Purification and cloning of the novel phosphoprotein copine III and characterization of its associated kinase activity

The copines, named and first described by Creutz et al. (1998), comprise a two C2 domain-containing protein family that can aggregate phosphatidylserine membranes in a calcium-dependent manner. Although no enzymatic function has been attributed to copines, their carboxyl terminus shows homology to the A domain found in integrins that allows binding of magnesium ions. The secondary structure of A domains resembles a Rossmann fold, which can bind dinucleotides and is present in a number of intracellular enzymes. Due to a crossreacting activity of Mik b 1, an antibody to the IL-2R b chain, we were able to serendipitously clone human copine III (CIII). CIII is 65% identical to copine I (CI) and the 5 kb CIII transcript is expressed ubiquitously as determined by a multitissue Northern blot. A polyclonal antibody generated against the carboxyl terminus of CIII recognized CIII in immunoblots and immunoprecipitations. Phosphorylation of CIII was observed on serine and threonine residues, as determined by phosphoamino acid analysis. ^ Experiments were designed to determine whether or not any enzymatic activity, specifically kinase activity, was intrinsic to or associated with CIII. In vitro and in gel kinase assays were performed using transfected HA-tagged CI and CIII, immunoprecipitated endogenous CIII and purified endogenous CIII. The exogenous substrate MBP was phosphorylated in all in vitro kinase assays containing CIII protein purification and column chromatography expertise with me. ^

RNA-Activated Protein Kinase, PKR

The double-stranded RNA (dsRNA) activated protein kinase, PKR, is one of the several enzymes induced by interferons and a key molecule mediating the antiviral effects of interferons. PKR contain an N-terminal, double-stranded RNA binding domain (dsRBD), which has two tandem copies of the motifs (dsRBM I and dsRBM II). Upon binding to viral dsRNA, PKR is activated via autophosphorylation. Activated PKR has several substrates; one of the examples is eukaryotic translation initiation factor 2 (eIF2a). The phosphorylation of eIF2a leads to the termination of cell growth by inhibiting protein synthesis in response to viral infection. The objective of this project was to characterize the dsRBM I and define the dsRNA binding using biophysical methods. First, the dsRBM I gene was cloned from a pET-28b to a pET-11a expression plasmid. N-terminal poly-histidine tags on pET-28b are for affinity purification; however, these tags can alter the structure and function of proteins, thus the gene of dsRBM I was transferred into the plasmid without tags (pET-11a) and expressed as a native protein. The dsRBM I was transformed into and expressed by Rosetta DE3plyS expression cells. Purification was done by FPLC using a Sepharose IEX ion exchange followed by Heparin affinity column; yielding pure protein was assayed by PAGE. Analytical Ultracentrifugation, Sedimentation Velocity, was used to characterize free solution association state and hydrodynamic properties of the protein. The slight decrease in S-value with concentration is due to the hydrodynamic non-ideality. No self association was observed. The obtained molecule weight was 10,079 Da. The calculated sedimentation constant at zero concentration at 20°C in water was 1.23 and its friction coefficient was 3.575 ´ 10-8. The frictional ratio of sphere and dsRBM I became 1.30. Therefore, dsRBM I must be non-globular and more asymmetric shape. Isolated dsRBM I exhibits the same tertiary fold as compared to context in the full domain but it exhibited weaker binding affinity than full domain to a 20 bp dsRNA. However, when the conditions allowed for its saturation, dsRBM I to 20 bp dsRNA has similar stoichiometry as full dsRBD.

DNA strand annealing is promoted by the yeast Rad52 protein.

The Saccharomyces cerevisiae RAD52 gene plays a pivotal role in genetic recombination. Here we demonstrate that yeast Rad52 is a DNA binding protein. To show that the interaction between Rad52 and DNA is direct and not mediated by other yeast proteins and to facilitate protein purification, a recombinant expression system was developed. The recombinant protein can bind both single- and double-stranded DNA and the addition of either Mg2+ or ATP does not enhance the binding of single-stranded DNA. Furthermore, a DNA binding domain was found in the evolutionary conserved N terminus of the protein. More importantly, we show that the protein stimulates DNA annealing even in the presence of a large excess of nonhomologous DNA. Rad52-promoted annealing follows second-order kinetics and the rate is 3500-fold faster than that of the spontaneous reaction. How this annealing activity relates to the genetic phenotype associated with rad52 mutant cells is discussed.

Purification of a ligand for the EPH-like receptor HEK using a biosensor-based affinity detection approach.

Advances in screening technologies allowing the identification of growth factor receptors solely by virtue of DNA or protein sequence comparison call for novel methods to isolate corresponding ligand growth factors. The EPH-like receptor tyrosine kinase (RTK) HEK (human EPH-like kinase) was identified previously as a membrane antigen on the LK63 human pre-B-cell line and overexpression in leukemic specimens and cell lines suggested a role in oncogenesis. We developed a biosensor-based approach using the immobilized HEK receptor exodomain to detect and monitor purification of the HEK ligand. A protein purification protocol, which included HEK affinity chromatography, achieved a 1.8 X 10(6)-fold purification of an approximately 23-kDa protein from human placental conditioned medium. Analysis of specific sHEK (soluble extracellular domain of HEK) ligand interactions in the first and final purification steps suggested a ligand concentration of 40 pM in the source material and a Kd of 2-3 nM. Since the purified ligand was N-terminally blocked, we generated tryptic peptides and N-terminal amino acid sequence analysis of 7 tryptic fragments of the S-pyridylethylated protein unequivocally matched the sequence for AL-1, a recently reported ligand for the related EPH-like RTK REK7 (Winslow, J.W., Moran, P., Valverde, J., Shih, A., Yuan, J.Q., Wong, S.C., Tsai, S.P., Goddard, A., Henzel, W.J., Hefti, F., Beck, K.D., & Caras, I.W. (1995) Neuron 14, 973-981). Our findings demonstrate the application of biosensor technology in ligand purification and show that AL-1, as has been found for other ligands of the EPH-like RTK family, binds more than one receptor.

Purification and characterisation of two cancer cachexia factors

Cachexia is a wasting phenomenon that often accompanies malignant disease. Its manifestation is associated with shortened survival and reduced responsiveness to anti-tumour therapy and as yet there is no established, effective amelioratory treatment. The MAC 16 model of cancer cachexia has been shown by many studies to closely mirror the human condition. Thus, cachexia is mediated by the presence of a small, slow-growing solid tumour that is mainly resistant to chemotherapy. In addition, the condition is largely attributable to aberrations in metabolic processes, while weight loss due to anorexia is negligible. Cachexia induced by the MAC 16 tumour, has been shown to be mediated by the production of tumour-derived circulatory catabolic factors, and the further elucidation of the structure of these molecules contributes towards the main content of this report. Thus, a factor with in vitro lipid-mobilising activity has been purified from the MAC 16 tumour, and has been found to have similarities to tumour-derived lipolytic factors published to date. Further work demonstrated that this factor was also purifiable from the urine of a patient with pancreatic cancer, and that it was capable of inducing weight loss in non tumour-bearing mice. Sequence analysis of the homogeneous material revealed an identity to Zn-α-2-glycoprotein, the significance of which is discussed. An additional factor, first detected as a result of its specific reactivity with a monoclonal antibody produced by fusion of splenocytes from MAC 16 tumour-bearing mice with mouse BALB/c myeloma cells, was identified as a co-purificant during studies to isolate the lipolytic factor. Subsequent purification of this material to homogeneity resulted in the determination of 18 of the N-terminal amino acids and revealed the highly glycosylated nature of its structure. Thus, this material (P24) was found to have an apparent molecular mass of 24kD of which 2kD was due to protein, while the remainder (92%) was due to the presence of carbohydrate groups. Sequence analysis of the protein core of P24 revealed an identity with Streptococcal pre-absorbing antigen (PA-Ag) in 11 of the amino acids, and the significance of this is discussed. P24 was shown to induce muscle protein breakdown in vitro and to induce cachexia in vivo, as measured by the depletion of fat (29%) and muscle (14%) tissue in the absence of a reduction of food and water intake. Further studies revealed that the same material was purifiable from the urine of patients with pancreatic cancer and was found to be detectable in the urine of cancer patients with weight loss greater than l.Skg/month. Thus, cachexia induced by the MAC 16 tumour in mice and by malignant disease in humans may be induced by similar mediators. Attempts to isolate the gene for P24 using information provided by the N-terminal protein sequence were unsuccessful. This was probably due to the low abundance o[ the material, as determined by protein purification studies; and the nature of the amino acids of the N-terminal sequence, which conferred a high degree o[ degeneracy to the oligonucleotides designed for the polymerase chain reaction.

Detergent-free purification of ABC (ATP-binding-cassette) transporters

ABC (ATP-binding-cassette) transporters carry out many vital functions and are involved in numerous diseases, but study of the structure and function of these proteins is often hampered by their large size and membrane location. Membrane protein purification usually utilizes detergents to solubilize the protein from the membrane, effectively removing it from its native lipid environment. Subsequently, lipids have to be added back and detergent removed to reconstitute the protein into a lipid bilayer. In the present study, we present the application of a new methodology for the extraction and purification of ABC transporters without the use of detergent, instead, using a copolymer, SMA (polystyrene-co-maleic acid). SMA inserts into a bilayer and assembles into discrete particles, essentially solubilizing the membrane into small discs of bilayer encircled by a polymer, termed SMALPs (SMA lipid particles). We show that this polymer can extract several eukaryotic ABC transporters, P-glycoprotein (ABCB1), MRP1 (multidrug-resistance protein 1; ABCC1), MRP4 (ABCC4), ABCG2 and CFTR (cystic fibrosis transmembrane conductance regulator; ABCC7), from a range of different expression systems. The SMALP-encapsulated ABC transporters can be purified by affinity chromatography, and are able to bind ligands comparably with those in native membranes or detergent micelles. A greater degree of purity and enhanced stability is seen compared with detergent solubilization. The present study demonstrates that eukaryotic ABC transporters can be extracted and purified without ever being removed from their lipid bilayer environment, opening up awide range of possibilities for the future study of their structure and function. © The Authors Journal compilation © 2014 Biochemical Society.

A novel vortex flow reactor for the purification of B-phycoerythrin from Porphyridium cruentum

The purification of B-phycoerythrin from a concentrated extract of disrupted Porphyridium cruentum cells was carried out using a new vortex flow reactor design for protein purification. The reactor behaved as an expanded bed in the laminar vortices flow regime where the Streamline DEAE resin was expanded by the axial flow and stabilized by the vortex flow. After the broth culture was centrifuged and resuspended in the adsorption buffer, the concentrated extract of disrupted cells was directly loaded into the vortex flow reactor. The purification of B-phycoerythrin was carried out in two steps: adsorption in the expanded bed and elution from the settled bed. 142.0 mg of B-phycoerythrin was eluted representing a total recovery yield of 86.6%. Prior to B-phycoerythrin purification, the protein adsorption of the vortex flow reactor was characterized through hydrodynamic studies and a dynamic capacity measurement using a standard protein.

Plant made anti-HIV microbicides-A field of opportunity

HIV remains a significant global burden and without an effective vaccine, it is crucial to develop microbicides to halt the initial transmission of the virus. Several microbicides have been researched with various levels of success. Amongst these, the broadly neutralising antibodies and peptide lectins are promising in that they can immediately act on the virus and have proven efficacious in in vitro and in vivo protection studies. For the purpose of development and access by the relevant population groups, it is crucial that these microbicides be produced at low cost. For the promising protein and peptide candidate molecules, it appears that current production systems are overburdened and expensive to establish and maintain. With recent developments in vector systems for protein expression coupled with downstream protein purification technologies, plants are rapidly gaining credibility as alternative production systems. Here we evaluate the advances made in host and vector system development for plant expression as well as the progress made in expressing HIV neutralising antibodies and peptide lectins using plant-based platforms. © 2012 Elsevier Inc.

Synthesis and modification of Alumina nanofibres and its applications

This thesis is a forward study of alumina nanofiber material in developing its applications biology field. It demonstrates that by applying proper modification strategy, alumina nanofiber is a promising material in protein purification and enzyme immobilization. The hydrophobic modification has dramatically improved the rejecting of protein molecular in purification system. On the other hand, utilisation of cross-linking agent firmly combined alumina nanofiber and target enzyme for immobilisation purpose. This step of progress could lead to inspiration of alumina nanofiber’s application in various area.

Investigation of the binding interactions between insulin and its receptor

This project investigated the interactions between insulin and its receptor. A combination of computational and experimental investigations resulted in the identification of four residues in non-canonical sites that, when mutated, had detrimental effects on insulin binding. An increased understanding of the binding mechanism will aid future research into diseases involving the insulin receptor and its relatives and could potentially lead to new therapeutic avenues to combat these health related issues.

Assay development for identifying inhibitors of the mycobacterial FadD32 activity

FadD32, a fatty acyl-AMP ligase (FAAL32) involved in the biosynthesis of mycolic acids, major and specific lipid components of the mycobacterial cell envelope, is essential for the survival of Mycobacterium tuberculosis, the causative agent of tuberculosis. The protein catalyzes the conversion of fatty acid to acyl-adenylate (acyl-AMP) in the presence of adenosine triphosphate and is conserved in all the mycobacterial species sequenced so far, thus representing a promising target for the development of novel antituberculous drugs. Here, we describe the optimization of the protein purification procedure and the development of a high-throughput screening assay for FadD32 activity. This spectrophotometric assay measuring the release of inorganic phosphate was optimized using the Mycobacterium smegmatis FadD32 as a surrogate enzyme. We describe the use of Tm (melting temperature) shift assay, which measures the modulation of FadD32 thermal stability, as a tool for the identification of potential ligands and for validation of compounds as inhibitors. Screening of a selected library of compounds led to the identification of five novel classes of inhibitors.

含铬或锰的新型固氮酶的纯化, 特性和结晶—棕色固氮菌突变种UW3中CrFe蛋白和MnFe蛋白的研究

以含MnSO4或Na2CrO4的无钼无氨的修改Burk’s培养基， 培养不能合成含钼固氮酶体系的棕色固氮菌 (Azotobacter vinelandii Lipmann) 突变种UW3， 发现在一定浓度范围内， MnSO4或Na2CrO4的加入有助于促进其生长。 菌体生长和C2H2还原活性曲线测定结果表明， 这种促进作用很可能是通过Mn或Cr取代Mo， 参与组装固氮酶中心原子簇， 从而影响固氮活性而实现的。 利用阴离子交换 (DEAE-52和Q-Sepharose FF) 和凝胶过滤 (Sephacryl S-200) 柱层析从两种菌体中纯化得到固氮酶组分Ⅰ蛋白 (分别命名为MnFe蛋白和CrFe蛋白)， 并对其进行了特性研究。 厌氧天然聚丙烯酰胺凝胶电泳 (PAGE) 和SDS-PAGE结果显示， 两种蛋白均为两种亚基组成的四聚体。 亚基可以与OP MoFe蛋白抗体发生免疫反应， 分子量分别略小于野生种OP MoFe蛋白的α和β亚基。 CrFe蛋白的C2H2还原活性， Ar下放氢活性和固氮活性分别相当于OP MoFe蛋白的36%， 38%和43%， 而MnFe蛋白活性相当于OP MoFe蛋白的50%左右， 并且两种蛋白与OP MoFe蛋白具有相似的固氮电子利用率。 对两种蛋白金属含量的测定证实其中分别含有Mn和Cr， 但仍存在少量Mo污染。 与OP MoFe蛋白相比，这两种蛋白圆二色谱的摩尔椭圆率 ([θ]) 除在450nm较接近外，在可见光区的其它波长处均显著降低。 与DT还原OP MoFe蛋白相似， CrFe蛋白和MnFe蛋白具有g≈4。3、3。7和2。0的特征EPR信号， 但各处信号强度比例不同。 在对污染Mo可能引起的信号进行校正后，CrFe蛋白的三个信号强度分别相当于DT还原OP MoFe蛋白的20%， 0%和10%， 而MnFe蛋白则分别相当于112%， 49%和65%。 上述结果表明， CrFe蛋白和MnFe蛋白与OP MoFe蛋白金属原子簇的主要差异很可能在于FeMco (M=Cr， Mn或Mo)的M种类， 而P-cluster结构和组成均未见大的差异。 利用气相扩散悬滴法对MnFe蛋白和CrFe蛋白结晶条件进行了筛选和初步优化， 确定了以Tris/Hepes， NaCl， MgCl2和PEG 8000为主要变量的沉淀剂体系， 寻找各组分对于晶体生长的最适浓度。 以此为基础探讨了应用气相扩散坐滴法和液-液扩散法对两种蛋白结晶条件的优化。 在一定条件下， 两种蛋白分别通过液-液扩散法获得了优质大单晶。 对从CrFe蛋白和MnFe蛋白制备物中培养出的蛋白质晶体的SDS-PAGE鉴定显示， 晶体由与OP MoFe蛋白相似的两种亚基组成。 通过 “神舟三号” 飞船搭载实验探讨了空间微重力对于厌氧蛋白质结晶的影响， 结果表明， 微重力有助于避免孪晶形成， 并具有长期培养后获得适于进行X-射线衍射分析的优质大单晶的潜在前景。 结合空间科学使固氮酶结构与功能研究得以发展， 这项工作是有意义并且可行的。

植物高赖氨酸蛋白质的分离和纯化及其N端序列核苷酸探针的合成

禾谷类作物水稻和小麦是人们的主要植物性食物来源．而这些作物种子蛋白质中人类不能合成的必需氨基酸含量不平衡，造成了优质蛋白质的缺乏和人体对蛋白质利用的极大浪费．大约有二分之一的谷类种子蛋白质和四分之一的大豆蛋白质不能被合理地利用。大多数禾本科作物包括水稻和小麦的种子蛋白质中第一限制性氨基酸是赖氨酸，纠正其不平衡现象可大大提商蛋白质的营养价值。本研究在高赖氨酸植物种的筛选、高赖氨酸种子储藏蛋白质的纯化及其基因的分离等方面开展了工作。 选用与禾本科亲缘关系较远的8个植物种为研究材料，它们分别属于榛科，十字花科、胡桃科、豆科、胡麻科和松科。氨基酸组分分析确定豆科和十字花科的三个植物种赖氨酸含量在5.5%以上，其中豆科植物四棱豆(Pso phocarpus tetragonolobus)种子全蛋白赖氨酸含量达7.9%．用5种提取液提取了四棱豆种子的清蛋白、球蛋白和全蛋白。经测定发现0.025M Tris.HCl(pH7.4)提取液提取的清蛋白赖氨酸含量高最．通过自然胶电泳，SDS-PAGB电泳，非变牲IEF和变性IEF／SDS双向电泳，对四棱豆种子清蛋白进行了定性研究。用变性IEF/ SDS双向电泳分析出60多种蛋白质和蛋白质亚基及多肽。研究中改进了等电聚焦电泳纯化蛋白质的方法，经处理的胶板显现出清晰的蛋白质带型，不需染色即可确定带的位置，从切下的胶条中洗脱的蛋白质，其纯度达到双向电泳纯和HPLC纯。用三种电溶方法(SDS-PAGE非变性IEF，变性IEF)纯化出三十一种蛋白质或多肽分子。分别进行了分子量确定和氨基酸组分分析，发现了一个赖氨酸含量高达11.4%的蛋白质，其分子量为18KD，并制备了该蛋白质的抗体，测定了18KD蛋白质N端30个氨基酸残基的顺序，根据这一顺序设计合成了一组17个核苷酸的基因探针．经鉴定单链DNA探针的纯度和总量达到了设计要求。用尿素法与CTAB法结合提取了四棱豆幼苗核基因组DNA，其分子量在50Kb以上，达到了构建GenormicDNA文库的要求．用bamHI EcoRI和HindⅢ三种酶切割提取的DNA，得到了分子量大小不同的片段。 对四棱豆种子蛋白质的定性、高赖氨酸蛋白质的纯化、18KD蛋白N端序列分析及寡核苷酸探针的合成以及GcnomicDNA的提取与酶切，尚未见有资料报道．这些工作为克隆高赖氨酸基因打下了良好的基础，对改良禾本科作物蛋白质品质意义深远．

Recent advance in the study of intein

Since the first intein was found, more and more attention were paid on it. It not only enrichs the content of the process that the gene transfers its information but also can be used in protein purification. The recent advance in the sequence characterist

Hydrodynamics in an expanded bed of large size ion-exchange resin, and natural product adsorption

Successful applications of expanded bed adsorption (EBA) technology have been widely reported in the literature for protein purification. Little has been reported on the recovery of natural products and active components of Chinese herbal preparations using EBA technology. In this study, the hydrodynamic behavior in an expanded bed of cation resin, 001 x 7 Styrene-DVB, was investigated. Ephedrine hydrochloride (EH) was used as a model natural product to test the dynamic binding capacity (DBC) in the expanded bed. EBA of EH directly from a feedstock containing powdered herbs has also been investigated. These particles are different from commercially available expanded bed adsorbents by virtue of their large size (20S to 1030 gm). When the adsorbent bed is expanded to approximately 1.3 to 1.5 times its settled bed height, the axial liquid-phase dispersion coefficient was found to be of the order 10(-5) m(2) s(-1), which falls into the range 1.0 x 10(-6) to 1.0 X 10(-5) m(2) s(-1) observed previously in protein purification. Because of the favorable column efficiency (low axial dispersion coefficient), the recovery yield and purification factor values of EH directly from a feedstock reached 86.5% and 18, respectively. The results suggest that EBA technology holds promise for the recovery of natural products and active components of Chinese herbal preparations.