Abstract:
:The recognition sequence of the Myb protein has been recently described to be pyAACKGHH (where py = T/C, K = G/T, and H = A/C/T), modifying the earlier identification as pyAACKG [Ording, E., et al. (1994) Eur. J. Biochem. 222, 113-120]. We had earlier determined the solution structure of the minimal cognate sequence TAACGG, choosing py = T and K = G, embeded in a 12-mer DNA duplex by NMR and related computational techniques [Radha, P. K., et al. (1995) Biochemistry 34, 5913-5912]. To understand the structural significance of the above modification and the role of the variability in the recognition sequence, we have investigated here the solution structure of a different DNA segment, d-ACAACTGCAGTTGT, which contains the extended Myb cognate site, CAACTGCA. The three-dimensional structure of the 14-mer duplex has been determined from NMR data by relaxation matrix and restrained molecular dynamics calculations. The structure of the above cognate sequence in the 14-mer duplex has been compared with that of the cognate sequence, TAACGG, in the 12-mer duplex and also with that in the NMR structure of the Myb DNA binding domain (R2R3)-DNA complex determined by Ogata et al. recently [Ogata, K., et al. (1994) Cell 79, 639-648]. The comparison highlighted differences in several structural parameters for the cognate sites in the DNA segments. Modeling studies by taking out the protein from the complex and presenting it with 12-mer and 14-mer DNA structures indicated that the protein induces structural alterations to drive the cognate site to a reasonably conserved structure. The extent of similarity of the derived structures was, however, dependent on the base sequences. Base changes in the minimal cognate sequence in the 12-mer-protein complex and in the 14-mer-protein complex so as to match the sequence of Ogata et al. produced a more conserved structure of the complex. A reverse exercise, in which the Ogata DNA in the complex was mutated to match the 12-mer and 14-mer minimal cognate sequences, complemented the above observations of the subtle sequence dependence of the structure in the complex. On the other hand, base changes in the extension did not influence the DNA-protein complex structure significantly. We also observed that the structural changes in the protein were very minor when different DNA sequences or different DNA structures were presented to it. These observations would be of interest from the point of view of DNA-Myb recognition.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Radha PK,Patel PK,Hosur RVdoi
10.1021/bi9806753subject
Has Abstractpub_date
1998-07-14 00:00:00pages
9952-63issue
28eissn
0006-2960issn
1520-4995pii
bi9806753journal_volume
37pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::STRA6 is a multitransmembrane domain protein not homologous to any other proteins with known function. It functions as the high-affinity receptor for plasma retinol binding protein (RBP) and mediates cellular uptake of vitamin A from the vitamin A-RBP complex. Consistent with the diverse roles of vitamin A and the wid...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8002082
更新日期:2008-05-13 00:00:00
abstract::Cibacron Blue F3GA dye has been used to probe subtle conformational changes in protein structure associated with the conversion of Escherichia coli glutamine synthetase (GS) between relaxed, taut, oxidized, and dissociated forms. Binding of the dye to each form of the enzyme elicits a different spectral perturbation o...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00324a017
更新日期:1985-01-29 00:00:00
abstract::Deuterium-labeled dihydroorotates bearing one, two, or three deuteriums at the pair of C4 and C5 positions have been synthesized in high isotopic and chiral purity and characterized by NMR and mass spectroscopy. These substrates have been used with the FMN-containing biosynthetic dihydroorotate oxidase from Crithidia ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00307a033
更新日期:1984-06-05 00:00:00
abstract::N-Linked sugar chains were liberated by hydrazinolysis from porcine zona pellucida glycoproteins obtained from ovarian follicular oocytes. Neutral sugar chains were separated from acidic ones by paper electrophoresis and fractionated with a serial lectin column chromatography and Bio-Gel P-4 column chromatography. The...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00222a012
更新日期:1991-02-26 00:00:00
abstract::A large fraction of a constitutively synthesized polypeptide, comprising 5% of the total Escherichia coli protein, is released when plasmolysed cells are subjected to osmotic shock into ice-cold water. Since the protein is not liberated by the conversion of cells to spheroplasts, it is not a typical periplasmic protei...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00656a008
更新日期:1976-06-01 00:00:00
abstract::The crystal structure of the particulate methane monooxygenase (pMMO) from Methylococcus capsulatus (Bath) has been reported recently [Lieberman, R. L., and Rosenzweig, A. C. (2005) Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane, Nature 434, 177-182]. Subsequent ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700883g
更新日期:2007-12-04 00:00:00
abstract::Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as determined by the high-resolution crystal structure of the D1.3-HEL comp...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi980148j
更新日期:1998-06-02 00:00:00
abstract::Modulation of endogenous gene function, through sequence-specific recognition of double helical DNA via oligonucleotide-directed triplex formation, is a promising approach. Compared to the formation of pyrimidine motif triplexes, which require relatively low pH, purine motif appears to be the most gifted for their sta...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1012589
更新日期:2011-05-17 00:00:00
abstract::Incorporation of nonproteinogenic amino acids in small polypeptides synthesized by nonribosomal peptide synthetases (NRPS) significantly contributes to their biological activity. In these peptides, conversion of L-amino acids to the corresponding D-isomer is catalyzed by specialized NRPS modules that utilize an epimer...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi011595t
更新日期:2001-12-25 00:00:00
abstract::Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyph...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi051779y
更新日期:2005-12-20 00:00:00
abstract::The goal of this study was to establish conditions for solubilization and characterization of CPTo, the malonyl-CoA sensitive form of mitochondrial carnitine palmitoyltransferase. CPTo of heart mitochondria is soluble in 1% octyl glucoside with retention of malonyl-CoA sensitivity. The degree of malonyl-CoA sensitivit...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00470a010
更新日期:1990-05-08 00:00:00
abstract::The contributions to thermostability of interactions within the beta-sheet region of rubredoxins (Rds) were investigated by examining proteins in which beta-strand sequences of Rds from the hyperthermophilic archaeon Pyrococcus furiosus (Pf) and the mesophilic bacterium Clostridium pasteurianum (Cp) were interchanged....
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970110r
更新日期:1997-08-26 00:00:00
abstract::Peptides prepared from the amino termini of pro alpha 1(I) and pro alpha 1(III) collagen chains inhibit the production of pro alpha 1(I) and pro alpha 2 by rat calvaria rna in a reticulocyte cell-free system. The synthesis of other proteins was not altered, suggesting a specific effect on collagen production. Various ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00589a034
更新日期:1979-10-30 00:00:00
abstract::The respiratory chain complexes can arrange into multienzyme assemblies, so-called supercomplexes. We present the first 3D map of a respiratory chain supercomplex. It was determined by random conical tilt electron microscopy analysis of a bovine supercomplex consisting of complex I, dimeric complex III, and complex IV...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700983h
更新日期:2007-11-06 00:00:00
abstract::A combined N- and C-terminal truncation variant of human apolipoprotein A-I (apoA-I) was designed, expressed in Escherichia coli, isolated, and characterized. Hydrodynamic experiments yielded a weight average molecular weight of 34000, indicating apoA-I-(44-186) exists in solution predominantly as a dimer. An axial ra...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0477135
更新日期:2005-03-22 00:00:00
abstract::Moesin binds to a large range of proteins through its N terminal FERM (band 4.1, ezrin, radixin, moesin) domain. In full-length moesin isolated from cells, this binding is masked by binding to the C-terminal domain of moesin (C-ERMAD). Activation takes place by phosphorylation of Thr 558 in the C-ERMAD, which releases...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi010419h
更新日期:2001-06-19 00:00:00
abstract::Adriamycin plays a prominent role in the treatment of leukemia and solid tumors in man. The mode of interaction of adriamycin with its nuclear target, responsible for its therapeutic effect, is known [Berman, H. M., & Young, P.R. (1981) Annu. Rev. Biophys. Bioeng. 10, 87-114]. The planar anthracycline moiety of adriam...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00380a043
更新日期:1987-03-24 00:00:00
abstract::31P nuclear magnetic resonance (NMR) saturation-transfer (ST) techniques have been used to measure steady-state flows through phosphate-adenosine 5'-triphosphate (ATP) exchange reactions in glucose-grown derepressed yeast. Our results have revealed that the reactions catalyzed by glyceraldehyde-3-phosphate dehydrogena...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00397a043
更新日期:1987-11-17 00:00:00
abstract::P16(INK4A) (also known as P16 and MTS1), a protein consisting exclusively of four ankyrin repeats, is recognized as a tumor suppressor mainly because of the prevalence of genetic inactivation of the p16(INK4A) (or CDKN2A) gene in virtually all types of human cancers. However, it has also been shown that an elevated le...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi200642e
更新日期:2011-06-28 00:00:00
abstract::Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5'-d-[(A)10TAATTTTAAATATTT]-3' (D1) and 5'-d[(T)10ATTAAAATTTATAAA]-3' (D2) in H2O and D2O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the de...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00226a012
更新日期:1991-03-26 00:00:00
abstract::The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate p...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00141a004
更新日期:1992-07-07 00:00:00
abstract::The effects of nonylphenol and 3,5-dibutyl-4-hydroxytoluene (BHT) on the activity of the (Ca2(+)-Mg2+)-ATPase of skeletal muscle sarcoplasmic reticulum have been studied. At high concentrations, both inhibit the ATPase activity of the ATPase either in native lipid or in bilayers of dioleoylphosphatidylcholine but, at ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00464a028
更新日期:1990-03-27 00:00:00
abstract::Kinetic study of a series of compounds containing the thrombin-directed peptide D-Phe-ProboroArg-OH had indicated that the structure of the N-terminal blocking group may be correlated with binding [Kettner, C., Mersinger, L., & Knabb, R. (1990) J. Biol. Chem. 265, 18289-18297]. In order to further study this phenomeno...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi952164b
更新日期:1996-07-30 00:00:00
abstract::Trifluoperazine (TFP) was shown to interact with the cyanogen bromide fragment 9 (CB9) (residues 84-135) of rabbit skeletal troponin C and with a synthetic peptide representing the N-terminal region of CB9. The phenothiazine did not affect the calcium binding property of CB9 as observed by proton magnetic resonance an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00276a010
更新日期:1983-03-29 00:00:00
abstract::Creatininase catalyzes the conversion of creatinine (a biosensor for kidney function) to creatine via a two-step mechanism: water addition followed by ring opening. Water addition is common to other known cyclic amidohydrolases, but the precise mechanism for ring opening is still under debate. The proton donor in this...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b01032
更新日期:2017-12-05 00:00:00
abstract::The amidotransferase family of enzymes utilizes the ammonia derived from the hydrolysis of glutamine for a subsequent chemical reaction catalyzed by the same enzyme. The ammonia intermediate does not dissociate into solution during the chemical transformations. A well-characterized example of the structure and mechani...
journal_title:Biochemistry
pub_type: 杂志文章,评审
doi:10.1021/bi990871p
更新日期:1999-06-22 00:00:00
abstract::In vivo bioluminescence imaging (BLI) has become a standard, non-invasive imaging modality for following gene expression or the fate of proteins and cells in living animals. Currently, bioluminescent reporters used in laboratories are mostly derivatives of two major luciferase families: ATP-dependent insect luciferase...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b01303
更新日期:2019-03-26 00:00:00
abstract::Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a monotopic membrane protein anchored to the membrane by an N-terminal in-plane amphipathic alpha-helix. This membrane anchor is essential for the assembly of a functional viral replication complex. Although amino acid sequences differ considerably, putative m...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0517685
更新日期:2006-02-21 00:00:00
abstract::We previously showed that a bulky ring-strained cycloalkyne possessing a rhodamine fluorophore directly reacts (via strain-promoted click chemistry) with the azido group incorporated (via ligand-directed tosyl chemistry) into Asp160 in the 49 kDa subunit of complex I in bovine heart submitochondrial particles [Masuya,...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.7b00612
更新日期:2017-08-15 00:00:00
abstract::The CCA-adding enzymes [ATP(CTP):tRNA nucleotidyl transferases] catalyze synthesis of the conserved and essential CCA sequence to the tRNA 3' end. These enzymes are divided into two classes of distinct structures that differ in the overall orientation of the head to tail domains. However, the catalytic core of the two...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0509402
更新日期:2005-09-27 00:00:00