Abstract：
:Conformational distributions of a four-way DNA junction have been examined by time-resolved fluorescence resonance energy transfer (FRET). A series of dye-labeled junctions were synthesized with donor (fluorescein) and acceptor (tetramethylrhodamine) dyes conjugated to the 5' termini of the duplex arms in all six pairwise combinations. The fluorescence decay of the donor in each junction was measured by time-correlated single-photon counting. The distributions of donor-acceptor (D-A) distances present between each pair of arms were recovered from the donor decays using a continuous Gaussian distribution model. The overall geometry of the four-way junction defined by the six mean D-A distances was consistent with a stacked-X structure, wherein pairs of duplex arms associate to form two continuous domains. Large differences were observed in the widths of the D-A distance distributions, depending on which pair of arms were labeled with the donor and acceptor dyes. Distances measured along the stacking domains were characterized by relatively narrow distributions, indicating that these domains were rigid, whereas distances between stacking domains had broader distributions, reflecting variability in the angle between the two domains. The distances described by broad distributions were overestimated by steady-state FRET measurements. These results suggest that an ensemble of stacked-X structures are present in solution, characterized by differences in the small angle between the stacking domains. Temperature and solvent effects on the recovered distribution widths provide an indication of flexibility in the four-way junction.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Eis PS,Millar DPdoi
10.1021/bi00213a014subject
Has Abstractpub_date
1993-12-21 00:00:00pages
13852-60issue
50eissn
0006-2960issn
1520-4995journal_volume
32pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract：:2,3-Butanedione monoxime (BDM) reversibly inhibits force production in muscle. At least part of its action appears to be directly on the contractile apparatus. To understand better its mechanism of action, we studied the effect of BDM on the steps of myosin subfragment 1 Mg(2+)-ATPase in 0.1 M potassium acetate, pH 7....
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00163a036
更新日期：1992-12-08 00:00:00
abstract：:S100A1, a member of the S100 protein family, is an EF-hand containing Ca(2+)-binding protein (93 residues per subunit) with noncovalent interactions at its dimer interface. Each subunit of S100A1 has four alpha-helices and a small antiparallel beta-sheet consistent with two helix-loop-helix calcium-binding domains [Ba...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0118308
更新日期：2002-01-22 00:00:00
abstract：:Human prolactin (hPRL) binds two human prolactin receptor molecules, creating active heterotrimeric complexes. Receptors bind dissimilar hormone surfaces termed site 1 and site 2 in an obligate ordered process. We sought to map the functional epitopes in site 1 of hPRL. Extensive alanine mutagenesis (102 of the 199 re...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi101838s
更新日期：2011-03-01 00:00:00
abstract：:The light harvesting 1 antenna (LH1) complex from Rhodobacter sphaeroides funnels excitation energy to the photosynthetic reaction center. Our ultimate goal is to build up the structure of LH1 from structures of its individual subunits, much as the antenna can self-assemble from its components in membrane-mimicking de...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi011576j
更新日期：2002-01-08 00:00:00
abstract：:Base excision repair (BER) plays a vital role in maintaining genomic integrity in mammalian cells. DNA polymerase λ (Pol λ) is believed to play a backup role to DNA polymerase β (Pol β) in base excision repair. Two oxidized abasic lesions that are produced by a variety of DNA-damaging agents, including several antitum...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi301592x
更新日期：2013-02-05 00:00:00
abstract：:Immunoglobulins fragments are composed of globular domains linked by extended polypeptide segments. The molecular flexibility inherent in this arrangement allows for significant potential differences between structures observed in the crystalline state and those attained in solution. Small-angle neutron scattering mea...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00541a011
更新日期：1982-06-08 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：:To understand relationships between membrane-binding properties of cytolytic peptides and resulting cytotoxicity, we investigated interactions of dermaseptin analogues with model bilayers by means of surface plasmon resonance. First, we tested the system by comparing two native dermaseptins, S1 and S4, whose binding p...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi034514x
更新日期：2003-11-11 00:00:00
abstract：:The multicatalytic proteinase complex (MPC, proteasome) is composed of 28 subunits organized into four rings surrounding a water-filled canal. The catalytic centers face the inner canal confining protein substrates to an enclosed space. Experimental findings obtained with MPC from archaebacteria suggest that degradati...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi990826h
更新日期：1999-11-02 00:00:00
abstract：:Lysophosphatidic acid (1-acyl-sn-glycero-3-phosphate or LPA) is a phospholipid mediator displaying numerous and widespread biological activities and thought to act via G-protein-coupled receptors. Here we have studied the effects on human platelets of a number of LPA analogues, including two enantiomers of both N-palm...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9816756
更新日期：1999-06-29 00:00:00
abstract：:An expression plasmid encoding the extracellular portion of the human tumor necrosis factor (TNF) type 1 receptor (TNF-R1) was constructed and used to generate a stable cell line secreting soluble TNF-R1 (sTNF-R1). The sTNF-R1 was purified, and its biochemical properties and its interactions with human TNF-alpha were ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00119a023
更新日期：1992-02-04 00:00:00
abstract：:The sensor kinase CitA and the response regulator CitB of Klebsiella pneumoniae form the paradigm of a subfamily of bacterial two-component regulatory systems that are capable of sensing tri- or dicarboxylates in the environment and then induce transporters for the uptake of these compounds. We recently showed that th...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi0340595
更新日期：2003-05-20 00:00:00
abstract：:To probe the mechanism of the reversible DNA phosphodiester bond cleavage and religation mechanism of the type I topoisomerase from vaccinia virus, we have synthesized DNA substrates carrying a single nonbridging Rp- or Sp-phosphorothioate (Ps) modification at the scissile phosphodiester (Pd) bond. Analysis of the ste...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi992429c
更新日期：2000-05-09 00:00:00
abstract：:Phosphorylation of phosphatidylinositol (PtdIns) by PtdIns 4-kinases is the first step in the synthesis of polyphosphoinositides, the lipid precursors of intracellular signaling molecules. We have recently identified a cytosolic PtdIns 4-kinase (cPI4K) in the bovine adrenal cortex that is distinguished from previously...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi9517493
更新日期：1996-03-19 00:00:00
abstract：:31P NMR measurements were made (at 121.5 MHz and 5 degrees C) on enzyme-bound substrate complexes of 3-phosphoglycerate kinase in order to address three questions pertaining to (i) the integrity of the enzyme-substrate complexes with Mg(II) in the presence of sulfate concentrations typical of those used for crystalliz...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00415a027
更新日期：1988-07-26 00:00:00
abstract：:The importance of the evolutionarily conserved Gly-4 residue for the affinity and kinetics of interaction of cystatin A with several cysteine proteinases was assessed by site-directed mutagenesis. Even the smallest replacement, by Ala, resulted in approximately 1000-, approximately 10- and approximately 6000-fold decr...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi980026r
更新日期：1998-05-19 00:00:00
abstract：:The association of membrane and cytoplasmic proteins with the cytoskeleton of resting and activated platelets was studied. Glycoproteins were identified by labeling with 125I-labeled lectins (concanavalin A, wheat germ agglutinin, and Lens culinaris). Polypeptides, which are embedded in the lipid bilayer, have been id...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00537a002
更新日期：1982-04-13 00:00:00
abstract：:We have combined equilibrium and steered molecular dynamics (SMD) simulations with principal component and correlation analyses to probe the mechanism of allosteric regulation in imidazole glycerol phosphate (IGP) synthase. An evolutionary analysis of IGP synthase revealed a conserved network of interactions leading f...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi061708e
更新日期：2007-02-27 00:00:00
abstract：:Recombinant human brain calbindin D(28K) (rHCaBP), human Cu,Zn-superoxide dismutase (HCuZnSOD), rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and bovine serum albumin (BSA) were found to be S-glutathiolated in decomposed S-nitrosoglutathione (GSNO) solutions. Tryptic or Glu-C digestion and MALDI-TOF ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi035924o
更新日期：2004-04-06 00:00:00
abstract：:Human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2, respectively) exhibit extensive genetic variations. It was postulated that much of this genetic variability stems from the low fidelity of the reverse transcription step. Both HIV reverse transcriptases (RTs) were shown to be particularly error-prone during...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00154a010
更新日期：1992-10-06 00:00:00
abstract：:Endonuclease V from bacteriophage T4 is a well characterized enzyme that initiates the repair of ultraviolet light induced pyrimidine dimers. Scission of the phosphodiester backbone between the pyrimidines within a dimer, or 3' to an abasic (AP) site, occurs by a beta-elimination mechanism. In addition, high concentra...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00027a031
更新日期：1995-07-11 00:00:00
abstract：:Replication protein A (RPA) is a heterotrimeric protein that is required for DNA replication and most DNA repair pathways. RPA has previously been shown to play a role in recognizing and binding damaged DNA during nucleotide excision repair (NER). RPA has also been suggested to play a role in psoralen DNA interstrand ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi800460d
更新日期：2008-09-23 00:00:00
abstract：:The folding of many globular proteins from the unfolded (U) to the native (N) state appears to be describable by a two-state N ↔ U model, which has led to the general belief that protein folding occurs in a highly cooperative manner. One reason for the widespread belief in "two-state folding" is that protein folding r...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/acs.biochem.8b00698
更新日期：2018-10-09 00:00:00
abstract：:(S)-Mandelate dehydrogenase from Pseudomonas putida belongs to a FMN-dependent enzyme family that oxidizes (S)-alpha-hydroxyacids. Despite a high degree of sequence and structural similarity, this family can be divided into three subgroups based on the different oxidants utilized in the second oxidative half-reaction....
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi049005p
更新日期：2004-08-24 00:00:00
abstract：:Human hemoglobin produced in the Escherichia coli coexpression system of Hernan et al. [(1992) Biochemistry 31, 8619-8628] has been transformed into a functionally homogeneous protein whose properties closely approximate those of normal hemoglobin A. Both of the alpha and beta chains of this hemoglobin contain a valin...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi981986g
更新日期：1999-01-19 00:00:00
abstract：:In the minor fraction of HDL3 containing alpha-tocopherol (alphaTocOH), selective one-electron oxidation of Trp and Tyr residues of apolipoproteins A-I and A-II by *Br2- radical-anions produces the corresponding semioxidized species, TyrO* and *Trp. Repair of TyrO* by endogenous alphaTocOH generates the alpha-tocopher...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi701419d
更新日期：2007-12-11 00:00:00
abstract：:The mechanism of the argininosuccinate lyase reaction has been probed by the measurement of the effects of isotopic substitution at the reaction centers. A primary deuterium isotope effect of 1.0 on both V and V/K is obtained with (2S,3R)-argininosuccinate-3-d, while a primary 15N isotope effect on V/K of 0.9964 +/- 0...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00365a004
更新日期：1986-08-26 00:00:00
abstract：:The biosynthesis of epothilones, a family of hybrid polyketide (PK)/nonribosomal peptide (NRP) antitumor agents, provides an ideal system to study a hybrid PK/NRP natural product with significant biomedical value. Here the third enzyme involved in epothilone production, the five domain 195 kDa polyketide synthase (PKS...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi020006w
更新日期：2002-04-30 00:00:00
abstract：:To probe the details of small amplitude motions in proteins, a dynamical analysis of the orientation fluctuations of two tyrosine side chains in the bovine pancreatic trypsin inhibitor is presented. Detailed results are given for the time history and correlation functions obtained for the ring motion from a molecular ...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00573a001
更新日期：1979-03-20 00:00:00
abstract：:The kinetics of ATP-induced Ca2+ uptake by vesicular dispersions of sarcoplasmic reticulum were determined with a time resolution of about 10 ms, depending on the temperature. Ca2+ uptake was initiated by the addition of ATP through the flash photolysis of P3-1-(2-nitrophenyl)-ethyl adenosine 5'-triphosphate utilizing...
journal_title：Biochemistry
pub_type： 杂志文章
doi：10.1021/bi00292a003
更新日期：1983-11-08 00:00:00
