Protein photocrosslinking reveals dimer of dimers formation on MarR protein in Escherichia coli

The multiple antibiotic resistance regulatory protein(MarR) binds to two promoter sites on the marO operator in Escherichia coli.Our study showed that more than one MarR dimer proteins bound to either of its two promoter sites(Site I and Site II),suggesting that MarR might form higher complexes than homodimers when bound to DNA inside E.coli cells.To further verify this hypothesis,we site-specifically incorporated a photocrosslinking probe at the interface between two MarR dimer proteins.Photolysis in living E.coli cells revealed a covalent linkage between the two interdimer subunits of MarR,suggesting that MarR forms dimer of dimers in vivo.     

MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

NMR elucidation of monomer–dimer transition and conformational heterogeneity in histone‐like DNA binding protein of Helicobacter pylori

Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone‐like DNA binding protein (Hup), which in its homo‐dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti‐H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup‐dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti‐H. pylori agents employing structure‐based‐rational drug discovery approach.     

Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.     

Binding of the Zn2+ ion to ferric uptake regulation protein from E. coli and the competition with Fe2+ binding: a molecular modeling study of the effect on DNA binding and conformational changes of Fur

The three dimensional structure of Ferric uptake regulation protein dimer from E. coli, determined by molecular modeling, was docked on a DNA fragment (iron box) and Zn²⁺ ions were added in two steps. The first step involved the binding of one Zn²⁺ ion to what is known as the zinc site which consists of the residues Cys 92, Cys 95, Asp 137, Asp141, Arg139, Glu 140, His 145 and His 143 with an average metal-Nitrogen distance of 2.5 Å and metal-oxygen distance of 3.1–3.2 Å. The second Zn²⁺ ion is bound to the iron activating site formed from the residues Ile 50, His 71, Asn 72, Gly 97, Asp 105 and Ala 109. The binding of the second Zn²⁺ ion strengthened the binding of the first ion as indicated by the shortening of the zinc-residue distances. Fe²⁺, when added to the complex consisting of 2Zn²⁺/Fur dimer/DNA, replaced the Zn²⁺ ion in the zinc site and when a second Fe²⁺ was added, it replaced the second zinc ion in the iron activating site. The binding of both zinc and iron ions induced a similar change in Fur conformations, but shifted residues closer to DNA in a different manner. This is discussed along with a possible role for the Zn²⁺ ion in the Fur dimer binding of DNA in its repressor activity. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Expression Characterization and Preparation of Human Amyloid Precursor Protein in Escherichia coli

To analyze whether expressed amyloid precursor protein(APP) existed in hydrophilic(cytoplasmid) or hy-drophobic(lipid bilayer) environment in E. coli and to obtain intact APP for study on its function, we investigated the expression characterization and preparation of the three intact isoforms APP770, APP751, and APP695 in E. coli. The results show that these expressed APPs existed both in hydrophilic cytoplasm region as inclusion bodies and hy-drophobic membrane region as membrane-bound state in E. coll. APPs in inclusion bodies were purified on an NTA-Ni2. agarose column after dissolving in the urea buffer and APPs in membrane-bound state were obtained by ultracentrifugation. The activity analysis indicates that APP770 and APP751 exhibited strong trypsin-inhibitory activity like the natural ones. These results indicate that E. coil cells can be used as host cells for the expression of human integral membrane protein like APP in either soluble or membrane-bound state unless the interest protein undergone post-translational modification is required.     

毛细管电泳技术分析PDGF-B基因启动子与蛋白质的复合物

 利用 1.0 %T ,0 %C的线性聚丙烯酰胺 (即丙烯酰胺和双丙烯酰胺的总质量分数是 1.0 % ,交联度为 0 % )作为筛分介质 ,对人体血小板长生因子 (PDGF) B基因启动子与核蛋白形成的复合物进行了分析。结果显示主要有两种核蛋白与PDGF B基因启动子具有较强的结合能力 ,能形成DNA蛋白质复合物。所得结论与传统凝胶电泳相似。该方法具有较高的分离度和良好的重现性 ,整个分析可在 5 0min内完成。该方法不失为一种基于PDGF为研究目标、用于PDGF与蛋白质复合物形成及抑制行为分析的快速、准确的实用方法。     

Spectral and molecular docking studies of nucleic acids/protein binding interactions of a novel organometallic palladium (II) complex containing bioactive PTA ligands: Its synthesis,anticancer effects and encapsulation in albumin nanoparticles

The organometallic palladium complex with nitrogen-containing heterocycles is a potent antitumor agent. Coordination of phosphorus ligands to organometallic complexes increases their hydrophilicity, promotes ligand−DNA interactions and damage level to cancer cells, and blocks division in target cells. In this study, a phosphaadamantane palladium complex ([Pd{(C,N)- (C₁₂H₈NH₂)} (PTA) Cl], PTA = 1,3,5-Triaza-7-phosphaadamantane) ( 2 ) was synthesized via the reaction of biologically active PTA with binuclear palladacycles [Pd₂{(C,N)-(C₁₂H₈NH₂)}₂(μ-Cl)₂] ( 1 ). In vitro studies of the complex with DNA (calf-thymus) explored by UV–Vis, emission titration, circular dichroism and helix melting methods showed that the complex interacts with DNA via an intercalative mechanism. Furthermore, competitive binding studies using warfarin, digoxin and ibuprofen site markers containing definite binding sites revealed the binding of the complex to site I on bovine serum albumin. The in vitro release mechanism of the palladium complex exhibited a biphasic pattern characterized by an initial burst release followed by a slower sustained release. Ultimately, in vitro evaluation of cytotoxicity and cell death showed that the complexes were able to decrease the viability of human cancer cell lines (MCF-7 and Jurkat) in a dose-dependent manner, but lower decreases were observed in the viability of normal fibroblast cells ASF-4 at the dosages evaluated. Finally, the order of in vitro anticancer activities was found to be consistent with the DNA-binding affinities.     

Structure Analysis of Streptococcal Protein G Fc Binding Domain

The gene fragment (191 bp) encoding protein G IgG Fc binding domain was isolated by PCR from group G streptococcus (CMCC32138), and a clone containing this gene fragment was found to give fine reactivity to human IgG when expressed in Escherichia coli. The complete nucleotide sequence of the gene fragment was determined. One base pair differs from previously reported protein Gnucleotide sequences, and resultsin an amino acid change (Ala-Thr), but this variation makes no difference in binding to the IgG Fc part by ELISA.The secondary structure of the protein G IgG Fc binding domain has been estimated by circular dichroism and assigned by computer algorithm.It shows a typical α-helix region in this domain.By breaking this α-helix region with recombinant DNA techniques, a 44 peptide, which contained the N-terminal 27 amino acid residues of this domain, was expressed in E. coli and showed no reactivity to IgG.The hydropathicity of this domain was also analyzed and compared with that of protein A relevant     

Sequential formation of yellow, red, and orange 1-phenyl-3,3-biphenylene-allene dimers prior to blue tetracene formation: Helicity reversal in trans-3,4-diphenyl-1,2-bis(fluorenylidene)cyclobutane

1-Phenyl-3,3-biphenyleneallene (2), the base-catalyzed rearrangement product of 9-phenylethynylfluorene (1) yields a yellow, head-to-tail dimer 6 that, upon gentle warming, is converted to the red tail-to-tail isomer trans-3,4-diphenyl-1,2-bis(fluorenylidene)cyclobutane (7), in which the two fluorenylidene moieties severely overlap. The helical sense of the fluorenylidene moieties in 7 matches that of the phenyl substituents, and the interplanar angle between the fluorenylidene moieties is 41 degrees . At 80 degrees C, 6 isomerizes to orange cis-3,4-diphenyl-1,2-bis(fluorenylidene)cyclobutane (8), which at 110 degrees C is converted to orange trans diastereomer 9, whereby the helicity of the overlapping fluorenylidene moieties is reversed from that in 7 such that they are aligned with the ring hydrogen atoms, and the interplanar angle between the fluorenylidene moieties is now 60 degrees . At 180 degrees C, 6 rearranges to dispirodihydrotetracene 3 and blue, electroluminescent diindenotetracene 4, which is readily oxidized to peroxide 5. In the solid state, both 3 and 4 adopt structures with Ci symmetry (only an inversion center) such that the central polycyclic framework is nonplanar. Deprotonation of yellow head-to-tail allene dimer 6 with tBuOK in DMSO and reprotonation with HOAc yields the [1,3]-hydrogen migration product 10, in which the proton originally on the cyclobutane ring is now sited at C9 on the exocyclic fluorenyl substituent. Analogously, deprotonation and reprotonation of orange dimer 9 furnishes [1,3]-hydrogen migration product 11. Side product 17, formed during the synthesis of 1 from 9-phenylethynylfluoren-9-ol, BF3 and Et3SiH, was shown to be a silyl-indene spiro-linked to C9 of fluorene. All products were characterized by NMR spectroscopy and X-ray crystallography, and the mechanisms of these interconversions are discussed.     

A novel detection of single-stranded DNA binding protein based on ss-DNA modified chip using surface plasmon resonance microscopy

An ss-DNA gold chip was prepared based on self-assembly of the thiol-derivatized oligonucleotide,and used for thedetermination of single-stranded binding protein(SSB)by surface plasmon resonance microscopy(SPR).The experiment resultsshowed that SSB binds ss-DNA with high specificity,and relative signal of SPR response is proportional to the concentration of SSBin the range of 0.1-100 ng/mL with a detection limit(S/N=3)of 0.07 ng/mL.     

蛋白质表面模块划分及其在结合位点预测中的应用

蛋白质-蛋白质复合物的结合位点预测是计算分子生物学的一个难题. 本文对蛋白质-蛋白质复合物数据集Benchmark 3.0 中的双链蛋白质复合物进行了研究, 计算了单体的残基溶剂可接近表面积和残基间的接触面积, 并据此提出了蛋白质表面模块划分方法. 发现模块的溶剂可接近表面积与其内部接触面积的乘积(PSAIA)值能够提供结合位点的信息. 在78 个双链蛋白质复合物中, 有74 个体系其受体或配体上具有最大或次大PSAIA值的模块是界面模块. 将该方法获得的结合位点信息应用在CAPRI竞赛Target 39 的复合物结构预测中取得了较好的结果. 本文提出的基于模块的蛋白质结合位点预测方法不同于以残基为基础且仅考虑表面残基的传统预测方法, 为蛋白质-蛋白质复合物结合位点预测提供了新思路.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

水产品中胂蛋白的提取方法研究

以蛤蜊为研究对象,建立了水产品中胂蛋白的提取方法.采用超声波细胞破碎法以Tris-HCl作为缓冲溶液提取蛤蜊中的胂蛋白;对提取的胂蛋白进行电泳分离纯化,采用氢化物发生-原子荧光光谱法对蛋白条带中As含量进行测定.根据实验结果分析,胂蛋白的最佳提取条件为:超声功率190 W,超声波每次辐射时间/间歇时间为5 s/5 s,...