conformational changes in this region appear to be responsible for the improved xylitol specificity.     

Disruption of an Amino Acid Transport Mutant of Neurospora crassa by KCl

A double amino acid transport-deficient mutant (Pm (-)NB) of Neurospora crassa is shown to be altered in the molecular structure of its cell wall or membrane. This alteration was revealed by a high degree of cellular disruption and cell-cell interaction following extraction by a high molar concentration of KCl.     

Tryptophan Metabolism of Rats Fed on an Amino Acid Diet Devoid of One Branched Chain Amino Acid

In an attempt to study on metabolic changes in rats fed on an amino acid diet devoid of one branched chain amino acid and of niacin, rats were force-fed a leucine-free, isoleucine-free, valine-free or complete amino acid diet for 3 or 4 days and killed 3 hr after the feeding on day 4 or 5 to observe the body weight changes, the urinary nitrogen and N¹-methylnicotinamide (MNA), and liver tryptophanpyrrolase (TPase) and tyrosine-α-keto-glutarate transaminase (TKase) activities.

The excretion of the urinary nitrogen and MNA, TPase and TKase activities, and fat content of livers of rats force-fed these amino acid deficient diets were higher than those fed the complete amino acid diet. It was further confirmed in the present study that changes in TPase activity of rats given diets devoid of one essential amino acid were in the same direction with changes in urinary MNA which was observed in the previous studies on rats given threonine-free, tryptophan-free, methionine-free, lysine-free and complete amino acid diets. However, such metabolic changes in rats fed the leucine-free diet were not so remarkable, compared with those of rats fed the other amino acid deficient diets.     

Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures

The α‐d‐phosphohexomutase superfamily comprises enzymes involved in carbohydrate metabolism that are found in all kingdoms of life. Recent biophysical studies have shown for the first time that several of these enzymes exist as dimers in solution, prompting an examination of the oligomeric state of all proteins of known structure in the superfamily (11 different proteins; 31 crystal structures) via computational and experimental analyses. We find that these proteins range in quaternary structure from monomers to tetramers, with 6 of the 11 known structures being likely oligomers. The oligomeric state of these proteins not only is associated in some cases with enzyme subgroup (i.e., substrate specificity) but also appears to depend on domain of life, with the two archaeal proteins existing as higher‐order oligomers. Within the oligomers, three distinct interfaces are observed, one of which is found in both archaeal and bacterial proteins. Normal mode analysis shows that the topological arrangement of the oligomers permits domain 4 of each protomer to move independently as required for catalysis. Our analysis suggests that the advantages associated with protein flexibility in this enzyme family are of sufficient importance to be maintained during the evolution of multiple independent oligomers. This study is one of the first showing that global motions may be conserved not only within protein families but also across members of a superfamily with varying oligomeric structures.     

Ninhydrin Positive Compounds Produced by Heating of Poly-l-amino Acids,Tripeptides and an Amino Acid Mixture

Glycosaminoglycans were isolated from bovine and human milk fat globule membrane (MFGM) preparations and characterized. The amount of glycosaminoglycans in human MFGM protein fraction was 5 ~ 10 times higher than that in bovine MFGM protein fraction. On Dowex-1 column chromatography most of the glycosaminoglycans were eluted with 1 M and 3 M NaCl. Cellulose acetate electrophoresis, chondroitinase digestion and nitrous acid degradation indicated that the major glycosaminoglycan in both bovine and human MFGM was heparan sulfate. Bovine MFGM was shown to contain chondroitin sulfate A/C in addition to heparan sulfate. The glycosaminoglycan composition of bovine colostral MFGM was similar to that of bovine normal MFGM. The glycosaminoglycan fraction prepared from MFGM of human colostrum, however, did not contain heparan sulfate, suggesting some compositional changes in glycosaminoglycans during the lactation period.     

Amino Acid incorporation by wheat chloroplasts

Isolated chloroplasts from wheat leaves incorporate radioactive amino acids into protein. Both physiological and biochemical evidence show that contaminating bacteria are not responsible for the activity. Activity is best in plastids from 5-day-old or younger seedlings; a sharp drop usually occurs by day 6 or 7. The system requires added adenosine triphosphate, guanosine triphosphate and Mg⁺⁺, and is inhibited by ribonuclease, puromycin and chloramphenicol. Preliminary evidence is presented that polyribosomes are present in the young leaf chloroplast fraction. Half of the protein that is formed in a 20-minute incubation is released in soluble form.     

五步蛇蛇毒类凝血酶N端的部分氨基酸序列

从五步蛇蛇毒中纯化得到的类凝血酶,在SDS-PAGE及IEF均为一条带,且分子质量约38 ku,等电点约为4.0。测定该酶N端15个氨基酸的序列是VIGGVECDINEHRFL,与其他的蛇毒类凝血酶有高度同源性。