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1.
Single-stranded DNA-binding proteins have in common their crucial roles in DNA metabolism, although they exhibit significant differences in their single-stranded DNA binding properties. To evaluate the correlation between the structure of different nucleoprotein complexes and their function, we have carried out a comparative study of the complexes that the single-stranded DNA-binding proteins of three related bacteriophages, ?29, Nf and GA-1, form with single-stranded DNA. Under the experimental conditions used, ?29 and Nf single-stranded DNA-binding proteins are stable monomers in solution, while GA-1 single-stranded DNA-binding protein presents a hexameric state, as determined in glycerol gradients. The thermodynamic parameters derived from quenching measurements of the intrinsic protein fluorescence upon single-stranded DNA binding revealed (i) that GA-1 single-stranded DNA-binding protein occludes a larger binding site (n=51 nt/oligomer) than ?29 and Nf SSBs (n=3.4 and 4.7 nt/monomer, respectively); and (ii) that it shows a higher global affinity for single-stranded DNA (GA-1 SSB, K(eff)=18.6 x 10(5) M(-1); o29 SSB, K(eff)=2.2 x 10(5) M(-1); Nf SSB, K(eff)=2.9 x 10(5) M(-1)). Altogether, these parameters justify the differences displayed by the GA-1 single-stranded DNA-binding protein and single-stranded DNA complex under the electron microscope, and the requirement of higher amounts of ?29 and Nf single-stranded DNA-binding proteins than of GA-1 SSB in gel mobility shift assays to produce a similar effect. The structural differences of the nucleoprotein complexes formed by the three single-stranded DNA-binding proteins with single-stranded DNA correlate with their different functional stimulatory effects in ?29 DNA amplification. 相似文献
2.
Wen Guo Xu Yuan Chun Zhang Shi Xiang Lu Rui Chun Zhang 《Journal of molecular modeling》2009,15(11):1329-1336
The equilibrium geometries, total energies, and vibrational frequencies of anions X2Y2
− (X = C, Si, Ge and Y = N, P, As) are theoretically investigated with density functional theory (DFT) method. Our calculation
shows that for C2N2
− species, the D
2h
isomer is the most stable four-membered structure, and for other species the C
2v
isomer in which two X atoms are contrapuntal is the most stable structure at the B3LYP/6-311 +G* level. Wiberg bond index (WBI) and negative nucleus-independent chemical shift (NICS) value indicate the existence of delocalization
in stable X2Y2
− structures. A detailed molecular orbital (MO) analysis further reveals that stable isomers of these species have strongly
aromatic character, which strengthens the structural stability and makes them closely connected with the concept of aromaticity. 相似文献
3.
LF Chin SM Kong HL Seng YL Tiong KE Neo MJ Maah AS Khoo M Ahmad TS Hor HB Lee SL San SM Chye CH Ng 《Journal of biological inorganic chemistry》2012,17(7):1093-1105
Two ternary Zn(II) complexes, with 1,10-phenanthroline (phen) as the main ligand and a carboxylate-containing ligand [dipicolinate (dipico) or L-threoninate (L-Thr)] as the subsidiary ligand, were prepared and characterized by elemental analysis, Fourier transform IR, UV, and fluorescence spectroscopy, X-ray diffraction, molar conductivity, and electrospray ionization mass spectrometry. X-ray structure analysis shows that both [Zn(phen)(dipico)(H(2)O)]·H(2)O (1) and [Zn(phen)(L-Thr)(H(2)O)Cl]·2H(2)O (2) have octahedral geometry about the Zn(II) atom. Both complexes can inhibit topoisomerase I, and have better anticancer activity than cisplatin against nasopharyngeal cancer cell lines, HK1 and HONE-1, with concentrations causing 50?% inhibition of cell proliferation (IC(50)) in the low micromolar range. Complex 2 has the highest therapeutic index for HK1. Both Zn(II) complexes can induce cell death by apoptosis. Changing the subsidiary ligand in the Zn(II) complexes affects the UV-fluorescence spectral properties of the coordinated phen ligand, the binding affinity for some DNA sequences, nucleobase sequence-selective binding, the phase at which cell cycle progression was arrested for treated cancer cells, and their therapeutic index. 相似文献
4.
Fu-de Ren Duan-lin Cao Wen-liang Wang Jun Ren Su-qing Hou Shu-sen Chen 《Journal of molecular modeling》2009,15(5):515-523
The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid
hydrogen of HF, HCl, HCN and H2C2 using MP2 and B3LYP methods at 6-311++G(2df,2p) and aug-cc-pVTZ levels. The binding energies follow the order of HB=BH...HF>HB=BH...HCl>HB=BH...HCN>HB=BH...H2C2. The hydrogen-bonded interactions in HB=BH...HX are found to be stronger than those in H2C=CH2...HX and OCB≡BCO...HX. The analyses of natural bond orbital (NBO) and the electron density shifts reveal that the nature
of the T-shaped X–H...π hydrogen-bonded interaction is that much of the lost density from the π-orbital of B=B bond is shifted
toward the hydrogen atom of the proton donor, leading to the electron density accumulation and the formation of the hydrogen
bond. The atoms in molecules (AIM) theory have also been applied to characterize bond critical points and confirm that the
B=B double bond can be a potential proton acceptor.
The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid
hydrogen of HF, HCl, HCN and H2C2 相似文献
5.
6.
7.
Calculation predicted the interacting forms of halopentafluorobenzene C6F5X (X=F, Cl, Br, I) with triethylphosphine oxide which is biologically interested and easily detected by 31P NMR. The interaction energy and geometric parameters of resultant halogen or π-hole bonding complexes were estimated and compared. Moreover, the bonding constants were determined by 31P NMR. Both theory and experiments indicated the C6F6 and C6F5Cl interact with triethylphosphine oxide by π-hole bonding pattern, while C6F5I by halogen/σ-hole bonding form. For C6F5Br, two interactions are comparative and should coexist competitively. The calculated interaction energies of σ-hole bonding complexes, ?5.07 kcal mol?1 for C6F5Br?O=P and ?8.25 kcal mol?1 for C6F5I?O=P, and π-hole bonding complexes, ?7.29 kcal mol?1 for C6F6?O=P and ?7.24 kcal mol?1 for C6F5Cl?O=P, are consistent with the changing tendency of bonding constants measured by 31P NMR, 4.37, 19.7, 2.42 and 2.23 M?1, respectively. Figure
The competitive σ-hole···O=P and π-hole···O=P bonds between C6F5X (X=F, Cl, Br, I) and O=PEt3 相似文献
8.
Liang Junxi Wang Yanbin Zhang Qiang Li Yu Geng Zhiyuan Wang Xiuhong 《Journal of molecular modeling》2013,19(4):1739-1750
Gas-phase reactions of ClO–/BrO– with RCl (R = CH3, C2H5, and C3H7) have been investigated in detail using the popular DFT functional BHandHLYP/aug-cc-pVDZ level of theory. As a result, our findings strongly suggest that the type of reaction is firstly initiated by a typical SN2 fashion. Subsequently, two competitive substitution steps, named as SN2-induced substitution and SN2-induced elimination, respectively, would proceed before the initial SN2 product ion-dipole complex separates, in which the former exhibits less reactivity than the latter. Those are consistent with relevant experimental results. Moreover, we have also explored reactivity difference for the title reactions in term of some factors derived from methyl group, p-π electronic conjugation, ionization energy (IE), as well as molecular orbital (MO) analysis. Figure
Energy profiles for the ClO– reactions and BrO–reactions, respectively 相似文献
9.
Geoffrey A. Mueller Eugene F. DeRose Thomas W. Kirby Robert E. London 《Biomolecular NMR assignments》2007,1(1):33-35
DNA Polymerase β is a multifunctional enzyme involved in base excision repair of nuclear DNA in vertebrate cells. We present
here the first assignments of the full-length protein (335 residues, 39 kDa) in the presence of a double gap—double hairpin
DNA (22 nucleotides, 7 kDa). 相似文献
10.
de Oliveira BG Araújo RC Chagas FF Carvalho AB Ramos MN 《Journal of molecular modeling》2008,14(10):949-955
The geometries of three isomers of the C2H4O···2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis
of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation
of infrared stretching modes, and Bader’s atoms in molecules (AIM) theory calculations was carried out in order to characterize
the hydrogen bonds in each isomer of the C2H4O···2HF complex. The most stable structure was determined through the identification of hydrogen bonds between C2H4O and HF, (O···H), as well as in the hydrofluoric acid dimer, (HFD–R···HFD). However, the existence of a tertiary interaction (Fλ···Hα) between the fluoride of the second hydrofluoric acid and the axial hydrogen atoms of C2H4O was decisive in the identification of the preferred configuration of the C2H4O···2HF system.
Figure Geometries of three isomers of the C2H4O···2HF tri-molecular heterocyclic hydrogen-bonded complex 相似文献
11.
Mireia Güell Josep M. Luis Miquel Solà Per E. M. Siegbahn 《Journal of biological inorganic chemistry》2009,14(2):229-242
Tyrosinase catalyzes the ortho hydroxylation of monophenols and the subsequent oxidation of the diphenolic products to the resulting quinones. In efforts
to create biomimetic copper complexes that can oxidize C–H bonds, Stack and coworkers recently reported a synthetic μ-η2:η2-peroxodicopper(II)(DBED)2 complex (DBED is N,N′-di-tert-butylethylenediamine), which rapidly hydroxylates phenolates. A reactive intermediate consistent with a bis-μ-oxo-dicopper(III)-phenolate
complex, with the O–O bond fully cleaved, is observed experimentally. Overall, the evidence for sequential O–O bond cleavage
and C–O bond formation in this synthetic complex suggests an alternative mechanism to the concerted or late-stage O–O bond
scission generally accepted for the phenol hydroxylation reaction performed by tyrosinase. In this work, the reaction mechanism
of this peroxodicopper(II) complex was studied with hybrid density functional methods by replacing DBED in the μ-η2:η2-peroxodicopper(II)(DBED)2 complex by N,N′-dimethylethylenediamine ligands to reduce the computational costs. The reaction mechanism obtained is compared with the
existing proposals for the catalytic ortho hydroxylation of monophenol and the subsequent oxidation of the diphenolic product to the resulting quinone with the aim
of gaining some understanding about the copper-promoted oxidation processes mediated by 2:1 Cu(I)O2-derived species.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
13.
Qiang Zhao 《Journal of molecular modeling》2014,20(10):1-6
The interplay between halogen and chalcogen bonding in the XCl???OCS and XCl???OCS???NH3 (X = F, OH, NC, CN, and FCC) complex was studied at the MP2/6-311++G(d,p) computational level. Cooperative effect is observed when halogen and chalcogen bonding coexist in the same complex. The effect is studied by means of binding distance, interaction energy, and cooperative energy. Molecular electrostatic potential calculation reveals the electrostatic nature of the interactions. Cooperative effect is explained by the difference of the electron density. Second-order stabilization energy was calculated to study the orbital interaction in the complex. Atoms in molecules analysis was performed to analyze the enhancement of the electron density in the bond critical point. 相似文献
14.
《Journal of inorganic biochemistry》1986,26(1):1-21
Two structurally different phases of a uric acid salt of magnesium, Mg(hydrogenurate)2 · 8H2O, have been prepared by crystallization from solution at pH = 7.5–8.0 and were investigated by x-ray crystallography, thermal analysis, and ir spectroscopy. Both phases are monoclinic, space group P21/c with a = 9.573(2), b = 14.627(3), c = 7.170(1) Å, β = 101.91(1)° (phase I) and a = 10.397(2), b = 14.306(3), c = 6.732(1) Å, β = 104.64(2)° (phase II). The crystal structures of both phases (R = 0.053 and 0.051, respectively) contain isolated octahedral [Mg(H2O)6]2+ cations, hydrogenurate monoanions, and two molecules of water of crystallization per formula unit. The structural formula representing these facts is [Mg(H2O)6] (hydrogenura-te)2·2H2O. The tautomeric form of the hydrogenurate molecule corresponds to the tri-keto form of uric acid deprotonated at N(3). Differences in bond length between uric acid and the hydrogenurate molecule may be described in terms of three additional resonance structures distributing the formal negative charge at N(3) within the pyrimidine (but not the imidazole) ring. Deprotonation at N(3) significantly decreases the internal C-N-C angle at N(3). Alternating pairs of medium-strong intermolecular N-HO hydrogen bonds lead to infinite chains of hydrogenurate molecules extending along the b axis of the unit cells in both phases. The main difference between the two phases lies in their stacking pattern of the hydrogenurate molecules. Infrared data confirm the hydrogen bonding characteristics resulting from the crystal structure analysis. Thermogravimetric measurements and differential scanning calorimetry data show that the dehydration of both phases occurs in two distinct steps with Mg(hydrogenurate)2.6H2O as an intermediate phase. The first dehydration step (−2H2O) is a topotactic reaction with three-dimensional preservation of the main structure elements of the octahydrate in the structure of the hexahydrate. 相似文献
15.
16.
《Inorganica chimica acta》1988,149(1):21-30
Dimeric copper(I) complexes L2Cu2X2 react with 1 and 2 mol of M(NS)2 reagents in aprotic solvents to give quantitative yields of products LMX2 and (NS)M(X,X)M(NS), respectively. Here, L = N,N,N′N′-tetraethylethylenediamine, X = Cl or Br, M = Co, Ni, Cu and Ns = S-methylisopropylidenehydrazinecarbodithioate. Dimers (NS)Cu(X,X)Cu(NS) are oxidatively unstable. LCoCl2 crystallizes in the monoclinic space group P21/c (C2h5): a = 7.345(1), b = 11.801(1), c = 17.478(2) Å, β = 104.98(1)°, Z = 4. The electronic spectra of LMX2 and (NS)M(X,X)M(NS) complexes are discussed. 相似文献
17.
An ab initio computational density functional theory (DFT) was used to study the formation of the first cyclic molecule (phenyl)
initiated by the ethynyl radical (C2H•). The study covers a competition reaction between the addition reactions of C2H• with ethyne (C2H2) and some molecular re-arrangement schemes. The minimum energy paths of the preferred cyclic formation route were characterized.
A thorough thermochemical analysis was performed by evaluating the differences in the energy of activation (ΔE), enthalpy
(ΔH), and Gibb's free energy (ΔG) of the optimized stable and transition state (TS) molecules. The reaction temperatures were
set to normal (T = 298 K) and combustion (T = 1,200 K) conditions.
相似文献
Romero M. SantiagoEmail: |
18.
《Inorganica chimica acta》1986,121(2):229-231
The formation of iron(III) complexes with six monoaminopolycarboxylate and monoaminopoly-alcohol ligands has been investigated by redox and pH measurements in acidic solutions at I=1 (NaClO4) and 25 °C. The stability of the complexes increases with the number of carboxylate groups and a further enhancement is observed when alcoholic groups are present. 相似文献
19.
20.
《Inorganica chimica acta》1987,129(1):119-121
The new bridging complexes Cp3UClClAlCl2 and Cp3UClClAlCl2·THF were synthesized by reaction of triscyclopentadienyl uranium chloride with aluminum trichloride in the presence of different solvents. The Cp3UClClAlCl2·THF complex id proposed to have a square bipyramidal structure with THF occupying the sixth position. A new inorganic cyclooctatetraene uranium complex, UCl2(S4N4), was also synthesized by uranium tetrachloride with tetrasulfur tetranitride. 相似文献