Abstract:
:C4'-oxidized (C4-AP) and C5'-oxidized abasic sites (DOB) that are produced following abstraction of a hydrogen atom from the DNA backbone reversibly form cross-links selectively with dA opposite a 3'-adjacent nucleotide, despite the comparable proximity of an opposing dA. A previous report on UvrABC incision of DNA substrates containing stabilized analogues of the ICLs derived from C4-AP and DOB also indicated that the latter is repaired more readily by nucleotide excision repair [Ghosh, S., and Greenberg, M. M. (2014) Biochemistry 53, 5958-5965]. The source for selective cross-link formation was probed by comparing the reactivity of ICL analogues of C4-AP and DOB that mimic the preferred and disfavored cross-links with that of reagents that indirectly detect distortion by reacting with the nucleobases. The disfavored C4-AP and DOB analogues were each more reactive than the corresponding preferred cross-link substrates, suggesting that the latter are more stable, which is consistent with selective ICL formation. In addition, the preferred DOB analogue is more reactive than the respective C4-AP ICL, which is consistent with its more efficient incision by UvrABC. The conclusions drawn from the chemical probing experiments are corroborated by UV melting studies. The preferred ICLs exhibit melting temperatures higher than those of the corresponding disfavored isomers. These studies suggest that oxidized abasic sites form reversible interstrand cross-links with dA opposite the 3'-adjacent thymidine because these products are more stable and the thermodynamic preference is reflected in the transition states for their formation.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Ghosh S,Greenberg MMdoi
10.1021/acs.biochem.5b00860subject
Has Abstractpub_date
2015-10-13 00:00:00pages
6274-83issue
40eissn
0006-2960issn
1520-4995journal_volume
54pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Pyruvate decarboxylase (PDC) uses thiamine diphosphate as an essential cofactor to catalyze the formation of acetaldehyde on the pathway of ethanol synthesis. Here we report the crystallographic image of a prereaction intermediate of a bacterial pyruvate decarboxylase prepared by cocrystallizing the enzyme with pyruva...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901864j
更新日期:2010-03-02 00:00:00
abstract::Comparative studies on the salt titration and the related kinetics for poly(dG-dC) X poly(dG-dC) in pH 7.0 and 3.8 solutions clearly suggest that base protonation facilitates the kinetics of B-Z interconversion although the midpoint for such a transition in acidic solution (2.0-2.1 M NaCl) is only slightly lower than ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00320a041
更新日期:1984-12-04 00:00:00
abstract::High hydrostatic pressure has been shown to cause reversible dissociation of the isolated apo beta 2 dimer of tryptophan synthase from Escherichia coli into enzymatically inactive monomers [Seifert, T., Bartholmes, P., & Jaenicke, R. (1982) Biophys. Chem. 15, 1-8]. Addition of the coenzyme pyridoxal 5'-phosphate affec...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00323a016
更新日期:1985-01-15 00:00:00
abstract::The periplasmic protein CusF, as a part of the CusCFBA efflux complex, plays a role in resistance to elevated levels of copper and silver in Escherichia coli. Although homologues have been identified in other Gram-negative bacteria, the substrate of CusF and its precise role in metal resistance have not been described...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0612622
更新日期:2006-09-19 00:00:00
abstract::Orthophosphate and phosphate derivatives including pyrophosphate, hexametaphosphate, ATP, ADP, and inositol hexaphosphate enhance the extent of DNA degradation by iron(II) bleomycin. These phosphate-containing compounds increase both the release of free nucleic base and that of base propenals which are DNA cleavage pr...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00335a034
更新日期:1985-07-02 00:00:00
abstract::ROS-GC represents a membrane guanylate cyclase subfamily whose distinctive feature is that it transduces diverse intracellularly generated Ca(2+) signals into the production of the second messenger cyclic GMP. An intriguing feature of the first subfamily member, ROS-GC1, is that it is both stimulated and inhibited by ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi990851n
更新日期:1999-09-28 00:00:00
abstract::Chemosensory cilia isolated from the olfactory epithelium of Rana catesbeiana were solubilized with Lubrol PX in the presence of supplementary lipid, forskolin, and sodium fluoride. Subsequent removal of the detergent by adsorption onto Biobeads SM2 results in the formation of proteoliposomes that display forskolin- a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00417a040
更新日期:1988-08-23 00:00:00
abstract::Kinetic studies of the effect of addition of Co2+ or Mn2+ to a highly purified dipeptidase from Ehrlich-Lettré mouse ascites tumor cells show that these metals specifically activate the hydrolyses of certain classes of dipeptides. This enzyme was previously (S. Hayman and E. K. Patterson, 1971, J. Biol. Chem. 246, 660...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00690a018
更新日期:1975-09-23 00:00:00
abstract::Mouse photoreceptor function and survival critically depend on Ca(2+)-regulated retinal membrane guanylyl cyclase (RetGC), comprised of two isozymes, RetGC1 and RetGC2. We characterized the content, catalytic constants, and regulation of native RetGC1 and RetGC2 isozymes using mice lacking guanylyl cyclase activating ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200491b
更新日期:2011-06-28 00:00:00
abstract::As part of a search for peptides that have specificity for selected protein kinases, the possibility that adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) recognizes the hydrogen-bonding potential of its peptide substrates was investigated. A-Kinase catalyzes the phosphorylation of five N alpha-met...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00388a041
更新日期:1987-07-14 00:00:00
abstract::Substitution of Co(II) for the catalytic site Zn(II) of horse liver alcohol dehydrogenase (LADH) yields an active enzyme derivative, CoIIE, with characteristic Co(II) charge-transfer and d-d electronic transitions that are sensitive to the events which take place during catalysis [Koerber, S. C., MacGibbon, A. K. H., ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00377a031
更新日期:1987-02-10 00:00:00
abstract::Two extremely potent inhibitors of citrate synthase, carboxyl and primary amide analogues of acetyl coenzyme A, have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.70- and 1.65-A resolution, respectively. The ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00191a002
更新日期:1994-06-28 00:00:00
abstract::To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101806b
更新日期:2011-04-19 00:00:00
abstract::The chemoreceptors of Escherichia coli are homodimeric membrane proteins that cluster in patches near the cell poles. They convert environmental stimuli into intracellular signals that control flagellar rotation. The functional domains of a receptor are physically separated by the cell membrane. Chemoeffectors bind to...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi048969d
更新日期:2005-02-01 00:00:00
abstract::D-Xylose isomerase (XI) is a heat-stable homotetrameric enzyme used in industry for the production of high-fructose corn syrups by isomerization of D-glucose into D-fructose. To carry out biochemical and structural studies of this enzyme and of its engineered variants, a rapid and convenient method of purification of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00125a009
更新日期:1992-03-17 00:00:00
abstract::The binding of 8-anilino-1-naphthalenesulfonate (ANS) to ciliary dynein ATPase leads to a marked increase in the dye's fluorescence intensity, accompanied by a blue shift in the observed fluorescence emission maximum. We found that dynein has 37 +/- 3 ANS binding sites and that experimentally applied ANS concentration...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00347a012
更新日期:1985-12-17 00:00:00
abstract::Myc and Max belong to the b-HLH-LZ family of transcription factors. Heterodimerization between Myc and Max or homodimerization of Max allows these proteins to bind their cognate DNA sequence known as the E-box (CACGTG). Recent evidence has suggested that the c-Myc/Max heterodimeric b-HLH-LZ could interact to form a he...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700076m
更新日期:2007-09-11 00:00:00
abstract::Stopped-flow and laser photolysis methods have been used to investigate the rates of electron-transfer reactions of fully reduced riboflavin and the three oxidation states of Clostridium pasteurianum flavodoxin. Both normal and 7,8-dichloroflavin analogues were studied. Redox reagents included oxygen, ferricyanide, fe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00521a005
更新日期:1981-09-01 00:00:00
abstract::It is generally accepted that electron transfer in bacterial photosynthesis is driven by the first singlet excited state of a special pair of bacteriochlorophylls (P*). We have examined the first steps of electron transfer in a mutant of the Rhodobacter sphaeroides reaction center in which charge separation from P* is...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9703756
更新日期:1997-06-10 00:00:00
abstract::The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9628228
更新日期:1997-04-22 00:00:00
abstract::Large conductance Ca(2+)-activated K(+) channels (BK(Ca)) contain an intracellular binding site for bovine pancreatic trypsin inhibitor (BPTI), a well-known inhibitor of various serine proteinase (SerP) enzymes. To investigate the structural basis of this interaction, we examined the activity of 11 BPTI mutants using ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi992140v
更新日期:2000-02-29 00:00:00
abstract::Pf1, a class II filamentous virus, has been investigated by ultraviolet resonance Raman (UVRR) spectroscopy with excitation wavelengths of 257, 244, 238, and 229 nm. The 257-nm UVRR spectrum is rich in Raman bands of the packaged single-stranded DNA (ssDNA) genome, despite the low DNA mass (6%) of the virion. Converse...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi981965m
更新日期:1999-03-09 00:00:00
abstract::Reticulocyte lysate contains a chaperone system that assembles glucocorticoid receptor (GR).hsp90 heterocomplexes. Using purified proteins, we have prepared a five-protein heterocomplex assembly system consisting of two proteins essential for heterocomplex assembly-hsp90 and hsp70-and three proteins that act as co-cha...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001671c
更新日期:2000-11-21 00:00:00
abstract::Murine epidermal growth factor (EGF), a 53 amino acid protein, has been modified by enzymic digestion, site-specific chemical reactions, and recombinant DNA technology. After trypsin digestion the EGF derivatives EGF1-48 (called EGF-T) and EGF1-45 (called EGF-T2) were separated from the residual EGF and the C-terminal...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00414a005
更新日期:1988-07-12 00:00:00
abstract::The kinetics of reduction of free flavin semiquinones of the individual components of 1:1 covalent and electrostatic complexes of yeast ferric and ferryl cytochrome c peroxidase and ferric horse cytochrome c have been studied. Covalent cross-linking between the peroxidase and cytochrome c at low ionic strength results...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00406a029
更新日期:1988-03-22 00:00:00
abstract::Human phenylalanine hydroxylase is a liver-specific enzyme that catalyzes the conversion of phenylalanine to tyrosine. Absence of enzymatic activity results in phenylketonuria, a genetic disorder that causes development of severe mental retardation in untreated children. In this paper we report the cloning and structu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00352a001
更新日期:1986-02-25 00:00:00
abstract::Extended-spectrum β-lactamases (ESBLs) pose a threat to public health because of their ability to confer resistance to extended-spectrum cephalosporins such as cefotaxime. The CTX-M β-lactamases are the most widespread ESBL enzymes among antibiotic resistant bacteria. Many of the active site residues are conserved bet...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi501195g
更新日期:2015-01-20 00:00:00
abstract::Dihydroorotate dehydrogenases (DHODs) oxidize dihydroorotate (DHO) to orotate using the FMN prosthetic group to abstract a hydride equivalent from C6 and a protein residue (Ser for Class 2 DHODs) to deprotonate C5. The fundamental question of whether the scission of the two DHO C-H bonds is concerted or stepwise was a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi060919g
更新日期:2006-12-19 00:00:00
abstract::We measured the time course of skeletal muscle actin polymerization at different actin concentrations. In 0.1 M KCl with 1 mM Mg2+, log/log plots of the rate of the early, slow phase of polymerization vs. actin concentration were linear with slopes from 1.0 to 1.3. Computer-assisted calculations of similar curves from...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00278a021
更新日期:1983-04-26 00:00:00
abstract::A 600 MHz 1H NMR study of toxin OSK1, blocker of small-conductance Ca2+-activated K+ channels, is presented. The unambiguous sequential assignment of all the protons of the toxin was obtained using TOCSY, DQF-COSY, and NOESY experiments at pH 3.0 (10, 30, and 45 degrees C) in aqueous solution. 3J(N alpha), 3J(alphabet...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9614390
更新日期:1997-02-11 00:00:00