当前位置： SCI文献检索 > BIOCHEMISTRY期刊下所有文献 > Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA.

Backbone and side chain dynamics of lac repressor headpiece (1-56) and its complex with DNA.

Abstract：

:The dynamics of the backbone and (some of) the side chains of lac headpiece (1-56; lac HP56) have been studied for the free protein and for its complex with lac half-operator DNA by 15N T1 and T1p relaxation measurements combined with [1H-15N] NOE experiments. For the structurally well-defined part of the free lac HP56 (i.e., residues 3-49) a rigid backbone was found for residues in the three alpha-helices and for the turn of the helix-turn-helix motif. The loop between helices II and III of lac headpiece, which was characterized by slight disorder in the structure calculations, shows increased mobility. The detected side chains are very mobile. These data are in full agreement with the rms deviations in the structural data of free lac HP56. When lac HP56 is complexed with DNA, several changes in mobility take place. The most remarkable change was found for the loop region between helices II and III: residue His-29 within this loop interacts with Thy-3 of the operator DNA. As a result this mobile loop adapts itself to the DNA and becomes more rigid. Moreover, most DNA-contacting side chains show a significant decrease in flexibility, although these side chains do not become as rigid as the backbone. These results suggest that the mobility of the regions within lac HP56 important for complexation, i.e., the loop and the DNA-contacting side chains, is essential for a good fit onto the counterparts of the target DNA.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Slijper M,Boelens R,Davis AL,Konings RN,van der Marel GA,van Boom JH,Kaptein R

doi

10.1021/bi961670d

subject

Has Abstract

pub_date

1997-01-07 00:00:00

pages

249-54

issue

1

eissn

0006-2960

issn

1520-4995

pii

bi961670d

journal_volume

36

pub_type

杂志文章

相关文献

BIOCHEMISTRY文献大全
  • Self-assembly of aqueous bilirubin ditaurate, a natural conjugated bile pigment, to contraposing enantiomeric dimers and M(-) and P(+) tetramers and their selective hydrophilic disaggregation by monomers and micelles of bile salts.

    abstract：:The solution behavior of bilirubin ditaurate (BDT), the first naturally occurring conjugated bile pigment to be physically and chemically characterized, was assessed in aqueous solution and in monomeric and micellar solutions of common taurine-conjugated bile salts (BS). Analytical ultracentrifugation revealed that BD...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi501251v

    authors： Neubrand MW,Carey MC,Laue TM

    更新日期：2015-02-24 00:00:00

  • Normal modes of prion proteins: from native to infectious particle.

    abstract：:Prion proteins (PrP) are the infectious agent in transmissible spongiform encephalopathies (i.e., mad cow disease). To be infectious, prion proteins must undergo a conformational change involving a decrease in α-helical content along with an increase in β-strand content. This conformational change was evaluated by mea...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi1010514

    authors： Samson AO,Levitt M

    更新日期：2011-03-29 00:00:00

  • Use of a Cholesterol Recognition Amino Acid Consensus Peptide To Inhibit Binding of a Bacterial Toxin to Cholesterol.

    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

    authors： Koufos E,Chang EH,Rasti ES,Krueger E,Brown AC

    更新日期：2016-08-30 00:00:00

  • Structure and interactions of plant cell-wall polysaccharides by two- and three-dimensional magic-angle-spinning solid-state NMR.

    abstract：:The polysaccharide-rich cell walls (CWs) of plants perform essential functions such as maintaining tensile strength and allowing plant growth. Using two- and three-dimensional magic-angle-spinning (MAS) solid-state NMR and uniformly (13)C-labeled Arabidopsis thaliana, we have assigned the resonances of the major polys...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi101795q

    authors： Dick-Pérez M,Zhang Y,Hayes J,Salazar A,Zabotina OA,Hong M

    更新日期：2011-02-15 00:00:00

  • Temperature dependence of the reduction potential of CuA in carbon monoxide inhibited cytochrome c oxidase.

    abstract：:The temperature dependence of the reduction potential of the CuA site in carbon monoxide inhibited cytochrome c oxidase has been measured with a spectroelectrochemical method adapted to the relatively weak near-infrared absorption of this copper ion. These measurements, together with parallel measurements on the 604-n...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00349a024

    authors： Wang H,Blair DF,Ellis WR Jr,Gray HB,Chan SI

    更新日期：1986-01-14 00:00:00

  • Kinetics and equilibria in ligand binding by nitrophorins 1-4: evidence for stabilization of a nitric oxide-ferriheme complex through a ligand-induced conformational trap.

    abstract：:Nitrophorins 1-4 (NP1-4) are ferriheme proteins from the blood-sucking insect Rhodnius prolixus that transport nitric oxide (NO) to the victim, sequester histamine, and inhibit blood coagulation. Here, we report kinetic and thermodynamic analyses for ligand binding by all four proteins and their reduction potentials. ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi000766b

    authors： Andersen JF,Ding XD,Balfour C,Shokhireva TK,Champagne DE,Walker FA,Montfort WR

    更新日期：2000-08-22 00:00:00

  • Structural investigation of the binding of a herpesviral protein to the SH3 domain of tyrosine kinase Lck.

    abstract：:Herpesvirus saimiri codes for a tyrosine kinase interacting protein (Tip) that interacts with both the SH3 domain and the kinase domain of the T-cell-specific tyrosine kinase Lck via two separate motifs. The activation of Lck by Tip is considered as a key event in the transformation of human T-lymphocytes during herpe...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi015986j

    authors： Schweimer K,Hoffmann S,Bauer F,Friedrich U,Kardinal C,Feller SM,Biesinger B,Sticht H

    更新日期：2002-04-23 00:00:00

  • Selective targeting of G-quadruplex using furan-based cyclic homooligopeptides: effect on c-MYC expression.

    abstract：:Quadruplex-specific molecules can serve as suitable drugs in cancer therapy. We have synthesized a pair of furan-based cyclic homooligopeptides, ligand 1 and ligand 2, to specifically target G-quadruplexes. We have shown by CD spectroscopy and UV melting that these ligands can effectively induce G-quadruplex structure...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi1005927

    authors： Agarwal T,Roy S,Chakraborty TK,Maiti S

    更新日期：2010-09-28 00:00:00

  • Studies of 1-deoxy-D-fructose, 1-deoxy-D-glucitol, and 1-deoxy-D-minnitol as antimetabolites.

    abstract：:1-Deoxy-D-fructose was synthesized in 27% yield from D-glucosamine in a three-step procedure involving Raney nickel desulfurization and oxidative deamination with 3,5-di-tert-butyl- 1,2-benzoquinone applied to appropriate intermediates. 1-Deoxyfructose and its reduction products, 1-deoxyglucitol and 1-deoxymannitol, w...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00665a027

    authors： Dills WL Jr,Meyer WL

    更新日期：1976-10-05 00:00:00

  • Formylglycinamide ribonucleotide synthetase from Escherichia coli: cloning, sequencing, overproduction, isolation, and characterization.

    abstract：:The purL gene of Escherichia coli encoding the enzyme formylglycinamidine ribonucleotide (FGAM) synthetase which catalyzes the conversion of formylglycinamide ribonucleotide (FGAR), glutamine, and MgATP to FGAM, glutamate, ADP, and Pi has been cloned and sequenced. The mature protein, as deduced by the structural gene...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00432a017

    authors： Schendel FJ,Mueller E,Stubbe J,Shiau A,Smith JM

    更新日期：1989-03-21 00:00:00

  • Efficiency of repair of an abasic site within DNA clustered damage sites by mammalian cell nuclear extracts.

    abstract：:Ionizing radiation induces clustered DNA damage sites which have been shown to challenge the repair mechanism(s) of the cell. Evidence demonstrating that base excision repair is compromised during the repair of an abasic (AP) site present within a clustered damage site is presented. Simple bistranded clustered damage ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi049560r

    authors： Lomax ME,Cunniffe S,O'Neill P

    更新日期：2004-08-31 00:00:00

  • Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187.

    abstract：:The nature of the putative general acid His187 in the reaction catalyzed by Escherichia coli uracil DNA glycosylase (UDG) was investigated using X-ray crystallography and NMR spectroscopy. The crystal structures of H187Q UDG, and its complex with uracil, have been solved at 1.40 and 1.60 A resolution, respectively. Th...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9910880

    authors： Drohat AC,Xiao G,Tordova M,Jagadeesh J,Pankiewicz KW,Watanabe KA,Gilliland GL,Stivers JT

    更新日期：1999-09-14 00:00:00

  • Equilibrium analysis of ethidium binding to DNA containing base mismatches and branches.

    abstract：:In the processes of DNA replication, recombination, and repair, duplex DNA can transiently form branched structures, such as Holliday junctions, as well as base pair mismatches and bulges. These stages have altered ligand and protein binding properties from normal double helical DNA. A variety of ligands have been rep...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00248a025

    authors： Hernández LI,Zhong M,Courtney SH,Marky LA,Kallenbach NR

    更新日期：1994-11-08 00:00:00

  • Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase.

    abstract：:The binding of bacteriophage T4 DNA polymerase (T4 pol) to primer-template DNA with 2-aminopurine (2AP) located at the primer terminus results in the formation of a hyperfluorescent 2AP state. Changes in this hyperfluorescent state were utilized to investigate the fractional concentration of primer-templates bound at ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi980074b

    authors： Beechem JM,Otto MR,Bloom LB,Eritja R,Reha-Krantz LJ,Goodman MF

    更新日期：1998-07-14 00:00:00

  • Deletion of the omega-loop in the active site of staphylococcal nuclease. 2. Effects on protein structure and dynamics.

    abstract：:It has been shown (Poole et al., 1991) that deletion of residues 44-49 from the sequence of staphylococcal nuclease (E43 SNase) results in an enzyme (E43 delta SNase) that is significantly more active than D43 SNase, an enzyme that differs from the wild-type enzyme by deletion of a single methylene group. In addition,...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00229a006

    authors： Baldisseri DM,Torchia DA,Poole LB,Gerlt JA

    更新日期：1991-04-16 00:00:00

  • Perturbing the water cavity surrounding the manganese cluster by mutating the residue D1-valine 185 has a strong effect on the water oxidation mechanism of photosystem II.

    abstract：:The active site of water oxidation in Photosystem II (PSII) is a Mn4CaO5 cluster that is located in a cavity between the D1 and CP43 protein subunits by which it is coordinated. The remainder of this cavity is filled with water molecules, which serve as a source of substrate and participate in poorly understood hydrog...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi400930g

    authors： Dilbeck PL,Bao H,Neveu CL,Burnap RL

    更新日期：2013-10-01 00:00:00

  • Heme-binding characteristics of the isolated PAS-A domain of mouse Per2, a transcriptional regulatory factor associated with circadian rhythms.

    abstract：:Neuronal PAS protein 2 (NPAS2), a heme-binding transcriptional regulatory factor, is involved in circadian rhythms. Period homologue (Per) is another important transcriptional regulatory factor that binds to cryptochrome (Cry). The resultant Per/Cry heterodimer interacts with the NPAS2/BMAL1 heterodimer to inhibit the...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi7023892

    authors： Kitanishi K,Igarashi J,Hayasaka K,Hikage N,Saiful I,Yamauchi S,Uchida T,Ishimori K,Shimizu T

    更新日期：2008-06-10 00:00:00

  • Acetylcholine receptor: evidence for a regulatory binding site in investigations of suberyldicholine-induced transmembrane ion flux in Electrophorus electricus membrane vesicles.

    abstract：:Suberyldicholine-induced ion translocation in the millisecond time region in acetylcholine receptor rich membrane vesicles prepared from the electric organ of Electrophorus electricus was investigated in eel Ringer's solution, pH 7.0, 1 degree C. A quench-flow technique with a time resolution of 5 ms was used to measu...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00294a041

    authors： Pasquale EB,Takeyasu K,Udgaonkar JB,Cash DJ,Severski MC,Hess GP

    更新日期：1983-12-06 00:00:00

  • Conformational flexibility of PEP mutase.

    abstract：:Previous work has indicated that PEP mutase catalyzes the rearrangement of phosphoenolpyruvate to phosphonopyruvate by a dissociative mechanism. The crystal structure of the mutase with Mg(II) and sulfopyruvate (a phosphonopyruvate analogue) bound showed that the substrate is anchored to the active site by the Mg(II),...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi036255h

    authors： Liu S,Lu Z,Han Y,Jia Y,Howard A,Dunaway-Mariano D,Herzberg O

    更新日期：2004-04-20 00:00:00

  • Binding of initiation factor 2 and initiator tRNA to the Escherichia coli 30S ribosomal subunit induces allosteric transitions in 16S rRNA.

    abstract：:The specific effect of the binding of IF2 and initiator fMET-tRNA(fMet) on Escherichia coli 16S rRNA has been probed by phosphate alkylation with ethylnitrosourea. The results show that IF2 does not significantly shield portions of 16S rRNA but induces both reductions and enhancements of reactivity scattered in the en...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00487a023

    authors： Wakao H,Romby P,Laalami S,Ebel JP,Ehresmann C,Ehresmann B

    更新日期：1990-09-04 00:00:00

  • DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein: promoter-dependent differences in the thermodynamics and kinetics of binding.

    abstract：:The equilibrium binding and association kinetics of the Saccharomyces cerevisiae TATA Binding Protein (TBP) to the E4 and Major Late promoters of adenovirus (TATATATA and TATAAAAG, respectively), have been directly compared by quantitative DNase I titration and quench-flow "footprinting". The equilibrium binding of TB...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi981072u

    authors： Petri V,Hsieh M,Jamison E,Brenowitz M

    更新日期：1998-11-10 00:00:00

  • Electronic structure studies of the adenosylcobalamin cofactor in glutamate mutase.

    abstract：:Glutamate mutase (GM) is a cobalamin-dependent enzyme that catalyzes the reversible interconversion of L-glutamate and L-threo-3-methylaspartate via a radical-based mechanism. To initiate catalysis, the 5'-deoxyadenosylcobalamin (AdoCbl) cofactor's Co-C bond is cleaved homolytically to generate an adenosyl radical and...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi051094y

    authors： Brooks AJ,Fox CC,Marsh EN,Vlasie M,Banerjee R,Brunold TC

    更新日期：2005-11-22 00:00:00

  • RNA-ligand interactions: affinity and specificity of aminoglycoside dimers and acridine conjugates to the HIV-1 Rev response element.

    abstract：:Semisynthetic aminoglycoside derivatives may provide a means to selectively target viral RNA sites, including the HIV-1 Rev response element (RRE). The design, synthesis, and evaluation of derivatives based upon neomycin B, kanamycin A, and tobramycin conjugates of 9-aminoacridine are presented. To evaluate the import...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi034766y

    authors： Luedtke NW,Liu Q,Tor Y

    更新日期：2003-10-07 00:00:00

  • Inhibition of protein phosphatase 2A activity by selective electrophile alkylation damage.

    abstract：:Protein serine/threonine phosphatase 2A (PP2A) is a critical regulator of numerous cellular signaling processes and a potential target for reactive electrophiles that dysregulate phosphorylation-dependent signal transduction cascades. The predominant cellular form of PP2A is a heterotrimeric holoenzyme consisting of a...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi060551n

    authors： Codreanu SG,Adams DG,Dawson ES,Wadzinski BE,Liebler DC

    更新日期：2006-08-22 00:00:00

  • Isolation and characterization of an anticoagulant protein homologous to botrocetin from the venom of Bothrops jararaca.

    abstract：:We previously isolated a unique anticoagulant protein named IX/X-bp (factor IX/factor X-binding protein) from the venom of the habu snake Trimeresurus flavoviridis. We recently determined its primary structure and found that this protein had a structure homologous to the carbohydrate-recognition domains of C-type lect...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00078a012

    authors： Sekiya F,Atoda H,Morita T

    更新日期：1993-07-13 00:00:00

  • Heterogeneous glycosylation of immunoglobulin E constructs characterized by top-down high-resolution 2-D mass spectrometry.

    abstract：:Posttranslational glycosylation is critical for biological function of many proteins, but its structural characterization is complicated by natural heterogeneity, multiple glycosylation sites, and different forms. Here, a top-down mass spectrometry (MS) characterization is applied to three constructs of the Fc segment...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi9919091

    authors： Fridriksson EK,Beavil A,Holowka D,Gould HJ,Baird B,McLafferty FW

    更新日期：2000-03-28 00:00:00

  • Role of GTP hydrolysis in microtubule polymerization: evidence for a coupled hydrolysis mechanism.

    abstract：:The relationship between GTP hydrolysis and microtubule assembly has been investigated by using a rapid filtration method. Microtubules assembled from phosphocellulose-purified tubulin, double-labeled with [gamma-32P]- and [3H]GTP, were trapped and washed free of unbound nucleotide on glass fiber filters. The transien...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00479a022

    authors： Stewart RJ,Farrell KW,Wilson L

    更新日期：1990-07-10 00:00:00

  • Identification of multiple glucocorticoid receptor binding sites in the rat osteocalcin gene promoter.

    abstract：:The biosynthesis of osteocalcin (OC), a bone-specific, noncollagenous protein, is stringently regulated during differentiation of the osteoblast phenotype. Glucocorticoids, and also 1,25(OH)2D3, mediate the developmental regulation of OC gene transcription. In this study, we established that the -1097 to +23 promoter ...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi00093a022

    authors： Heinrichs AA,Bortell R,Rahman S,Stein JL,Alnemri ES,Litwack G,Lian JB,Stein GS

    更新日期：1993-10-26 00:00:00

  • Investigations of photolysis and rebinding kinetics in myoglobin using proximal ligand replacements.

    abstract：:We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound H93G myoglobin (Mb) mutants to study the influence of the proximal ligand on the CO rebinding kinetics. In H93G mutants, where the proximal linkage with the protein is eliminated and the heme can bind exogenous ligands (e.g., imidazole, 4-b...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi049077g

    authors： Cao W,Ye X,Sjodin T,Christian JF,Demidov AA,Berezhna S,Wang W,Barrick D,Sage JT,Champion PM

    更新日期：2004-08-31 00:00:00

  • Crystal structures of antibiotic-bound complexes of aminoglycoside 2''-phosphotransferase IVa highlight the diversity in substrate binding modes among aminoglycoside kinases.

    abstract：:Aminoglycoside 2''-phosphotransferase IVa [APH(2'')-IVa] is a member of a family of bacterial enzymes responsible for medically relevant resistance to antibiotics. APH(2'')-IVa confers high-level resistance against several clinically used aminoglycoside antibiotics in various pathogenic Enterococcus species by phospho...

    journal_title：Biochemistry

    pub_type： 杂志文章

    doi：10.1021/bi200747f

    authors： Shi K,Houston DR,Berghuis AM

    更新日期：2011-07-19 00:00:00