Studies of electrons trapped in X-irradiated rhamnose crystals

The electrons trapped in single crystals of rhamnose X-irradiated at low temperature were studied by ENDOR spectroscopy. Hyperfine couplings of protons in the environs of the electron have been determined from ENDOR measurements, including those of some of the more remote carbon-bound hydrogen atoms. The likely site of electron trapping in the crystal structure of rhamnose was inferred from calculations of the electric potential generated by the dipoles of hydroxy groups about preexisting void spaces. Electron-proton distances for nonexchangeable hydrogen atoms from points within the void were calculated from the crystal structure and compared with distances obtained from hyperfine couplings. Good agreement was obtained between experimental and calculated values.     

High-throughput trapping of secretory pathway genes in mouse embryonic stem cells

High-throughput gene trapping is a random approach for inducing insertional mutations across the mouse genome. This approach uses gene trap vectors that simultaneously inactivate and report the expression of the trapped gene at the insertion site, and provide a DNA tag for the rapid identification of the disrupted gene. Gene trapping has been used by both public and private institutions to produce libraries of embryonic stem (ES) cells harboring mutations in single genes. Presently, approximately 66% of the protein coding genes in the mouse genome have been disrupted by gene trap insertions. Among these, however, genes encoding signal peptides or transmembrane domains (secretory genes) are underrepresented because they are not susceptible to conventional trapping methods. Here, we describe a high-throughput gene trapping strategy that effectively targets secretory genes. We used this strategy to assemble a library of ES cells harboring mutations in 716 unique secretory genes, of which 61% were not trapped by conventional trapping, indicating that the two strategies are complementary. The trapped ES cell lines, which can be ordered from the International Gene Trap Consortium (http://www.genetrap.org), are freely available to the scientific community.     

Electron trapping and reactions in rhamnose by ESR and ENDOR.

The main objective for a reinvestigation of rhamnose was to devise a mechanistic link between the trapped electron detected previously and the secondary radicals observed at 77 K and at room temperature. Single crystals of rhamnose were X-irradiated at temperatures between 15 and 300 K and examined using ESR, ENDOR, and field-swept ENDOR techniques. After low-temperature irradiation a C3 H-abstraction radical is formed following the visible light-induced decay of the trapped electron. This species was previously assigned erroneously to a C2 H-abstraction species. At temperatures above 120 K, this radical deprotonates at the C3 hydroxy group. Furthermore, a C2 H-abstraction radical is formed following the thermally induced decay of the trapped electron. The C2 and C3 H-abstraction radicals did not convert into each other. A third radical species formed at low temperatures is a C5 H-abstraction radical. It is unstable above 250 K and decays without any apparent successor. The C2 and C3 H-abstraction radicals are formed thermally and photochemically from the parent trapped electron. The conversions are mediated by hydrogen atoms formed intermediately or by elimination of hydride ions. The thermal decomposition pathway requires further studies, in particular with respect to the possible role of water. Recently, Box et al. analyzed the site of the trapped electron in rhamnose crystals. The present results support the results obtained by these authors (Radiat. Res. 121, 262 (1990)). In particular, trapped electron vs proton distances closely match the conversion mechanisms suggested.     

Trapping of electrons and acceleration of the electron bunch in a wake wave

The process of electron trapping by a wake wave excited by a laser pulse in a plasma channel in the case where the electron bunches are injected into the vicinity of the maximum of the wakefield potential at a velocity lower than the wave phase velocity is considered. The mechanism for the formation of a compact electron bunch in the trapping region when only the electrons of the injected bunch that are trapped in the focusing phase mainly undergo the subsequent acceleration in the wakefield is analyzed. The influence of the spatial dimensions of the injected bunch and its energy spread on the length of the trapped electron bunch and the fraction of trapped electrons is studied analytically and numerically. For electron bunches with different ratios of their spatial dimensions to the characteristic dimensions of the wake wave, the influence of the injection energy on the parameters of the high-energy electron bunch trapped and accelerated in the wake-field is studied.     

Free radical yields in crystalline DNA X-irradiated at 4 K

The objective of this work is to determine the extent to which various structural factors influence the yield of trapped free radicals, G(tfr), in DNA irradiated at 4 K. G(tfr) was measured in a series of 13 different oligodeoxynucleotides using electron paramagnetic resonance (EPR) spectroscopy. Each sample consisted of crystalline duplex DNA for which the crystal structure was verified to be that reported in the literature. We find that the G(tfr) of these samples is remarkably high, ranging from 0.55 to 0.75 micromol/J. The standard deviation in G(tfr) for a given crystal structure is generally small, typically less than +/-10%. Furthermore, G(tfr) does not correlate with DNA base sequence, conformation, counterion or length of base stacking. Two observations point to the importance of DNA packing: (1) The radical yields in crystalline DNA are greater than those determined previously for DNA films (0.2 to 0.5 micromol/J); and (2) the variability in G(tfr) is less in DNA crystals than in DNA films. We conclude that closely packed DNA maximizes radical trapping by minimizing the interhelical solvent space. Furthermore, the high efficiency of electron and hole trapping at 4 K is not consistent with DNA possessing properties of a metallic conductor. Indeed, it behaves as an insulator, whether it is in A-, B-, or Z-form and whether base stacking is short- (8 bp) or long-range (>1000 bp).     

The disulfide bond isomerase DsbC is activated by an immunoglobulin-fold thiol oxidoreductase: crystal structure of the DsbC-DsbDalpha complex

The Escherichia coli disulfide bond isomerase DsbC rearranges incorrect disulfide bonds during oxidative protein folding. It is specifically activated by the periplasmic N-terminal domain (DsbDalpha) of the transmembrane electron transporter DsbD. An intermediate of the electron transport reaction was trapped, yielding a covalent DsbC-DsbDalpha complex. The 2.3 A crystal structure of the complex shows for the first time the specific interactions between two thiol oxidoreductases. DsbDalpha is a novel thiol oxidoreductase with the active site cysteines embedded in an immunoglobulin fold. It binds into the central cleft of the V-shaped DsbC dimer, which assumes a closed conformation on complex formation. Comparison of the complex with oxidized DsbDalpha reveals major conformational changes in a cap structure that regulates the accessibility of the DsbDalpha active site. Our results explain how DsbC is selectively activated by DsbD using electrons derived from the cytoplasm.     

Controlled rotation of biological microscopic objects using optical line tweezers

Controlled, continuous rotation of cells or intracellular objects was achieved using optical tweezers with an elliptic beam profile (line tweezers), which was generated by placing a cylindrical lens in the path of the trapping beam. By rotating the cylindrical lens, rotation of the elliptic trapping beam and hence of the object trapped therein was achieved. Compared to previously reported techniques for rotation of microscopic objects, this approach is much simpler, gives better utilization of available laser power and also allows much easier control of the trap beam profile. We have used this approach for rotation of biological objects varying in size from 2 to 40 m. At 25 mW trapping beam power at the object plane E. coli bacteria could be rotated at speeds approaching 10 Hz and an intracellular object (presumably a calcium oxalate crystal) trapped inside Elodea densa plant cell could be rotated with speeds of up to 4 Hz. To our knowledge, this is the first report for rotation of an intracellular object.     

AZI基因被捕获的鉴定实验

目的 确立基因捕获细胞中被捕获的基因名称. 方法 Southern印迹确定合适的限制性内切酶,用质粒拯救（plasmid rescue）获得含有细胞染色体DNA的质粒,测序.结果 本次实验中,被捕获载体整合的基因是AZI基因. 结论质粒拯救方法能确立质粒整合细胞染色体上准确的位置.     

Trapping of transition metal-nucleotide complexes in myosin subfragment 1 by cross-linking thiols; divalent transition metal probes of the active site

Recent experiments [Wells, J., & Yount, R. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 4966] have shown it is possible to trap MgADP and other nucleotides stably at the active site of myosin by cross-linking two thiol groups. A variety of cross-linking reagents including chelation of the two thiols by cobalt (III) phenanthroline or covalent reaction with N,N'-p-phenylenedimaleimide (pPDM) are effective trapping agents. No trapping of nucleotides occurs in the absence of divalent metals. Thus far Mg2+, Mn2+, Co2+, Ni2+, and Ca2+ but not Zn2+ all function to promote trapping of the 1:1 divalent metal-ADP complex and to enhance the rate of ATPase inactivation. Substitution-inert Cr(III) complexes of ADP, ATP, or pyrophosphate that bind very weakly or not at all to the active site are not trapped by cross-linking. While the stability of the trapped divalent metals varies, e.g., t1/2 of 0.5-7 days at 0 degree C, they are stable enough to permit accurate spectral measurements of the Mn2+ and Co2+ trapped complexes. Electron paramagnetic resonance (EPR) measurements of Mn2+ bound to 5'-adenylyl imidodiphosphate or complexed to myosin chymotryptic subfragment 1 indicate that the metal is bound at the active site. Circular dichroism (CD) and visible absorption studies of the Co2+ . ADP trapped complex indicate the metal ion is in an asymmetric octahedral environment. EPR and CD measurements show that the environment of the metal nucleotide is the same whether bound reversibly or stably trapped at the active site.     

Substrate orientation in xanthine oxidase: crystal structure of enzyme in reaction with 2-hydroxy-6-methylpurine

Xanthine oxidoreductase catalyzes the final two steps of purine catabolism and is involved in a variety of pathological states ranging from hyperuricemia to ischemia-reperfusion injury. The human enzyme is expressed primarily in its dehydrogenase form utilizing NAD+ as the final electron acceptor from the enzyme's flavin site but can exist as an oxidase that utilizes O2 for this purpose. Central to an understanding of the enzyme's function is knowledge of purine substrate orientation in the enzyme's molybdenum-containing active site. We report here the crystal structure of xanthine oxidase, trapped at the stage of a critical intermediate in the course of reaction with the slow substrate 2-hydroxy-6-methylpurine at 2.3A. This is the first crystal structure of a reaction intermediate with a purine substrate that is hydroxylated at its C8 position as is xanthine and confirms the structure predicted to occur in the course of the presently favored reaction mechanism. The structure also corroborates recent work suggesting that 2-hydroxy-6-methylpurine orients in the active site with its C2 carbonyl group interacting with Arg-880 and extends our hypothesis that xanthine binds opposite this orientation, with its C6 carbonyl positioned to interact with Arg-880 in stabilizing the MoV transition state.     

用基因诱捕法制作Ayu17-449基因敲除小鼠模型

为了探明Ayu17-449基因在小鼠生长发育过程中的功能, 用特殊的诱捕载体（Gene trapping vector）导入小鼠ES细胞中,5′RACE、Southern blot方法鉴定成功地单一捕获Ayu17-449基因后,由这种ES制作了Ayu17-449 敲除小鼠并用Northern blot方法该基因在突变小鼠体内的表达。结果在Ayu17-449 敲除小鼠体内,诱捕载体位于Ayu17-449基因的翻译起始密码上游,Ayu17-449基因的转录被抑制。表明Ayu17-449敲除小鼠为分析Ayu17-449基因的功能提供了可靠的实验材料。      

Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase

The Escherichia coli adenine DNA glycosylase, MutY, plays an important role in the maintenance of genomic stability by catalyzing the removal of adenine opposite 8-oxo-7,8-dihydroguanine or guanine in duplex DNA. Although the x-ray crystal structure of the catalytic domain of MutY revealed a mechanism for catalysis of the glycosyl bond, it appeared that several opportunistically positioned lysine side chains could participate in a secondary beta-elimination reaction. In this investigation, it is established via site-directed mutagenesis and the determination of a 1.35-A structure of MutY in complex with adenine that the abasic site (apurinic/apyrimidinic) lyase activity is alternatively regulated by two lysines, Lys142 and Lys20. Analyses of the crystallographic structure also suggest a role for Glu161 in the apurinic/apyrimidinic lyase chemistry. The beta-elimination reaction is structurally and chemically uncoupled from the initial glycosyl bond scission, indicating that this reaction occurs as a consequence of active site plasticity and slow dissociation of the product complex. MutY with either the K142A or K20A mutation still catalyzes beta and beta-delta elimination reactions, and both mutants can be trapped as covalent enzyme-DNA intermediates by chemical reduction. The trapping was observed to occur both pre- and post-phosphodiester bond scission, establishing that both of these intermediates have significant half-lives. Thus, the final spectrum of DNA products generated reflects the outcome of a delicate balance of closely related equilibrium constants.     

Photochemical mapping of the active site of myosin.

The active sites of myosin from skeletal, smooth and scallop muscle have been partly characterized by use of a series of photoreactive analogues of ATP. Specific labelling was attained by trapping these analogues in their diphosphate forms at the active sites by either cross-linking two reactive thiols (skeletal myosin) or by formation of stable vanadate-metal ion transition state-like complexes (smooth muscle and scallop myosin). By use of this approach combined with appropriate chemistry, several key residues in all three myosins have been identified which bind at or near the adenine ring, the ribose ring and to the gamma-phosphate of ATP. This information should aid in the solution of the crystal structure of the heads of myosin and in defining a detailed structure of the ATP binding site.     

Reinvestigation of the catalytic mechanism of formyl-CoA transferase, a class III CoA-transferase

Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transferase has a unique three-dimensional fold composed of two interlaced subunits locked together like rings of a chain. We here present an intermediate in the reaction, formyl-CoA transferase containing the covalent beta-aspartyl-CoA thioester, adopting different conformations in the two active sites of the dimer, which was identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid. The formation of the enzyme-CoA thioester was also confirmed by mass spectrometric data. Further structural data include a trapped aspartyl-formyl anhydride protected by a glycine loop closing down over the active site. In a crystal structure of the beta-aspartyl-CoA thioester of an inactive mutant variant, oxalate was found bound to the open conformation of the glycine loop. Together with hydroxylamine trapping experiments and kinetic as well as mutagenesis data, the structures of these formyl-CoA transferase complexes provide new information on the Class III CoA-transferase family and prompt redefinition of the catalytic steps and the modified reaction mechanism of formyl-CoA transferase proposed here.     

Study of the validity of channeling for hrem diffraction

The computation of many beam dynamical electron diffraction can be done numerically using rather sophisticated computer programs so that the physical insight is often lost. It will be shown that, in a crystal in zone oriëntation, the electrons are trapped in the atom columns which then acts as channels. In this way a one to one correspondence between the electron wavefunction and the structure of the object is maintained. This channeling approach enables to describe the diffraction in a much simpler way: the wavefunction is expanded in eigenfunctions of the Hamiltonian. For most kind of columns in a zone axis oriëntation only one bound state will occur which leads to a perfectly oscillatory motion of the electron in the column which can be expressed in a very simple form. The validity is confirmed by comparison with complete dynamical calculations.     

Investigating the free radical trapping ability of NXY-059, S-PBN and PBN

The spin trapping ability of the nitrones 2,4-disulphophenyl-N-tert-butyl nitrone (NXY-059), 2-sulphophenyl-N-tert-butyl nitrone (S-PBN) and alpha-phenyl-N-tert-butyl nitrone (PBN) for both hydroxyl and methanol radicals was investigated using electron paramagnetic resonance (EPR) spectroscopy. The radicals of interest were generated in situ in the spectrometer under constant flow conditions in the presence of each nitrone. The spin adducts formed were detected by EPR spectroscopy. This approach allowed for quantitative comparison of the EPR spectra of the spin adducts of each nitrone. The results obtained showed that NXY-059 trapped a greater number of hydroxyl and methanol radicals than the other two nitrones, under the conditions studied.     

Spin trapping: ESR parameters of spin adducts

Spin trapping has become a valuable tool for the study of free radicals in biology and medicine. The electron spin resonance hyperfine splitting constants of spin adducts of interest in this area are tabulated. The entries also contain a brief comment on the source of the radical trapped.     

Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound

Bifurcated electron transfer during ubiquinol oxidation is the key reaction of cytochrome bc1 complex catalysis. Binding of the competitive inhibitor 5-n-heptyl-6-hydroxy-4,7-dioxobenzothiazole to the Qo site of the cytochrome bc1 complex from Saccharomyces cerevisiae was analyzed by x-ray crystallography. This alkylhydroxydioxobenzothiazole is bound in its ionized form as evident from the crystal structure and confirmed by spectroscopic analysis, consistent with a measured pKa = 6.1 of the hydroxy group in detergent micelles. Stabilizing forces for the hydroxyquinone anion inhibitor include a polarized hydrogen bond to the iron-sulfur cluster ligand His181 and on-edge interactions via weak hydrogen bonds with cytochrome b residue Tyr279. The hydroxy group of the latter contributes to stabilization of the Rieske protein in the b-position by donating a hydrogen bond. The reported pH dependence of inhibition with lower efficacy at alkaline pH is attributed to the protonation state of His181 with a pKa of 7.5. Glu272, a proposed primary ligand and proton acceptor of ubiquinol, is not bound to the carbonyl group of the hydroxydioxobenzothiazole ring but is rotated out of the binding pocket toward the heme bL propionate A, to which it is hydrogen-bonded via a single water molecule. The observed hydrogen bonding pattern provides experimental evidence for the previously proposed proton exit pathway involving the heme propionate and a chain of water molecules. Binding of the alkyl-6-hydroxy-4,7-dioxobenzothiazole is discussed as resembling an intermediate step of ubiquinol oxidation, supporting a single occupancy model at the Qo site.