Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Double Bind Interaction”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed2000

The cysteine- and glycine-rich LIM domain protein CRP2 specifically interacts with a novel human protein (CRP2BP).

We used the interaction trap to isolate a novel human protein that specifically interacts with the double LIM domain protein CRP2. This protein, designated CRP2BP (for CRP2 binding partner), was previously postulated by sequencing contigs of human chromosome 20. The observed interaction is mediated via the LIM1 domain of CRP2 and is of functional relevance in cellular environment. This novel single copy gene spans approximately 45-bp and is organized into at least ten exons. CRP2BP is expressed in all human tissues tested, with a major mRNA of 4-kb in size and an additional 3.2-kb transcript in placenta.

Adaptor Proteins, Signal Transducing↗
PubMed2003

RP4 repressor protein KorB binds to the major groove of the operator DNA: a Raman study.

KorB is a member of the ParB family of bacterial partitioning proteins. The protein encoded by the conjugative plasmid RP4 is part of the global control circuit and regulates the expression of plasmid genes, the products of which are involved in replication, transfer, and stable inheritance. KorB is a homodimeric protein which binds to palindromic 13 bp DNA sequences [5'-TTTAGC((G)/(C))GCTAAA-3'] present 12 times in the 60 kb plasmid. Each KorB subunit is composed of two domains; the C-domain is responsible for the dimerization of the protein, whereas the N-terminal domain recognizes and binds to the operator sequence (O(B)). Here we describe results of a Raman spectroscopic study of the interaction of the N-domain with a double-stranded model oligonucleotide composed of the palindromic binding sequence and terminal 5'-A(Br)U and AG-3' bases. Comparison of the Raman spectra of the free KorB N-domain and O(B) DNA with the spectrum of the complex reveals large differences. KorB-N binds in the major groove of the O(B) DNA, and the interactions induce changes in the DNA backbone and in the secondary structure of the protein.

DNA Primase↗
PubMed2004

Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains.

Colloidal probe microscopy has been used to study the interaction between model cellulose surfaces and the role of cellulose binding domain (CBD), peptides specifically binding to cellulose, in interfacial interaction of cellulose surfaces modified with CBDs. The interaction between pure cellulose surfaces in aqueous electrolyte solution is dominated by double layer repulsive forces with the range and magnitude of the net force dependent on electrolyte concentration. AFM imaging reveals agglomeration of CBD adsorbed on cellulose surface. Despite an increase in surface charge owing to CBD binding to cellulose surface, force profiles are less repulsive for interactions involving, at least, one modified surface. Such changes are attributed to irregularity of the topography of protein surface and non-uniform distribution of surface charges on the surface of modified cellulose. Binding double CBD hybrid protein to cellulose surfaces causes adhesive forces at retraction, whereas separation curves obtained with cellulose modified with single CBD show small adhesion only at high ionic strength. This is possibly caused by the formation of the cross-links between cellulose surfaces in the case of double CBD.

Cellulose↗
PubMed1994

Effect of pH on interactions between DNA and high-mobility group protein HMG1.

Fluorescence quenching was used to test the effect of pH changes on the binding of high-mobility group protein 1 (HMG1) to double-stranded and single-stranded DNA. At pH 7.5, the binding constant K for double-stranded DNA was 3 x 10(6) M-1, the binding site size n was 13, and the cooperativity factor q was 78, while at pH 6 the corresponding values were K = 12 x 10(6) M-1, n = 54, and q = 770. For the binding of HMG1 to single-stranded DNA at pH 7.5, the values were K = 2 x 10(6) M-1, n = 7, and q = 60, whereas at pH 6 they were K = 3 x 10(6) M-1, n = 14, and q = 440. Denaturation of HMG1 by oxidation of its sulfhydryl groups substantially affected the binding parameters. At pH 6, double-stranded DNA bound oxidized HMG1 with K = 6 x 10(6) M-1, n = 16, and q = 200, and single-stranded DNA bound with K = 3 x 10(6) M-1, n = 7, and q = 180. The sensitivity of the double-stranded DNA-HMG1 interaction to pH, along with an earlier report of a sharp optimum of binding at 140 mM NaCl, reveals a potential for in vivo regulation of the strength and mode of HMG1 binding by DNA through the action of analogous factors in the cellular milieu.

DNA↗
PubMed1997

Direct interaction of the KRAB/Cys2-His2 zinc finger protein ZNF74 with a hyperphosphorylated form of the RNA polymerase II largest subunit.

We previously identified ZNF74 as a developmentally expressed gene commonly deleted in DiGeorge syndrome. ZNF74 encodes an RNA-binding protein tightly associated with the nuclear matrix and belongs to a large subfamily of Cys2-His2 zinc finger proteins containing a KRAB (Kruppel-associated box) repressor motif. We now report on the multifunctionality of the zinc finger domain of ZNF74. This nucleic acid binding domain is shown here to function as a nuclear matrix targeting sequence and to be involved in protein-protein interaction. By far-Western analysis and coimmunoprecipitation studies, we demonstrate that ZNF74 interacts, via its zinc finger domain, with the hyperphosphorylated largest subunit of RNA polymerase II (pol IIo) but not with the hypophosphorylated form. The importance of the phosphorylation in this interaction is supported by the observation that phosphatase treatment inhibits ZNF74 binding. Double immunofluorescence experiments indicate that ZNF74 colocalizes with the pol IIo and the SC35 splicing factor in irregularly shaped subnuclear domains. Thus, ZNF74 sublocalization in nuclear domains enriched in pre-mRNA maturating factors, its RNA binding activity, and its direct phosphodependent interaction with the pol IIo, a form of the RNA polymerase functionally associated with pre- mRNA processing, suggest a role for this member of the KRAB multifinger protein family in RNA processing.

Animals↗
PubMed1998

Activities of adenovirus virus-associated RNAs: purification and characterization of RNA binding proteins.

Most human adenoviruses encode two virus-associated (VA) RNAs, VA RNAI and VA RNAII, that accumulate to high levels in the cytoplasm of infected cells. The function of VA RNAI in blocking the activation of the cellular kinase PKR is well known, but the role of VA RNAII is obscure. Herein we characterize and purify several human proteins that interact preferentially with VA RNAII in Northwestern blot assays. Two of these proteins were identified as RNA helicase A and NF90, a component of the heterodimeric nuclear factor of activated T cells (NFAT). They copurified with the smaller NFAT subunit, NF45, which did not bind VA RNAII, and with an unidentified protein, p97, which did bind VA RNAII. Both RNA helicase A and NF90 contain two copies of a double-stranded (ds) RNA binding motif and bind strongly to dsRNA. NF90 interacts with RNAs in the following order of affinity: dsRNA > VA RNAII > VA RNAI > single-stranded RNA. Furthermore, VA RNAII is more effective than VA RNAI as an inhibitor of RNA helicase activity. These data identify RNA helicase A and NF90 as cellular proteins with an affinity for dsRNA and other structured RNA molecules and suggest that their functions are subject to regulation by RNA ligands including VA RNAII.

Adenoviridae↗
PubMed1997

Preferred interaction of D-peptidyl-anthraquinones with double-stranded B-DNA.

The quest for more specific drugs in antitumor chemotherapy led us to the design of anthraquinone-peptide conjugates capable of selective recognition of the nucleic acid. We present here the DNA binding characteristics, sequence specificity and geometry of interaction of a pair of enantiomers containing the lysine-glycine dipeptide in the side chains. The D enantiomer binds right handed double stranded DNA more efficiently than the L form under all conditions tested. The source of higher binding affinity is not electrostatic in nature and rests in the more favorable hydrophobic contacts of the D-lysyl side chains in the drug-DNA complex. Both derivatives exhibit preference for alternating GC base sequences and intercalate into DNA in a threading mode as suggested by chiroptical and theoretical studies. The D enantiomer, being a peptidyl derivative that contains a non-natural amino acid, has the considerable advantage of being less susceptible to enzymatic hydrolysis and could therefore represent a lead compound for further development.

Anthraquinones↗
PubMed1992

DNA conformational change induced by the bacteriophage phi 29 connector.

Translocation of viral DNA inwards and outwards of the capsid of double-stranded DNA bacteriophages occurs through the connector, a key viral structure that is known to interact with DNA. It is shown here that phage phi 29 connector binds both linear and circular double-stranded DNA. However, DNA-mediated protection of phi 29 connectors against Staphylococcus aureus endoprotease V8 digestion suggests that binding to linear DNA is more stable than to circular DNA. Endoprotease V8-protection assays also suggest that the length of the linear DNA required to produce a stable phi 29 connector-DNA interaction is, at least, twice longer than the phi 29 connector channel. This result is confirmed by experiments of phi 29 connector-protection of DNA against DNase I digestion. Furthermore, DNA circularization assays indicate that phi 29 connectors restrain negative supercoiling when bound to linear DNA. This DNA conformational change is not observed upon binding to circular DNA and it could reflect the existence of some left-handed DNA coiling or DNA untwisting inside of the phi 29 connector channel.

Bacillus Phages↗
PubMed1997

The human ALL-1/MLL/HRX antigen is predominantly localized in the nucleus of resting and proliferating peripheral blood mononuclear cells.

The ALL-1 gene is an important regulator of embryonal and hematopoietic development, and structural variants of the human gene generated by chromosomal translocations and other genomic alterations presumably act as oncogenes in the pathogenesis of acute leukemias and other hematological malignancies. Antisera against two different epitopes of the human ALL-1 protein (anti-ALL1-N and anti-ALL1-C) were produced. Both sera revealed indistinguishable patterns of antigen localization in human peripheral blood mononuclear cells (PBMCs). In resting PBMCs, the antigen was distributed in a speckled pattern across the nuclei, with an increased density at the nuclear envelope and the nuclear indentation. In mitotically stimulated PBMCs, the antigen surrounded the condensing chromosomes but did not colocalize with chromatin or the nuclear scaffold. The antigen is considered a marker for a novel nuclear subcompartment, a perichromosomal area termed the "chromosomal envelope." In Western blot experiments, the anti-ALL1-N serum reacted with a polypeptide corresponding to the expected full-length 430-kDa ALL-1 protein. Recombinant proteins representing the AT-hook and zinc binding subdomains of the ALL-1 protein interacted in vitro with a degenerate mixture of double-stranded oligodeoxynucleotides. Thus, the ALL-1 protein probably is a DNA-binding protein with both a sequence-unspecific (AT-hook) and a sequence-specific (zinc binding subdomains) double-stranded DNA binding mode.

Animals↗
PubMed1985

Interconvertible molecular-weight forms of the bifunctional chorismate mutase-prephenate dehydratase from Acinetobacter calcoaceticus.

Acinetobacter calcoaceticus belongs to a large phylogenetic cluster of gram-negative procaryotes that all utilize a bifunctional P-protein (chorismate mutase-prephenate dehydratase) [EC 5.4.99.5-4.2.1.51] for phenylalanine biosynthesis. These two enzyme activities from Ac. calcoaceticus were inseparable by gel-filtration or DEAE-cellulose chromatography. The molecular weight of the P-protein in the absence of effectors was 65,000. In the presence of L-tyrosine (dehydratase activator) or L-phenylalanine (inhibitor of both P-protein activities), the molecular weight increased to 122,000. Maximal activation (23-fold) of prephenate dehydratase was achieved at 0.85 mM L-tyrosine. Under these conditions, dehydratase activity exhibited a hysteretic response to increasing protein concentration. Substrate saturation curves for prephenate dehydratase were hyperbolic at L-tyrosine concentrations sufficient to give maximal activation (yielding a Km,app of 0.52 mM for prephenate), whereas at lower L-tyrosine concentrations the curves were sigmoidal. Dehydratase activity was inhibited by L-phenylalanine, and exhibited cooperative interactions for inhibitor binding. A Hill plot yielded an n' value of 3.1. Double-reciprocal plots of substrate saturation data obtained in the presence of L-phenylalanine indicated cooperative interactions for prephenate in the presence of inhibitor. The n values obtained were 1.4 and 3.0 in the absence or presence of 0.3 mM L-phenylalanine, respectively. The hysteretic response of chorismate mutase activity to increasing enzyme concentration was less dramatic than that of prephenate dehydratase. A Km,app for chorismate of 0.63 mM was obtained. L-Tyrosine did not affect chorismate mutase activity, but mutase activity was inhibited both by L-phenylalanine and by prephenate. Interpretations are given about the physiological significance of the overall pattern of allosteric control of the P-protein, and the relationship between this control and the effector-induced molecular-weight transitions. The properties of the P-protein in Acinetobacter are considered within the context of the ubiquity of the P-protein within the phylogenetic cluster to which this genus belongs.

Acinetobacter↗
PubMed2003

DNA interactions of monofunctional organometallic ruthenium(II) antitumor complexes in cell-free media.

Modifications of natural DNA in a cell-free medium by antitumor monodentate Ru(II) arene compounds of the general formula [(eta(6)-arene)Ru(en)Cl](+) (arene = biphenyl, dihydroanthracene, tetrahydroanthracene, p-cymene, or benzene; en = ethylenediamine) were studied by atomic absorption, melting behavior, transcription mapping, circular and linear dichroism, plasmid unwinding, competitive ethidium displacement, and differential pulse polarography. The results indicate that these complexes bind preferentially to guanine residues in double-helical DNA. The data are consistent with DNA binding of the complexes containing biphenyl, dihydroanthracene, or tetrahydroanthracene ligands that involves combined coordination to G N7 and noncovalent, hydrophobic interactions between the arene ligand and DNA, which may include arene intercalation and minor groove binding. In contrast, the single hydrocarbon rings in the p-cymene and benzene ruthenium complexes cannot interact with double-helical DNA by intercalation. Interestingly, the adducts of the complex containing p-cymene ligand, which has methyl and isopropyl substituents, distort the conformation and thermally destabilize double-helical DNA distinctly more than the adducts of the three multiring ruthenium arene compounds. It has been suggested that the different character of conformational alterations induced in DNA, and the resulting thermal destabilization, may affect differently further "downstream" effects of damaged DNA and consequently may result in different biological effects of this new class of metal-based antitumor compounds. The results point to a unique profile of DNA binding for Ru(II) arene compounds, suggesting that a search for new anticancer compounds based on this class of complexes may also lead to an altered profile of biological activity in comparison with that of metal-based antitumor drugs already used in the clinic or currently on clinical trials.

Animals↗
PubMed2005

Positron binding energies for alkali hydrides.

Ab initio multireference single- and double-excitation configuration interaction (MRD-CI) calculations are carried out to study the interactions of positrons with the members of the alkali hydride class of molecules. A new computer program has been constructed for this purpose that makes use of the Table-Direct-CI method for construction of the required Hamiltonian matrixes and electronic/positronic wave functions. The calculations indicate that the binding energy (positron affinity PA) of a single positron to these systems increases by an increment of 0.2-0.3 eV as the atomic number of the alkali atom is increased. It is found that the positron prefers a location in the more electronegative regions of such molecules, similarly as has been found in earlier calculations for the urea and acetone molecules. The positron orbital itself possesses a diffuse charge distribution with relatively small expectation values of the kinetic energy in all four systems considered. Each of the four positronic molecules is stable with respect to formation of either positronium (Ps) or HPs according to the present calculations. Relatively large changes in the equilibrium bond distance of the hydrides occur as a result of the positron interaction. The importance of bond dipole moments in producing the binding of positrons to molecules is discussed, as well as the role that the electronegativity of the constituent atoms plays in determining the magnitude of the PA for a given system.

Journal Article↗
PubMed1989

Identification of two distinct functional domains on vinculin involved in its association with focal contacts.

We report here on the identification of two distinct functional domains on chicken vinculin molecule, which can, independently, mediate its interaction with focal contacts in living cells. These findings were obtained by immunofluorescent labeling of COS cells transfected with a series of chicken vinculin-specific cDNA constructs derived from clones cVin1 and cVin5 (Bendori, R., D. Salomon, and B. Geiger. 1987. EMBO [Eur. Mol. Biol. Organ.] J. 6:2897-2905). These included a chimeric construct consisting of 5' sequences of cVin1 attached to the complementary 3' region of cVin5, as well as several constructs of either cVin1 or cVin5 from which 3' or 5' sequences were deleted. We show here that the products of both cVin1 and cVin5, and of the cVin1/cVin5 chimera, readily associated with focal contacts in transfected COS cells. Furthermore, 78 and 45 kD NH2-terminal fragments encoded by a deleted cVin1 and the 78-kD COOH-terminal portion of vinculin encoded by cVin5 were capable of binding specifically to focal contact areas. In contrast 3'-deletion mutants prepared from clone cVin5 and a 5'-deletion mutant of cVin1, lacking both NH2- and COOH-terminal sequences, failed to associate with focal contacts in transfected cells. The loss of binding was accompanied by an overall disarray of the microfilament system. These results, together with previous in vitro binding studies, suggest that vinculin contains at least two independent sites for binding to focal contacts; the NH2-terminal domain may contain the talin binding site while the COOH-terminal domain may mediate vinculin-vinculin interaction. Moreover, the disruptive effect of the double-deleted molecule (lacking the two focal-contact binding sites) on the organization of actin suggests that a distinct region involved in the binding of vinculin to the microfilament system is present in the NH2-terminal 45-kD region of the molecule.

Animals↗
PubMed2002

DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability.

The mutagenic and cytotoxic effects of many endogenous and exogenous alkylating agents are mitigated by the actions of O(6)-alkylguanine-DNA alkyltransferase (AGT). In humans this protein protects the integrity of the genome, but it also contributes to the resistance of tumors to DNA-alkylating chemotherapeutic agents. Here we report properties of the interaction between AGT and short DNA oligonucleotides. We show that although AGT sediments as a monomer in the absence of DNA, it binds cooperatively to both single-stranded and double-stranded deoxyribonucleotides. This strong cooperative interaction is only slightly perturbed by active site mutation of AGT or by alkylation of either AGT or DNA. The stoichiometry of complex formation with 16-mer oligonucleotides, assessed by analytical ultracentrifugation and electrophoretic mobility shift assays, is 4:1 on single-stranded and duplex DNA and is unchanged by several active site mutations or by protein or DNA alkylation. These results have significant implications for the mechanisms by which AGT locates and interacts with repairable alkyl lesions to effect DNA repair.

Alkylation↗
PubMed1982

The interactions of androgen receptor with poly(A)-containing RNA and polyribonucleotides.

The androgen receptor from mouse kidney cytosol binds not only to DNA but also to RNA as assayed by competition with DNA-cellulose centrifugation or by direct binding with agarose-polynucleotides. The dihydrotestosterone-receptor complex interacts more strongly to poly(A)-containing mRNA than to native natural DNA; it binds much more tightly to synthetic poly(G) than to natural DNA and other homopolyribonucleotides such as poly(U), poly(A), or poly(C). Poly(U) is moderately effective in competing for the complex, whereas poly(A) and poly(C) re not effective. Competition studies with heteropolyribonucleotides show that polymers containing G are most effective on binding to the androgen receptor, whereas those containing U are moderately effective, and those containing only A and C are least effective. Several analogues of poly(G), such as poly(X), poly(I), and poly(m7G) interact very well with the dihydrotestosterone-receptor with some differences in the bindings. A double-stranded polymer, poly(I) . poly(C) competes poorly for the androgen receptor. The observations that the androgen receptor binds to RNA and interacts with polyribonucleotides selectively suggest that androgen receptor-RNA interaction could play important roles in gene regulation.

Animals↗
PubMed2003

Promyelocytic leukemia protein sensitizes tumor necrosis factor alpha-induced apoptosis by inhibiting the NF-kappaB survival pathway.

The promyelocytic leukemia protein (PML) is a growth/tumor suppressor essential for induction of apoptosis by diverse apoptotic stimuli. The mechanism by which PML regulates cell death remains unclear. In this study we found that ectopic expression of PML potentiates cell death by apoptosis in the tumor necrosis factor alpha (TNFalpha)-resistant cell line U2OS and other cell lines. Treatment with TNFalpha significantly sensitized these cells to apoptosis in a p53-independent manner. PML/TNFalpha-induced cell death is associated with DNA fragmentation, activation of caspase-3, -7, and -8, and degradation of DNA fragmentation factor/inhibitor of CAD. PML/TNFalpha-induced cell death could be blocked by the caspase-8 inhibitors CrmA and c-FLIP but not by Bcl-2. These findings indicate that this cell death event is initiated through the death receptor-dependent apoptosis pathway. PML is a transcriptional repressor of NF-kappaB by interacting with RelA/p65 and prevents its binding to the cognate enhancer through the C terminus. Coimmunoprecipitation and double-color immunofluorescence staining demonstrated that PML physically interacts with RelA/p65 in vivo and the two proteins colocalized at the endogenous levels. Overexpression of NF-kappaB rescued cell death induced by PML/TNFalpha. Furthermore, PML(-/-) mouse embryo fibroblasts are more resistant to TNFalpha-induced apoptosis. Together this study defines a novel mechanism by which PML induces apoptosis through repression of the NF-kappaB survival pathway.

Animals↗
PubMed1986

Identification of the 9-aminoacridine/DNA complex responsible for photodynamic inactivation of P22.

Acridine dyes bound to the condensed DNA within phage particles sensitize them to inactivation by visible light. The mechanism involves absorption of photons by an acridine/DNA complex, generating singlet oxygen, which covalently damages nearby proteins needed for DNA injection [Bryant, J., & King, J. (1985) J. Mol. Biol. 180, 837-863]. Acridines and related dyes interact with double-stranded DNA through a number of binding modes. To determine in condensed phage DNA the binding mode responsible for this inactivation, we have studied the formation of the DNA/acridine target complexes for photoinactivation. Analysis of the kinetics of 9-aminoacridine binding to Salmonella phage P22 particles revealed the formation of two binding species, one of which appeared more rapidly and was apparently an intermediate in the formation of the second. The rapidly forming species represented DNA sites with intercalated acridines, while the more slowly forming species represented the subsequent binding of additional acridine molecules to the DNA backbone of sites already containing intercalated dye. The rates of photoinactivation correlated with the rate of binding of 9-aminoacridine to the DNA backbone. This suggests that the most effective species for sensitizing phage to light-induced damage has acridine molecules stacked alongside the backbone of a region with intercalated molecules.

Aminacrine↗