Abstract:
:Inherently curved DNA segments, associated with short runs of adenines, have been identified in many gene regulatory regions, yet their physiological significance remains unknown. The observations reported in this study indicate that intrinsically bent nucleic acid fragments are characterized by substantially attenuated affinities toward DNA-binding proteins involved in structural functions, such as H1 histone and protamine, as well as toward various DNA-modifying enzymes including ligases and exo- and endonucleases. Two mechanisms might be responsible for the altered binding properties. According to the first mechanism, the attenuated binding affinities and the bending represent two independent consequences of the unique structural parameters exhibited by A-tracts. Indeed, analysis of the degradation products obtained upon exposure of the curved sequences to various chemical nucleases points toward the narrowing of the DNA minor groove, a conformational modulation known to characterize A-tracts and to run along the axially-bent motifs, as a potential determinant of the observed binding attenuation. Alternatively, the conformational constraints which result from the stable bending might act to modulate the strength of DNA-protein interactions. Although the factor directly responsible for the altered binding affinities revealed by the bent sequences cannot as yet be conclusively resolved, it is proposed that a reiteration of this specific factor, being either an A-tract or a bend, in phase with the DNA helical repeat acts to amplify the modulation of the binding.(ABSTRACT TRUNCATED AT 250 WORDS)
journal_name
Biochemistryjournal_title
Biochemistryauthors
Shatzky-Schwartz M,Hiller Y,Reich Z,Ghirlando R,Weinberger S,Minsky Adoi
10.1021/bi00123a019subject
Has Abstractpub_date
1992-03-03 00:00:00pages
2339-46issue
8eissn
0006-2960issn
1520-4995journal_volume
31pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Human acidic mammalian chitinase (AMCase), a member of the family 18 glycosyl hydrolases, is one of the important proteins involved in Th2-mediated inflammation and has been implicated in asthma and allergic diseases. Inhibition of AMCase results in decreased airway inflammation and airway hyper-responsiveness in a mo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0525977
更新日期:2006-04-11 00:00:00
abstract::Nitrosylhemoglobin (HbFe(II)NO) has been shown to be generated in vivo from the reaction of deoxyHb with NO(*) as well as with nitrite. Despite the physiological importance attributed to this form of Hb, its reactivity has not been investigated in detail. In this study, we showed that the rate of oxidation of HbFe(II)...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0475929
更新日期:2005-04-26 00:00:00
abstract::To probe the mechanism of chaperone substrate selection, we have investigated the kinetics of complex formation and dissociation between the molecular chaperone DnaK and a short peptide (Cro, representing amino acids 1-12 of the cro repressor protein). The Cro protein was N-terminally labeled with the environmentally ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00047a024
更新日期:1995-11-28 00:00:00
abstract::Cystathionine gamma-synthase (CGS) is a pyridoxal phosphate-dependent enzyme that catalyzes a gamma-replacement reaction, in which the succinyl group of an O-succinyl-L-homoserine (L-OSHS) is displaced by the thiol of L-cysteine to form L-cystathionine, in the first step of the bacterial transsulfuration pathway. The ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035107o
更新日期:2003-09-30 00:00:00
abstract::The third intracellular loop (IL3) of G protein-coupled receptors (GPCRs) is an important contact domain between GPCRs and their G proteins. Previously, the IL3 of Ste2p, a Saccharomyces cerevisiae GPCR, was suggested to undergo a conformational change upon activation as detected by differential protease susceptibilit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200254h
更新日期:2011-08-16 00:00:00
abstract::A visual pigment consists of an opsin protein and a chromophore, 11-cis-retinal, which binds to a specific lysine residue of opsin via a Schiff base linkage. The Schiff base chromophore is protonated in pigments that absorb visible light, whereas it is unprotonated in ultraviolet-absorbing visual pigments (UV pigments...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7003763
更新日期:2007-05-29 00:00:00
abstract::First identified on the surface of lymphoids as a type II transmembrane protein, CD38 has now been established to have dual functions not only as a receptor but also as a multifunctional enzyme,catalyzing the synthesis of and hydrolysis of a general calcium messenger molecule, cyclic ADP-ribose(cADPR). The receptorial...
journal_title:Biochemistry
pub_type: 杂志文章
doi:
更新日期:2008-12-30 00:00:00
abstract::Oxidative damage by transition metals bound to proteins may be an important pathogenic mechanism. Ceruloplasmin (Cp) is a Cu-containing plasma protein thought to be involved in oxidative modification of lipoproteins. We have previously shown that Cp increased cell-mediated low-density lipoprotein (LDL) oxidation by a ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi981137t
更新日期:1998-10-06 00:00:00
abstract::The reactivity of the mitochondrial (pI = 5) isoenzyme of horse liver aldehyde dehydrogenase was determined by studying the effects of pH on steady-state velocity, burst magnitude, and molecular weight of the enzyme in the absence and presence of Mg2+ ions. The Mg2+ ion activation of the steady-state velocity at pH 7....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00524a049
更新日期:1981-10-13 00:00:00
abstract::Homoserine transacetylase catalyzes one of the required steps in the biosynthesis of methionine in fungi and several bacteria. We have determined the crystal structure of homoserine transacetylase from Haemophilus influenzae to a resolution of 1.65 A. The structure identifies this enzyme to be a member of the alpha/be...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051951y
更新日期:2005-12-06 00:00:00
abstract::Mutation of Pro94 to phenylalanine or alanine significantly alters the redox properties of the type I copper center of amicyanin. Each mutation increases the redox midpoint potential (E(m)) value by at least 140 mV and shifts the pK(a) for the pH dependence of the E(m) value to a more acidic value. Atomic resolution (...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi049634z
更新日期:2004-07-27 00:00:00
abstract::FLI1 (Friend leukemia integration 1) is a metazoan transcription factor that is upregulated in a number of cancers. In addition, rearrangements of the fli1 gene cause sarcomas, leukemias, and lymphomas. These rearrangements encode oncogenic transcription factors, in which the DNA binding domain (DBD or ETS domain) of ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01121
更新日期:2015-12-22 00:00:00
abstract::The removal of cylclobutane pyrimidine dimers from cellular DNA occurs preferentially in actively transcribed genes of cells subjected to ultraviolet radiation. In contrast, reports concerning the transcription-dependent repair of N-methylpurines formed in cellular DNA following exposure to methylating agents are quit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00005a037
更新日期:1995-02-07 00:00:00
abstract::Here we explore the use of ethidium to determine relative affinities of different gene delivery vectors for DNA and describe an improved method for studying the interaction. Specifically, we investigate the binding of poly(amidoamine) dendrimers and show that the DNA-dendrimer-ethidium system is far from thermodynamic...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1015887
更新日期:2011-02-22 00:00:00
abstract::Fluorescence resonance energy transfer (FRET) has been used to investigate the conformation of the single stranded region for a series of fluorescent DNA template-primers bound to the Klenow fragment (KF) of Escherichia coli DNA polymerase I. Fluorescent derivatives of template-primer DNA, modified with tetramethylrho...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9719758
更新日期:1998-03-03 00:00:00
abstract::Enzyme IIA(Glc) (EIIA(Glc)) of the phosphoenolpyruvate phosphotransferase system for the uptake of glucose in Escherichia coli and Salmonella inhibits the maltose ATP-binding cassette transporter (MalE-FGK2) by interaction with the nucleotide-binding and -hydrolyzing subunit MalK, a process termed inducer exclusion. W...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.6b00721
更新日期:2016-09-27 00:00:00
abstract::Gluconacetobacter diazotrophicus stands out among the acetic acid bacteria as it fixes dinitrogen and is a true endophyte. It has a set of constitutive enzymes to oxidize ethanol and acetaldehyde which is upregulated during N(2)-dependent growth. The membrane-bound alcohol dehydrogenase (ADH) is a heterodimer (subunit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9015007
更新日期:2010-03-23 00:00:00
abstract::Ceruloplasmin is unique among the multicopper oxidases in that in addition to the usual copper stoichiometry of one Type 1 copper site and a Type 2/Type 3 trinuclear copper cluster, it contains two other Type 1 sites. This assignment of copper sites, based on copper quantitation, sequence alignment, and crystallograph...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi980434v
更新日期:1998-06-30 00:00:00
abstract::The synthesis of two potential arginine-directed purine-based analogues, 6-chloro-9-(3,4-dioxopentyl)purine (6) and 9-(3,4-dioxopentyl)hypoxanthine (7), is reported. Compound 7 was extensively tested as a potential affinity label of purine nucleoside phosphorylase (EC 2.4.2.1) from human erythrocytes. Evidence that 7 ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00268a010
更新日期:1982-12-07 00:00:00
abstract::Avian magnetoreception is assumed to occur in the retina. Although its molecular mechanism is unclear, magnetic field-dependent formation and the stability of radical-containing photointermediate(s) are suggested to play key roles in a hypothesis called the radical pair mechanism. Chicken cryptochrome4 (cCRY4) has bee...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00495
更新日期:2020-09-29 00:00:00
abstract::Weak or nonexistent smallpox immunity in today's human population raises concerns about the possibility of natural or provoked genetic modifications leading to re-emergence of variola virus and other poxviruses. Thus, the development of new antiviral strategies aimed at poxvirus infections in humans is a high priority...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700726a
更新日期:2007-10-23 00:00:00
abstract::We have previously shown that introduction of an engineered Met160 residue in ascorbate peroxidase (S160M variant) leads to the formation of a covalent link between Met160 and the heme vinyl group [Metcalfe, C. L., et al. (2004) J. Am. Chem. Soc. 126, 16242-16248]. In this work, we have used electronic spectroscopy, H...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7015316
更新日期:2007-11-20 00:00:00
abstract::The physiological effects of anesthetics have been ascribed to their interaction with hydrophobic sites within functionally relevant CNS proteins. Studies have shown that volatile anesthetics compete for luciferin binding to the hydrophobic substrate binding site within firefly luciferase and inhibit its activity (Fra...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi800544d
更新日期:2008-09-09 00:00:00
abstract::It is shown that the protochlorophyllide ester pool of etiolated higher plants is a faithful copy of the protochlorophyllide pool. It is made up of both monovinyl- and divinylprotochlorophyllide esters. Although the two tetrapyrroles exhibited similar emission maxima, they were distinguishable by their Soret excitatio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00562a027
更新日期:1980-10-14 00:00:00
abstract::Human genomic clones that span the entire protein S expressed gene (PS alpha) and the 3' two-thirds of the protein S pseudogene (PS beta) have been isolated and characterized. The PS alpha gene is greater than 80 kilobases in length and contains 14 introns and 15 exons, as well as 6 repetitive "Alu" sequences. Exons I...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00486a010
更新日期:1990-08-28 00:00:00
abstract::The importance of the fully conserved active site proline, Pro168, for the reaction mechanism of triosephosphate isomerase (TIM) has been investigated by studying the enzymatic and crystallographic properties of the P168A variant of trypanosomal TIM. In TIM, Pro168 follows the key catalytic residue Glu167, situated at...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi061683j
更新日期:2006-12-26 00:00:00
abstract::Nonribosomal peptide synthetases (NRPSs) are megasynthetases that require complex and specific interactions between multiple domains and proteins to functionally produce a metabolite. MbtH-like proteins (MLPs) are integral components of many NRPSs and interact directly with the adenylation domain of the megasynthetase...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00552
更新日期:2018-07-17 00:00:00
abstract::Protein S is an anticoagulant protein containing a Gla (enclosing gamma-carboxyglutamic acids) module, a TSR (thrombin sensitive region) module, four EGF (epidermal growth factor)-like modules, and a SHBG (sex hormone binding globulin)-like region. Protein S is a cofactor to activated protein C (APC) in the degradatio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0601151
更新日期:2006-09-05 00:00:00
abstract::Formiminotransferase-cyclodeaminase denatured in 6 M guanidine hydrochloride (Gdn.HCl) refolds and reassembles to the native octameric structure upon dilution into buffer. Both enzymic activities are recovered to greater than 90%, and the renatured enzyme "channels" the formiminotetrahydropteroylpentaglutamate interme...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00409a042
更新日期:1988-05-03 00:00:00
abstract::A fluorescent derivative of lysine-258 isolated from the active site of aspartate aminotransferase modified by treatment of the apoenzyme with pyridoxal 5'-sulfate has been characterized as a substituted 2H-pyrrolo[3,4-c]pyridine. Similar pyrrolopyridines are produced in up to 20% yield by reaction of pyridoxal sulfat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00264a016
更新日期:1982-10-12 00:00:00