Abstract:
:The solution conformation of the DNA duplex d(C1G2C3A4C5L6C7A8C9G10C11).d(G12C13G14T15G16T17G18T19G20C21G22 ) containing the 2'-deoxyribonolactone lesion (L6) in the middle of the sequence has been investigated by NMR spectroscopy and restrained molecular dynamics calculations. Interproton distances have been obtained by complete relaxation matrix analysis of the NOESY cross-peak intensities. These distances, along with torsion angles for sugar rings and additional data derived from canonical A- and B-DNA, have been used for structure refinement by restrained molecular dynamics (rMD). Six rMD simulations have been carried out starting from both regular A- and B-DNA forms. The pairwise rms deviations calculated for each refined structure are <1 A, indicating convergence to essentially the same geometry. The accuracy of the rMD structures has been assessed by complete relaxation matrix back-calculation. The average sixth-root residual index (Rx = 0.052 +/- 0.003) indicated that a good fit between experimental and calculated NOESY spectra has been achieved. Detailed analysis revealed a right-handed DNA conformation for the duplex in which both the T17 nucleotide opposite the abasic site and the lactone ring are located inside the helix. No kinking is observed for this molecule, even at the abasic site step. This structure is compared to that of the oligonucleotide with the identical sequence containing the stable tetrahydrofuran abasic site analogue that we reported previously [Coppel, Y., Berthet, N., Coulombeau, C., Coulombeau, Ce., Garcia, J., and Lhomme, J. (1997) Biochemistry 36, 4817-4830].
journal_name
Biochemistryjournal_title
Biochemistryauthors
Jourdan M,Garcia J,Defrancq E,Kotera M,Lhomme Jdoi
10.1021/bi982743rsubject
Has Abstractpub_date
1999-03-30 00:00:00pages
3985-95issue
13eissn
0006-2960issn
1520-4995pii
bi982743rjournal_volume
38pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::In order to study in detail the generality of the NUX (N = A, U, G, or C; X = A, U, or C) rule for the GUC triplet adjacent to the cleavage site in hammerhead ribozymes, two kinetic parameters, namely, kcat and Km, were determined for substrates with mutations in this triplet, which included double mutants with mutati...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00011a020
更新日期:1995-03-21 00:00:00
abstract::The nontransformed steroid receptors contain several non-steroid binding proteins, such as hsp90, hsp70, and p59. Recently, we and others have shown that p59 (FKBP59) is an immunophilin which binds two potent immunosuppressants, FK506 and rapamycin. This raises the possibility that FK506 or rapamycin may modify the fu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00201a014
更新日期:1994-09-06 00:00:00
abstract::The effects of metal ion binding on the optical spectroscopic properties and temperature stability of two single tryptophan mutants of chicken skeletal TnC, F78W and F154W, have been examined. The absence of tyrosine and other tryptophan residues allowed the unambiguous assignment of the spectral signal from the intro...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi982048j
更新日期:1999-09-14 00:00:00
abstract::We identified amino acid residues important for activity of sod2, the Na+/H+ antiporter of Schizosaccharomyces pombe. We mutated all eight His residues of sod2 into Arg. Only His367-->Arg affected function and resulted in complete inability of sod2 to allow growth of S. pombe in LiCl-containing medium. Mutant S. pombe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9801457
更新日期:1998-06-09 00:00:00
abstract::The hydrogen-bonded ring NH nuclear magnetic resonance (NMR) spectra of several transfer ribonucleic acid (RNA) species have been examined with particular emphasis on the extreme low-field portion. Betwen --13.8 and --15 ppm there are two extra resonances which are not derived from cloverleaf base pairs. A combined ap...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00585a025
更新日期:1979-09-04 00:00:00
abstract::Amyloid fibrils have been classically defined as linear, nonbranched polymeric proteins with a cross beta-sheet structure and the ability to alter the optical properties of the amyloid-specific dye Congo Red. Mounting evidence suggests that soluble oligomeric peptide assemblies approximately 2-20 nm in diameter are cr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700247y
更新日期:2007-06-19 00:00:00
abstract::A hallmark of penicillin-binding protein 2 (PBP2) from penicillin-resistant strains of Neisseria gonorrhoeae is insertion of an aspartate after position 345. The insertion resides on a loop near the active site and is immediately adjacent to an existing aspartate (Asp346) that forms a functionally important hydrogen b...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi5011317
更新日期:2014-12-09 00:00:00
abstract::The single reactive sulfhydryl group, located in the active site of each subunit of dimeric creatine kinase from rabbit muscle (isozyme MM), was selectively labeled with 3-(4-maleimidylphenyl)-7-(diethylamino)-4-methylcoumarin (CPM). Isozyme BB, purified to homogeneity from rabbit brain, was conjugated with the sulfhy...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00292a018
更新日期:1983-11-08 00:00:00
abstract::Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi300957f
更新日期:2012-10-23 00:00:00
abstract::The interaction of the 20-kDa pore-forming domain of colicin A with phospholipid vesicles was investigated by gel permeation chromatography, analytical centrifugation, and electron microscopy. Under the experimental conditions of this study, this peptide was found to interact only with vesicles containing negatively c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00445a029
更新日期:1989-09-19 00:00:00
abstract::Six rhodopsin mutants containing disulfide cross-links between different cytoplasmic regions were prepared: disulfide bond 1, between Cys65 (interhelical loop I-II) and Cys316 (end of helix VII); disulfide bond 2, between Cys246 (end of helix VI) and Cys312 (end of helix VII); disulfide bond 3, between Cys139 (end of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9912443
更新日期:1999-09-28 00:00:00
abstract::This study presents an approach to identifying surface residues on membrane proteins that are exposed toward the membrane-aqueous interface. The method employs a lipid Ni(II) chelate that localizes the metal ion to a region near the membrane-aqueous interface. Lateral diffusion of the lipid chelate results in Heisenbe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi015828s
更新日期:2002-01-29 00:00:00
abstract::Intrastrand cross-links (IaCL) connecting two purine nucleobases in DNA pose a challenge to high-fidelity replication in the cell. Various repair pathways or polymerase bypass can cope with these lesions. The influence of the phosphodiester linkage between two neighboring 2'-deoxyguanosine (dG) residues attached throu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01078
更新日期:2015-12-29 00:00:00
abstract::The substrate-bound form of the enzyme heme oxygenase (HO), which catalyzed the stereospecific alpha-meso bridge cleavage of hemin to yield biliverdin IX alpha, has been investigated by 1H NMR in both its primarily high-spin and its cyanide-inhibited low-spin forms. Both derivatives yield 1H NMR spectra indicative of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00187a033
更新日期:1994-05-31 00:00:00
abstract::Recognition of and binding to cholesterol on the host cell membrane is an initial step in the mechanism of numerous pathogens, including viruses, bacteria, and bacterial toxins; however, a viable method of inhibiting this interaction has not yet been uncovered. Here, we describe the mechanism by which a cholesterol re...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00430
更新日期:2016-08-30 00:00:00
abstract::The bacteriophage T7 DNA helicase/primase (gene 4 protein) is a ring-like hexamer that encircles ssDNA and requires forked DNA to catalyze DNA unwinding. We report that optimal rates of unwinding of forked DNA require ssDNA tails of 55 nucleotides on the 5'-to-3' strand and 15 nucleotides on the 3'-to-5' strand. Surpr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971644v
更新日期:1997-11-18 00:00:00
abstract::Cadherins are single pass transmembrane glycoproteins which mediate calcium dependent cell-cell adhesion by homophilic interactions. To reveal the molecular details of calcium binding and homoassociation, we recombinantly expressed in Escherichia coli a domain pair consisting of the first two domains of E-cadherin (EC...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9705624
更新日期:1997-06-24 00:00:00
abstract::Mismatches in DNA occur naturally during replication and as a result of endogenous DNA damaging agents, but the mismatch repair (MMR) pathway acts to correct mismatches before subsequent rounds of replication. Rhodium metalloinsertors bind to DNA mismatches with high affinity and specificity and represent a promising ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi2015822
更新日期:2011-12-20 00:00:00
abstract::Cyclobutane pyrimidine dimers (Pyr < > Pyr) are the major DNA photoproducts induced by the UV component of solar radiation. Photoreactivating enzyme (DNA photolyase) repairs DNA by utilizing the energy of visible light to break the cyclobutane ring of the dimer. Photolyases are monomeric proteins of 50-60 kDa with sto...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi00167a001
更新日期:1994-01-11 00:00:00
abstract::The amidotransferase family of enzymes utilizes the ammonia derived from the hydrolysis of glutamine for a subsequent chemical reaction catalyzed by the same enzyme. The ammonia intermediate does not dissociate into solution during the chemical transformations. A well-characterized example of the structure and mechani...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi990871p
更新日期:1999-06-22 00:00:00
abstract::The complete amino acid sequence of the major component myoglobin from the dwarf sperm whale, Kogia simus, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequenator. Three easily separable peptides were obtained by cleaving the protein at its two...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00624a010
更新日期:1977-03-08 00:00:00
abstract::The EcoRV restriction/modification system consists of two enzymes that recognize the DNA sequence GATATC. The EcoRV restriction endonuclease cleaves DNA at this site, but the DNA of Escherichia coli carrying the EcoRV system is protected from this reaction by the EcoRV methyltransferase. However, in vitro, the EcoRV n...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00500a003
更新日期:1990-12-04 00:00:00
abstract::Tissue factor pathway inhibitor (TFPI) from different cell lines shows up to 15-fold differences in the ratio of anticoagulant to chromogenic activity. The anticoagulant activity was dependent on the purification procedure used and it was possible to isolate two fractions of recombinant TFPI. Only one of these fractio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00107a002
更新日期:1991-10-29 00:00:00
abstract::The structure of the dimeric form of the protein L7/L12 from ribosomes from Escherichia coli was studied by using the heterobifunctional cross-linker 4-(6-formyl-3-azidophenoxy)butyrimidate. The imidate group of the cross-linker reacts very specifically with Lys-51 of L7/L12. Subsequent cross-linking of this modified ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00507a057
更新日期:1981-02-17 00:00:00
abstract::NADPH-cytochrome P450 oxidoreductase (P450 reductase, EC 1.6.2.4) is an essential component of the P450 monooxygenase complex and binds FMN, FAD, and NADPH cofactors. Residues Tyr140 and Tyr178 are known to be involved in FMN binding. A third aromatic side chain, Phe181, is also located in the proximity of the FMN rin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011147l
更新日期:2001-11-13 00:00:00
abstract::ATP and the fluorescent substrate analogue TNP-ATP bind competitively to the gastric H,-K-ATPase. Substrate and product completely reverse the fluorescence enhancement caused by TNP-ATP binding to the enzyme. The fluorophore is displaced monophasically from apoenzyme. However, ATP displaces TNP-ATP from the Mg2+-quenc...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00442a034
更新日期:1989-08-08 00:00:00
abstract::The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have sh...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00025
更新日期:2018-05-01 00:00:00
abstract::Cytochrome b(561) in adrenal chromaffin vesicle membranes conveys electron equivalents from extravesicular ascorbate to the intravesicular monodehydroascorbate radical. We conducted a stopped-flow study on the reaction of ascorbate with purified cytochrome b(561) in the detergent-solubilized state for the first time. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0267588
更新日期:2003-07-15 00:00:00
abstract::Using lattice statistical mechanics, we develop theory to account for the folding of a heteropolymer molecule such as a protein to the globular and soluble state. Folding is assumed to be driven by the association of solvophobic monomers to avoid solvent and opposed by the chain configurational entropy. Theory predict...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00327a032
更新日期:1985-03-12 00:00:00
abstract::The Escherichia coli siderophore enterobactin is assembled from 2,3-dihydroxybenzoate (2,3-DHB) and l-serine by the nonribosomal peptide synthetases EntB and EntF. The processive thiol-template strategy used can be sabotaged by EntB misacylation. Through in vitro kinetic analysis, we demonstrate two potential routes t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi802207t
更新日期:2009-01-27 00:00:00