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 505 records · Page 28Linked to original sources
PubMed1981

Equilibrium studies of ethidium--polynucleotide interactions.

We report equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.U (or T) and I.C base pairs. The results are interpreted in terms of the neighbor exclusion model of drug binding, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively. Both DNA and the alternating copolymers examined [poly[d(A-T)] and poly[d(I-C)]] showed high affinity (10(4)--10(5) M-1) in 1 M salt. Homopolynucleotides showed a more complicated pattern of affinities: poly(rA).poly(rU), poly(rA).poly(dT), and poly(dA).poly(rU) showed high affinity, whereas poly(dA).poly(dT), poly(rI).poly(rC), and poly(dI).poly(dC) showed low affinity (less than or equal to 10(3) M-1). The neighbor exclusion range was inferred to be two base pairs for DNA or B family helices and three for RNA or A family helices. Generally, polynucleotides showed some cooperativity in their ethidium binding. The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively.

Animals↗
PubMed1996

The central domain of colicin N possesses the receptor recognition site but not the binding affinity of the whole toxin.

Colicin N is a three-domain pore-forming colicin which kills enterobacterial cells following an initial binding to its receptor, the outer membrane porin OmpF. The receptor-binding domain of colicin N alone, and attached to the translocation domain, was overexpressed and purified using a hexahistidine tag. The receptor domain attached to the pore-forming domain was obtained by enzymatic digestion. Circular dichroism spectroscopy showed that the domains have structure in keeping with the known structure of colicin N. The receptor domain was stable, retaining both secondary and tertiary structure in 2 M guanidine hydrochloride and at low pH. It bound to both OmpF and PhoE porin-producing Escherichia coli with no toxicity and protected sensitive E. coli against intact colicin N toxicity at high domain/ colicin N ratios. Its in vitro affinity for OmpF, as determined by isothermal titration microcalorimetry, was found to be approximately 50-fold weaker than that of native colicin N. The receptor domain was readily out-competed by native colicin N in in vivo fluorescence assays which, coupled with its structural stability, suggests that its interaction with OmpF is one of weak, reversible binding. Since neither of the double domain constructs shows wild-type binding affinity either, it appears that the molecular recognition is a property of the receptor domain but that affinity is influenced by the entire molecule.

Bacterial Outer Membrane Proteins↗
PubMed1998

Rational design of a triple helix-specific intercalating ligand.

DNA triple helices offer new perspectives toward oligonucleotide-directed gene regulation. However, the poor stability of some of these structures might limit their use under physiological conditions. Specific ligands can intercalate into DNA triple helices and stabilize them. Molecular modeling and thermal denaturation experiments suggest that benzo[f]pyrido[3, 4-b]quinoxaline derivatives intercalate into triple helices by stacking preferentially with the Hoogsteen-paired bases. Based on this model, it was predicted that a benzo[f]quino[3,4-b]quinoxaline derivative, which possesses an additional aromatic ring, could engage additional stacking interactions with the pyrimidine strand of the Watson-Crick double helix upon binding of this pentacyclic ligand to a triplex structure. This compound was synthesized. Thermal denaturation experiments and inhibition of restriction enzyme cleavage show that this new compound can indeed stabilize triple helices with great efficiency and specificity and/or induce triple helix formation under physiological conditions.

Animals↗
PubMed2004

The brain-specific double-stranded RNA-binding protein Staufen2: nucleolar accumulation and isoform-specific exportin-5-dependent export.

The mammalian double-stranded RNA-binding proteins Staufen (Stau1 and Stau2) are involved in RNA localization in polarized neurons. In contrast to the more ubiquitously expressed Stau1, Stau2 is mainly expressed in the nervous system. In Drosophila, the third double-stranded RNA-binding domain (RBD3) of Staufen is essential for RNA interaction. When conserved amino acids within the RBD3 of Stau2 were mutated to render Stau2 defective for RNA binding, the mutant Stau2 proteins accumulate predominantly in the nucleolus. This is in contrast to wild type Stau2 that mostly localizes in the cytosol. The nuclear import is dependent on a nuclear localization signal in close proximity to the RBD3. The nuclear export of Stau2 is not dependent on CRM1 but rather on Exportin-5. We show that Exportin-5 interacts with the RBD3 of wild type Stau2 in an RNA-dependent manner in vitro but not with mutant Stau2. When Exportin-5 is down-regulated by RNA interference, only the largest isoform of Stau2 (Stau2(62)) preferentially accumulates in the nucleolus. It is tempting to speculate that Stau2(62) binds RNA in the nucleus and assembles into ribonucleoparticles, which are then exported via the Exportin-5 pathway to their final destination.

Animals↗
PubMed1983

Increased accessibility of bases in DNA upon binding of acridine orange.

Acridine orange (AO) forms 1:1 complexes with dsDNA which are insoluble in aqueous media, exhibit red luminescence, have minimal green luminescence and resemble complexes of AO with ss nucleic acids. During formation and/or dissociation of these complexes, accessibility of DNA bases to two conformational probes, formaldehyde and diethyl pyrocarbonate is increased, suggesting that the base pairing is destroyed and DNA at least partially denatured. Adriamycin and Ellipticine, but not Ethidium Bromide exert similar destabilizing effects. The results confirm our earlier predictions based on thermodynamic calculations that the double helix undergoes destabilization upon binding an intercalator characterized by high cooperativity in interaction with ss nucleic acids. Thus, the highly cooperative ligand binding to ss sections during the "breathing" of the polymer may progressively destabilize the adjacent ds structure.

Acridine Orange↗
PubMed2002

Complex formation by the human Rad51B and Rad51C DNA repair proteins and their activities in vitro.

The human Rad51 protein is essential for DNA repair by homologous recombination. In addition to Rad51 protein, five paralogs have been identified: Rad51B/Rad51L1, Rad51C/Rad51L2, Rad51D/Rad51L3, XRCC2, and XRCC3. To further characterize a subset of these proteins, recombinant Rad51, Rad51B-(His)(6), and Rad51C proteins were individually expressed employing the baculovirus system, and each was purified from Sf9 insect cells. Evidence from nickel-nitrilotriacetic acid pull-down experiments demonstrates a highly stable Rad51B.Rad51C heterodimer, which interacts weakly with Rad51. Rad51B and Rad51C proteins were found to bind single- and double-stranded DNA and to preferentially bind 3'-end-tailed double-stranded DNA. The ability to bind DNA was elevated with mixed Rad51 and Rad51C, as well as with mixed Rad51B and Rad51C, compared with that of the individual protein. In addition, both Rad51B and Rad51C exhibit DNA-stimulated ATPase activity. Rad51C displays an ATP-independent apparent DNA strand exchange activity, whereas Rad51B shows no such activity; this apparent strand exchange ability results actually from a duplex DNA destabilization capability of Rad51C. By analogy to the yeast Rad55 and Rad57, our results suggest that Rad51B and Rad51C function through interactions with the human Rad51 recombinase and play a crucial role in the homologous recombinational repair pathway.

Adenosine Triphosphate↗
PubMed2001

A short sequence within domain C of duck carboxypeptidase D is critical for duck hepatitis B virus binding and determines host specificity.

Virus-cell surface receptor interactions are of major interest. Hepadnaviruses are a family of partially double-stranded DNA viruses with liver tropism and a narrow host range of susceptibility to infection. At least in the case of duck hepatitis B virus (DHBV), host specificity seems controlled partly at the receptor level. The middle portion in the pre-S region of the viral large envelope protein binds specifically to duck carboxypeptidase D (DCPD) but not to its human or chicken homologue. Although domain C of DCPD is implicated in ligand binding, the exact pre-S contact site remains to be determined. We prepared and tested a panel of chimeric constructs consisting of DCPD and human carboxypeptidase D (HCPD). Our results indicate that a short region at the N terminus of domain C (residues 920 to 949) is critical to DHBV binding and is a major determinant for the host specificity of DHBV infection. Replacing this region of the DCPD molecule with its human homologue abolished the DHBV interaction, whereas introducing this DCPD sequence into HCPD conferred efficient DHBV binding. Extensive analysis of site-directed mutants revealed that both conserved and nonconserved residues were important for the pre-S interaction. There were primary sequence variations and secondary structural differences that contributed to the inability of HCPD to bind the DHBV pre-S domain.

Amino Acid Sequence↗
PubMed1994

Transcription of a human neurotropic virus promoter in glial cells: effect of YB-1 on expression of the JC virus late gene.

We have isolated a partial recombinant cDNA clone from a HeLa expression library which encodes a protein capable of binding to the central region of the human neurotropic JC virus (JCV) enhancer/promoter, termed the B region. Sequence analysis revealed a complete homology of the partial cDNA clone to the N-terminal region, of a previously described DNA-binding protein, termed YB-1. Band shift analyses have indicated that the bacterially produced YB-1 interacts specifically with the double-stranded B oligonucleotide as well as the corresponding single-stranded DNA fragment representing the early promoter sequence. Further analysis indicated that the YB-1 protein binds specifically to the C/T-rich sequence of the B domain, which is located in close proximity to the TATA box within the virus enhancer/promoter. Results from cotransfection experiments demonstrated that the full-length (YB-1) but not the partial cDNA enhances expression of the JCV late (JCVL) promoter in glial cells. Cointroduction into glial cells of a recombinant expressing the YB-1 and JCVL deletion mutants indicated that removal of the C/T-rich sequence of the B domain reduces the level of activation of the virus promoter by YB-1. Further cotransfection experiments revealed that the virus transactivating protein T antigen appears to diminish the ability of YB-1 to activate JCVL gene expression. RNA studies indicated that YB-1 is expressed in several cell types and tissues. Examination of YB-1 RNA from mouse brain at various stages of development revealed high levels of YB-1 RNA at early stages of development and lower levels at all subsequent developmental stages.

Antigens, Viral, Tumor↗
PubMed2004

Characterization of serotonin in protein and membrane mimetic environments: a spectroscopic study.

As a first step toward using the photophysical properties of serotonin to probe its interactions with biological target sites, we have examined its interactions with human serum albumin (HSA), chosen as a surrogate for the actual receptor proteins in physiological systems, and with sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/heptane/water reverse micelles, chosen as a biomembrane mimetic environment for the transmembrane portion of the receptor protein. Although the emission maximum of serotonin is relatively insensitive to the polarity of the local environment, which is attributed to lack of solvent dipolar reorientation of the 5-hydroxyindole chromophore, the fluorescence anisotropy (r) served as a useful and sensitive parameter from which the binding constants (K) and Gibbs energy changes (deltaG) were estimated for serotonin-HSA and serotonin-AOT reverse micellar interactions. Fluorescence-decay studies of serotonin show double-exponential kinetics in homogeneous aqueous solvent due to the structural heterogeneity arising from different rotamers of serotonin. In contrast, upon binding to HSA, a single-exponential fluorescence-decay profile was observed indicating the occurrence of a single structural species of serotonin in the protein environment. Furthermore, far-UV-circular-dichroism (CD) spectroscopic data indicate that the secondary structural features of HSA remain essentially intact after binding to serotonin. This preliminary research can be expected to open the door to extensive future studies on interactions of serotonin with relevant target proteins and associated cell membranes involved in its diverse physiological functions.

Biomimetic Materials↗
PubMed1998

Triple helices containing arabinonucleotides in the third (Hoogsteen) strand: effects of inverted stereochemistry at the 2'-position of the sugar moiety.

Arabinonucleic acid, the 2'-stereoisomer of RNA, was tested for its ability to recognize double-helical DNA, double-helical RNA and RNA-DNA hybrids. A pyrimidine oligoarabinonucleotide (ANA) was shown to form triple-helical complexes only with duplex DNA and hybrid DNA (Pu):RNA (Py) with an affinity that was slightly lower relative to the corresponding pyrimidine oligodeoxynucleotide (DNA) third strand. Neither the ANA nor DNA third strands were able to bind to duplex RNA or hybrid RNA (Pu):DNA (Py). In contrast, an RNA third strand recognized all four possible duplexes (DD, DR, RD and RR), as previously demonstrated. Such an understanding can be applied to the design of sequence-selective oligonucleotides which interact with double-stranded nucleic acids and emphasizes the role of the 2'-OH group as a general recognition and binding determinant of RNA.

Arabinonucleotides↗
PubMed2002

Mechanism of calcium-independent synaptotagmin binding to target SNAREs.

Synaptic vesicle exocytosis requires three SNARE (soluble N-ethylmaleimide-sensitive-factor attachment protein receptor) proteins: syntaxin and SNAP-25 on the plasma membrane (t-SNAREs) and synaptobrevin/VAMP on the synaptic vesicles (v-SNARE). Vesicular synaptotagmin 1 is essential for fast synchronous SNARE-mediated exocytosis and interacts with the SNAREs in brain material. To uncover the step at which synaptotagmin becomes linked to the three SNAREs, we purified all four proteins from brain membranes and analyzed their interactions. Our study reveals that, in the absence of calcium, native synaptotagmin 1 binds the t-SNARE heterodimer, formed from syntaxin and SNAP-25. This interaction is both stoichiometric and of high affinity. Synaptotagmin contains two divergent but conserved C2 domains that can act independently in calcium-triggered phospholipid binding. We now show that both C2 domains are strictly required for the calcium-independent interaction with the t-SNARE heterodimer, indicating that the double C2 domain structure of synaptotagmin may have evolved to acquire a function beyond calcium/phospholipid binding.

Animals↗
PubMed1999

DNA-surfactant interactions: coupled cooperativity in ligand binding leads to duplex stabilization.

The cooperative nature of interaction of cationic surfactants with short oligonucleotides leading to eventual stabilization of DNA duplexes is demonstrated. At submicellar concentrations and DNA:surfactant charge ratios of 0.2 to 0.8, the association of single chain (CTAB) and double chain (DOTAP) surfactants to oligonucleotides is initiated by electrostatic interaction of cationic ligands with polyanionic DNA that aligns the surfactant molecules on the DNA template. This is followed by binding of new surfactant ligands to the initial complex, driven cooperatively by the hydrophobic forces, leading to in situ formation of surfactant-bound and bare duplexes as separate species. These exhibit independent melting behaviour characterised by double transition in thermal UV profiles, with a higher T(m) for surfactant-DNA complexes. Understanding the cooperative binding of the cationic surfactants to the DNA described here may have implications for rational design of DNA binding drugs and DNA delivery systems.

Base Sequence↗
PubMed2006

Cooperative hydrogen bond interactions in the streptavidin-biotin system.

The thermodynamic and structural cooperativity between the Ser45- and D128-biotin hydrogen bonds was measured by calorimetric and X-ray crystallographic studies of the S45A/D128A double mutant of streptavidin. The double mutant exhibits a binding affinity approximately 2x10(7) times lower than that of wild-type streptavidin at 25 degrees C. The corresponding reduction in binding free energy (DeltaDeltaG) of 10.1 kcal/mol was nearly completely due to binding enthalpy losses at this temperature. The loss of binding affinity is 11-fold greater than that predicted by a linear combination of the single-mutant energetic perturbations (8.7 kcal/mol), indicating that these two mutations interact cooperatively. Crystallographic characterization of the double mutant and comparison with the two single mutant structures suggest that structural rearrangements at the S45 position, when the D128 carboxylate is removed, mask the true energetic contribution of the D128-biotin interaction. Taken together, the thermodynamic and structural analyses support the conclusion that the wild-type hydrogen bond between D128-OD and biotin-N2 is thermodynamically stronger than that between S45-OG and biotin-N1.

Biotin↗
PubMed1996

Preferential binding of Escherichia coli RecF protein to gapped DNA in the presence of adenosine (gamma-thio) triphosphate.

Escherichia coli RecF protein binds, but does not hydrolyze, ATP. To determine the role that ATP binding to RecF plays in RecF protein-mediated DNA binding, we have determined the interaction between RecF protein and single-stranded (ss)DNA, double-stranded (ds)DNA, and dsDNA containing ssDNA regions (gapped [g]DNA) either alone or in various combinations both in the presence and in the absence of adenosine (gamma-thio) triphosphate, gamma-S-ATP, a nonhydrolyzable ATP analog. Protein-DNA complexes were analyzed by electrophoresis on agarose gels and visualized by autoradiography. The type of protein-DNA complexes formed in the presence of gamma-S-ATP was different with each of the DNA substrates and from those formed in the absence of gamma-S-ATP. Competition experiments with various combinations of DNA substrates indicated that RecF protein preferentially bound gDNA in the presence of gamma-S-ATP, and the order of preference of binding was gDNA > dsDNA > ssDNA. Since gDNA has both ds- and ssDNA components, we suggest that the role for ATP in RecF protein-DNA interactions in vivo is to confer specificity of binding to dsDNA-ssDNA junctions, which is necessary for catalyzing DNA repair and recombination.

Adenosine Triphosphate↗
PubMed1996

Mutations of non-canonical base-pairs in the 3' major domain of Escherichia coli 16 S ribosomal RNA affect the initiation and elongation of protein synthesis.

Three single-point mutations and two multibase substitutions were introduced into the lower half of the 3' major domain of Escherichia coli 16 S ribosomal RNA. The three single mutations were located in helix 29 (U1341C) or in helix 43 (U1351C or A1357C) and replaced highly conserved non-canonical base-pairs with Watson-Crick base-pairs. The two multibase substitutions were located at the base of helix 42, where they transformed an irregular portion into a Watson-Crick [correction of Waston-Crick] segment. Each of the single mutations could be expressed in vivo from the rrnB operon of a multicopy plasmid under control of constitutive promoters, and none of them affected growth-rate. However, mutation A1357C, but not U1341C or U1351C, severely retarded cell growth, when expressed together with another mutation in the upper half of the 3' major domain, C1192U. The latter mutation is located in helix 34 and abolishes the binding of spectinomycin, a protein synthesis inhibitor. The proportion of mutated ribosomes was high in polysomes, suggesting that the A1357C and C1192U double mutation did not affect the initiation but rather the elongation of protein synthesis. The effect of the double mutation reveals a functional interplay between helices 34 and 43. Furthermore, an interaction between helices 34 and 43 was also suggested by studies of protection by spectinomycin against chemical attack, that showed that the binding site of spectinomycin was restored with ribosomes bearing another double mutation, U1351C and C1192U. In contrast to the single mutations, the multiple mutations in helix 42 could not be expressed in vivo under control of the strong constitutive promoters, but could be expressed under control of the weaker, thermoinducible lambda PL promoter. They did not affect cell growth, whether expressed in the absence or the presence of the C1192U mutation. However, under conditions where protein synthesis depended exclusively on ribosomes with plasmid-encoded rRNA, cells transformed with plasmids altered in helix 42 could not grow. Analysis of the plasmid-borne 16 S rRNA distribution in bacteria transformed with these mutant plasmids showed that mutant 16 S rRNA was present in a high proportion in the free 30 S subunits but was underrepresented in 70 S ribosomes and polysomes. Extension inhibition assays (toeprinting) demonstrated that this altered distribution resulted from an impaired capacity of the mutant 30 S subunits to form translation initiation complexes.

Bacterial Proteins↗
PubMed1978

[Ribosome binding to the membranes of Candida albicans].

The in vitro binding of free ribosomes to the membranes of polyenoic antibiotics-sensitive and resistant strains of Candida albicans, considerably differing in the composition of their sterol components, was studied. It was shown that the extent and type of membrane-ribosome interaction is similar in both cases. The dependence of binding on ribosome concentration in the incubation mixture is double-phase, as was shown for different membrane fractions of both sensitive and resistant strains. The role of lipid membrane components, particularly that of sterols in the membrane-ribosome interactions is discussed.

Candida albicans↗
PubMed2006

Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces.

We have studied the stability and the yield of the folded WW domains in a spherical nanopore to provide insights into the changes in the folding characteristics due to interactions of the polypeptide (SP) with the walls of the pore. Using different models for the interactions between the nanopore and the polypeptide chain we have obtained results that are relevant to a broad range of experiments. (a) In the temperature and the strength of the SP-pore interaction plane (lambda), there are four "phases," namely, the unfolded state, the native state, the molten globule phase (MG), and the surface interaction-stabilized (SIS) state. The MG and SIS states are populated at moderate and large values of lambda, respectively. For a fixed pore size, the folding rates vary non-monotonically as lambda is varied with a maximum at lambda approximately 1 at which the SP-nanopore interaction is comparable to the stability of the native state. At large lambda values, the WW domain is kinetically trapped in the SIS states. Using multiple sequence alignment, we conclude that similar folding mechanism should be observed in other WW domains as well. (b) To mimic the changes in the nature of the allosterically driven SP-GroEL interactions we consider two models for the dynamic Anfinsen cage (DAC). In DAC1, the SP-cavity interaction cycles between hydrophobic (lambda>0) and hydrophilic (lambda=0) with a period tau. The yield of the native state is a maximum for an optimum value of tau=tau(OPT). At tau=tau(OPT), the largest yield of the native state is obtained when tau(H) approximately tau(P) where tau(H)(tau(P)) is the duration for which the cavity is hydrophobic (hydrophilic). Thus, in order to enhance the native state yield, the cycling rate, for a given loading rate of the GroEL nanomachine, should be maximized. In DAC2, the volume of the cavity is doubled (as happens when ATP and GroES bind to GroEL) and the SP-pore interaction simultaneously changes from hydrophobic to hydrophilic. In this case, we find greater increase in yield of the native state compared to DAC1 at all values of tau.

Mathematics↗