DNA charge transport within the cell.

Abstract:

:The unique characteristics of DNA charge transport (CT) have prompted an examination of roles for this chemistry within a biological context. Not only can DNA CT facilitate long-range oxidative damage of DNA, but redox-active proteins can couple to the DNA base stack and participate in long-range redox reactions using DNA CT. DNA transcription factors with redox-active moieties such as SoxR and p53 can use DNA CT as a form of redox sensing. DNA CT chemistry also provides a means to monitor the integrity of the DNA, given the sensitivity of DNA CT to perturbations in base stacking as arise with mismatches and lesions. Enzymes that utilize this chemistry include an interesting and ever-growing class of DNA-processing enzymes involved in DNA repair, replication, and transcription that have been found to contain 4Fe-4S clusters. DNA repair enzymes containing 4Fe-4S clusters, that include endonuclease III (EndoIII), MutY, and DinG from bacteria, as well as XPD from archaea, have been shown to be redox-active when bound to DNA, share a DNA-bound redox potential, and can be reduced and oxidized at long-range via DNA CT. Interactions between DNA and these proteins in solution, in addition to genetics experiments within Escherichia coli, suggest that DNA-mediated CT can be used as a means of cooperative signaling among DNA repair proteins that contain 4Fe-4S clusters as a first step in finding DNA damage, even within cells. On the basis of these data, we can consider also how DNA-mediated CT may be used as a means of signaling to coordinate DNA processing across the genome.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Grodick MA,Muren NB,Barton JK

doi

10.1021/bi501520w

subject

Has Abstract

pub_date

2015-02-03 00:00:00

pages

962-73

issue

4

eissn

0006-2960

issn

1520-4995

journal_volume

54

pub_type

杂志文章,评审
  • Postulated role of calsequestrin in the regulation of calcium release from sarcoplasmic reticulum.

    abstract::Ca2+ release from heavy sarcoplasmic reticulum (SR) vesicles was induced by 2 mM caffeine, and the amount (A) and the rate constant (k) of Ca2+ release were investigated as a function of the extent of Ca2+ loading. Under both passive and active loading conditions, the A value increased monotonically in parallel to Ca2...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00442a033

    authors: Ikemoto N,Ronjat M,Mészáros LG,Koshita M

    更新日期:1989-08-08 00:00:00

  • Effects of peptide length and composition on binding to an empty class I MHC heterodimer.

    abstract::Class I major histocompatibility complex (MHC) proteins present peptide antigens to T cells during the immune response against viruses. Peptides are loaded into newly synthesized class I heterodimers in the endoplasmic reticulum such that most or all cell surface class I molecules contain peptides derived from endogen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00192a020

    authors: Fahnestock ML,Johnson JL,Feldman RM,Tsomides TJ,Mayer J,Narhi LO,Bjorkman PJ

    更新日期:1994-07-05 00:00:00

  • Regulation of biological functions by an insulin receptor monoclonal antibody in insulin receptor beta-subunit mutants.

    abstract::We investigated the effects of MA-5, a human-specific monoclonal antibody to the insulin receptor alpha-subunit, on transmembrane signaling in cell lines transfected with and expressing both normal human insulin receptors and receptors mutated in their beta-subunit tyrosine kinase domains. In cell lines expressing nor...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00116a025

    authors: Sung CK,Han XL,Brunetti A,Maddux B,Yamamoto-Honda R,Goldfine ID

    更新日期:1992-01-14 00:00:00

  • Resonance energy transfer as a direct monitor of GTP-binding protein-effector interactions: activated alpha-transducin binding to the cGMP phosphodiesterase in the bovine phototransduction cascade.

    abstract::Resonance energy-transfer approaches have been used to directly monitor the interactions of the GTP gamma S-bound alpha subunit of transducin (alpha T GTP gamma S) with the retinal cyclic GMP phosphodiesterase (PDE). The PDE was labeled with 5-(iodoacetamido) fluorescein (IAF-PDE) and served as the fluorescence donor ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00243a011

    authors: Erickson JW,Cerione RA

    更新日期:1991-07-23 00:00:00

  • Ti(IV) uptake and release by human serum transferrin and recognition of Ti(IV)-transferrin by cancer cells: understanding the mechanism of action of the anticancer drug titanocene dichloride.

    abstract::The organometallic anticancer agent titanocene dichloride, Cp(2)TiCl(2), is now in phase II clinical trials as an anticancer drug, but its mechanism of action is poorly understood. We show here that the interactions of Cp(2)TiCl(2) with human serum transferrin (hTF) and that of Ti(2)-hTF with adenosine triphosphate (A...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000798z

    authors: Guo M,Sun H,McArdle HJ,Gambling L,Sadler PJ

    更新日期:2000-08-22 00:00:00

  • Metal-selective DNA-binding response of Escherichia coli NikR.

    abstract::The NikR transcription factor from Escherichia coli is a Ni(II)-dependent repressor that regulates production of the nickel ion transporter encoded by the nik operon. In the previous paper in this issue (Wang, S. C., Dias, A., Bloom, S. L., and Zamble, D. B. (2004) Selectivity of Metal Binding and Metal-Induced Stabil...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049404k

    authors: Bloom SL,Zamble DB

    更新日期:2004-08-10 00:00:00

  • Geometry of the phosphodiester backbone in the A form of deoxyribonucleic acid determined by phosphorus-31 nuclear magnetic resonance spectroscopy.

    abstract::31P NMR spectra were obtained from poly(dA-dT) . poly(dA-dT) fibers which gave an X-ray diffraction pattern similar to that of the A form of natural deoxyribonucleic acid (DNA). The analysis of the line shape indicated that the A form of poly(dA-dT) . poly(dA-dT) has a single uniform backbone conformation; the orienta...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00507a013

    authors: Shindo H,Wooten JB,Zimmerman SB

    更新日期:1981-02-17 00:00:00

  • Membrane topography of the photosynthetic reaction center polypeptides of Rhodopseudomonas sphaeroides.

    abstract::The topography of the photosynthetic reaction center (RC) polypeptides (H, M, and L) was investigated by proteolysis and radioiodination of membrane vesicles isolated from Rhodopseudomonas sphaeroides. Chromatophores, obtained from French-pressed cell lysates, are closed vesicles' and oriented inside out with respect ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00519a012

    authors: Bachmann RC,Gillies K,Takemoto JY

    更新日期:1981-08-04 00:00:00

  • Direct observation and elucidation of the structures of aged and nonaged phosphorylated cholinesterases by 31P NMR spectroscopy.

    abstract::31P NMR spectroscopy of butyrylcholinesterase (BChE), acetylcholinesterase (AChE), and chymotrypsin (Cht) inhibited by pinacolyl methylphosphonofluoridate (soman), methylphosphonodifluoridate (MPDF), and diisopropyl phosphorofluoridate (DFP) allowed direct observation of the OP-linked moiety of aged (nonreactivatable)...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00212a009

    authors: Segall Y,Waysbort D,Barak D,Ariel N,Doctor BP,Grunwald J,Ashani Y

    更新日期:1993-12-14 00:00:00

  • Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease.

    abstract::The pK(a) values measured previously for the internal Lys-66, Asp-66, and Glu-66 in variants of a highly stable form of staphylococcal nuclease are shifted by as many as 5 pK(a) units relative to normal pK(a) values in water. These shifts cannot be reproduced with continuum electrostatics calculations with static stru...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi902114m

    authors: Karp DA,Stahley MR,García-Moreno B

    更新日期:2010-05-18 00:00:00

  • Simple method for selecting catalytic monoclonal antibodies that exhibit turnover and specificity.

    abstract::Monoclonal antibodies were raised against a mono-p-nitrophenyl phosphonate ester to elicit catalytic antibodies capable of hydrolyzing the analogous p-nitrophenyl ester or carbonate. Potential catalytic antibody producing clones were selected, by use of a competitive inhibition assay, on the basis of their affinity fo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00494a023

    authors: Tawfik DS,Zemel RR,Arad-Yellin R,Green BS,Eshhar Z

    更新日期:1990-10-23 00:00:00

  • Role of structural and energetic factors in regulating repair of a bulky DNA lesion with different opposite partner bases.

    abstract::Extensive molecular modeling with molecular dynamics simulations and van der Waals energy analyses were used to elucidate the striking finding that a mutagenic benzo[a]pyrene-derived DNA lesion, the base-displaced intercalated 10R-(+)-cis-anti-B[a]P-N(2)-dG (G*), manifests large differences in nucleotide excision repa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi4009177

    authors: Mu H,Kropachev K,Chen Y,Zhang H,Cai Y,Geacintov NE,Broyde S

    更新日期:2013-08-20 00:00:00

  • Evaluation of copper2+ affinities for the prion protein.

    abstract::The prion protein (PrP) is a cell-surface Cu2+ binding glycoprotein which can bind six copper ions. The role of Cu2+ in PrP function, misfolding, and prion disease has generated much interest; however, the field has been hampered by a lack of consensus with regard to the affinity of Cu2+ for PrPC. Here we build on our...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9011397

    authors: Nadal RC,Davies P,Brown DR,Viles JH

    更新日期:2009-09-29 00:00:00

  • A 106-kDa aminopeptidase is a putative receptor for Bacillus thuringiensis Cry11Ba toxin in the mosquito Anopheles gambiae.

    abstract::Bacillus thuringiensis (Bt) insecticidal toxins bind to receptors on midgut epithelial cells of susceptible insects, and binding triggers biochemical events that lead to insect mortality. Recently, a 100-kDa aminopeptidase N (APN) was isolated from brush border membrane vesicles (BBMV) of Anopheles quadrimaculatus and...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801181g

    authors: Zhang R,Hua G,Andacht TM,Adang MJ

    更新日期:2008-10-28 00:00:00

  • Solution structure of the N-terminal EGF-like domain from human factor VII.

    abstract::Blood coagulation is initiated by Ca(2+)-dependent binding of coagulation factor VIIa (FVIIa) to its cofactor, tissue factor (TF). The TF:FVIIa complex activates factors IX and X, ultimately leading to the formation of thrombin and the coagulation of blood. FVII consists of an N-terminal gamma-carboxyglutamic-acid-con...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980522f

    authors: Muranyi A,Finn BE,Gippert GP,Forsén S,Stenflo J,Drakenberg T

    更新日期:1998-07-28 00:00:00

  • Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy.

    abstract::The ferritin IRE, a highly conserved (96-99% in vertebrates) mRNA translation regulatory element in animal mRNA, was studied by molecular modeling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg2+. IRE isoforms in other mRNAs regulate mRNA translation or stabilit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9719814

    authors: Gdaniec Z,Sierzputowska-Gracz H,Theil EC

    更新日期:1998-02-10 00:00:00

  • Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.

    abstract::In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). I...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801831r

    authors: Zhang P,Martin PD,Purcarea C,Vaishnav A,Brunzelle JS,Fernando R,Guy-Evans HI,Evans DR,Edwards BF

    更新日期:2009-02-03 00:00:00

  • Regulation of the cardiac muscle ryanodine receptor by O(2) tension and S-nitrosoglutathione.

    abstract::The cardiac and skeletal muscle sarcoplasmic reticulum ryanodine receptor Ca(2+) release channels contain thiols that are potential targets of endogenously produced reactive oxygen and nitrogen intermediates. Previously, we showed that the skeletal muscle ryanodine receptor (RyR1) has O(2)-sensitive thiols; only when ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi8012627

    authors: Sun J,Yamaguchi N,Xu L,Eu JP,Stamler JS,Meissner G

    更新日期:2008-12-30 00:00:00

  • Design and synthesis of a globin fold.

    abstract::We propose a simple method to find an amino acid sequence that is foldable into a globular protein with a desired structure based on a knowledge-based 3D-1D compatibility function. An asymmetric alpha-helical single-domain structure of sperm whale myoglobin consisting of 153 amino acid residues was chosen for the desi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi983006y

    authors: Isogai Y,Ota M,Fujisawa T,Izuno H,Mukai M,Nakamura H,Iizuka T,Nishikawa K

    更新日期:1999-06-08 00:00:00

  • Structure-Based Identification of Inhibitors for the SLC13 Family of Na(+)/Dicarboxylate Cotransporters.

    abstract::In mammals, citric acid cycle intermediates play a key role in regulating various metabolic processes, such as fatty acid synthesis and glycolysis. Members of the sodium-dependent SLC13 transporter family mediate the transport of di- and tricarboxylates into cells. SLC13 family members have been implicated in lifespan...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.5b00388

    authors: Colas C,Pajor AM,Schlessinger A

    更新日期:2015-08-11 00:00:00

  • Physical behavior of the hydrophobic core of membranes: properties of 1-stearoyl-2-linoleoyl-sn-glycerol.

    abstract::Phospholipids containing a saturated fatty acid in the primary position and an unsaturated fatty acid in the secondary position are a major structural part of biological membranes. The mixed-chain hydrophobic core of the membranes is the diacylglycerol part. To better understand the core properties of membranes we hav...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00051a015

    authors: Di L,Small DM

    更新日期:1995-12-26 00:00:00

  • Pyridoxal 5'-phosphate binding site of pig heart alanine aminotransferase.

    abstract::After borohydride reduction, carboxymethylation, and tryptic digestion of the holoenzyme of pig heart alanine aminotransferase, a single icosapeptide containing the N6-(phosphopyridoxyl)lysine residue was isolated by a combination of gel filtration and ion-exchange chromatogrpahy. Its primary structure was determined ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00581a015

    authors: Tanase S,Kojima H,Morino Y

    更新日期:1979-07-10 00:00:00

  • Thermodynamics and specificity of the Mbp1-DNA interaction.

    abstract::The DNA binding domain of the yeast transcription factor Mbp1 is a winged helix-turn-helix structure, with an extended DNA binding site involving C-terminal "tail" residues. The thermodynamics of the interaction of the DNA binding domain with its target DNA sequence have been determined using fluorescence anisotropy a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi702339q

    authors: Deleeuw L,Tchernatynskaia AV,Lane AN

    更新日期:2008-06-17 00:00:00

  • Copurification of the FpvA ferric pyoverdin receptor of Pseudomonas aeruginosa with its iron-free ligand: implications for siderophore-mediated iron transport.

    abstract::The Pseudomonas aeruginosa FpvA receptor is a TonB-dependent outer membrane transport protein that catalyzes uptake of ferric pyoverdin across the outer membrane. Surprisingly, FpvA expressed in P. aeruginosa grown in an iron-deficient medium copurifies with a ligand X that we have characterized by UV, fluorescence, a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi990421x

    authors: Schalk IJ,Kyslik P,Prome D,van Dorsselaer A,Poole K,Abdallah MA,Pattus F

    更新日期:1999-07-20 00:00:00

  • Direct interaction of the inhibitory gamma-subunit of Rod cGMP phosphodiesterase (PDE6) with the PDE6 GAFa domains.

    abstract::Retinal rod and cone cGMP phosphodiesterases (PDE6 family) function as the effector enzyme in the vertebrate visual transduction cascade. The activity of PDE6 catalytic subunits is controlled by the Pgamma-subunits. In addition to the inhibition of cGMP hydrolysis at the catalytic sites, Pgamma is known to stimulate a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi015935m

    authors: Muradov KG,Granovsky AE,Schey KL,Artemyev NO

    更新日期:2002-03-26 00:00:00

  • Near-infrared resonance Raman spectra of Chloroflexus aurantiacus photosynthetic reaction centers.

    abstract::Resonance Raman spectra of the photosynthetic reaction center isolated from the green bacterium Chloroflexus aurantiacus have been obtained with excitation in the near-infrared absorption bands of the special pair (P) and the accessory bacteriochlorophyll (B) using shifted-excitation Raman difference spectroscopy (SER...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00015a044

    authors: Cherepy NJ,Holzwarth AR,Mathies RA

    更新日期:1995-04-18 00:00:00

  • Ethylene enhances reactivity of superoxide with peroxidase to form the oxy-ferrous complex.

    abstract::Ethylene and its analogues acetylene, carbon monoxide, and propylene inhibited the rate of oxidation of indole-3-acetic acid by peroxidase. Annulment of this effect by addition of superoxide dismutase showed that inhibition occurred only in the presence of the superoxide anion radical (O2-.). Kinetic and spectral data...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00276a019

    authors: Smith AM,Morrison WL,Milham PJ

    更新日期:1983-03-29 00:00:00

  • Biochemical characterization of the minichromosome maintenance (MCM) protein of the crenarchaeote Aeropyrum pernix and its interactions with the origin recognition complex (ORC) proteins.

    abstract::Replication in archaea is carried out by proteins that are homologues of eukaryotic counterparts. However, the archaeal systems tend to be much simpler with fewer different genes encoding the core functions than in eukaryotic counterparts. In many archaea, there is a single minichromosome maintenance (MCM) homologue, ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801479s

    authors: Atanassova N,Grainge I

    更新日期:2008-12-16 00:00:00

  • Kinetic and spectroscopic characterization of fluorescent ribose-modified ATP analogs upon interaction with skeletal muscle myosin subfragment 1.

    abstract::The interaction of fluorescent ATP analog 2'(3')-O-[N-[2-[3-(5-fluoresceinyl)thioureido]-ethyl]carbamoyl]adenosine 5'-triphosphate (FEDA-ATP) with rabbit skeletal myosin subfragment 1 (S1) and acto-S1 was studied. This and related ATP analogs are potentially useful for determination of the ATPase activity of single my...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi951824+

    authors: Conibear PB,Jeffreys DS,Seehra CK,Eaton RJ,Bagshaw CR

    更新日期:1996-02-20 00:00:00

  • Influence of the extent of branching on solution conformations of complex oligosaccharides: a molecular dynamics and NMR study of a penta-antennary "bisected" N-glycan.

    abstract::The solution conformation of an agalactosyl penta-antennary "bisected" N-linked glycan from hen ovomucoid has been determined using a combination of 1H-NMR NOE measurements and restrained molecular dynamics (MD) simulations. The majority of glycosidic linkages exhibited restricted torsional fluctuations about the glob...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00043a018

    authors: Rutherford TJ,Neville DC,Homans SW

    更新日期:1995-10-31 00:00:00