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Results for “Double Bind Interaction”

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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↗

PubMed1998

Ferrous sulphate interacts with captopril.

AIMS: To determine if iron binds strongly to captopril and reduces captopril absorption. METHODS: A variety of in vitro experiments was conducted to examine iron binding to captopril and a randomized, double-blind, placebo controlled, cross-over study design was used to assess the in vivo interaction. Captopril (25 mg) was coingested with either ferrous sulphate (300 mg) or placebo by seven healthy adult volunteers. Subjects were phlebotomized and had blood pressure measured at 0, 0.25, 0.5, 1, 2, 4, 6, 8, and 12 h post ingestion. A 1 week washout period was used. RESULTS: The coingestion of ferrous sulphate and captopril was associated with a 37% (134 ng ml(-1) h, 95% CI 41-228 ng ml(-1) h, P = 0.03) decrease in area under the curve (AUC) for unconjugated plasma captopril. There were no substantial changes in Cmax (mean difference; -32; 95% CI -124-62 ng ml(-1) (P = 0.57)) or in tmax (mean difference; 0; 95% CI -18-18 min (P = 0.65)) for unconjugated captopril when captopril was ingested with iron. There was a statistically insignificant increase in AUC for total plasma captopril of 43% (1312 ng ml(-1) h, 95% CI -827-3451 ng ml(-1) h P = 0.27) when captopril was ingested with iron. The addition of ferric chloride to captopril resulted in the initial rapid formation of a soluble blue complex which rapidly disappeared to be replaced by a white precipitant. The white precipitate was identified as captopril disulphide dimer. There were no significant differences in systolic and diastolic blood pressures between the treatment and placebo groups. CONCLUSIONS: Co-administration of ferrous sulphate and iron results in decreased unconjugated captopril levels likely due to a chemical interaction between ferric ion and captopril in the gastrointestinal tract. Care is required when coprescribing captopril and iron salts.

Adult↗

PubMed1991

Gene product dsbA of bacteriophage T4 binds to late promoters and enhances late transcription.

Gene product 33 of phage T4 is known to be essential in late transcription. Upstream from gene 33 and overlapping its 5' terminal sequence by 20 bp, we identified an open reading frame coding for a binding protein for double-stranded DNA (DsbA). Gene product DsbA is composed of 89 amino acid residues with a Mr of 10376 kDa. We purified this protein to homogeneity from over-expressing cells. Gel retardation assays reveal that it binds to DNA and footprint analyses disclose that it interacts preferentially with T4 late promoter regions. At the sites of binding the protein introduces nicks in double-stranded DNA. In vitro transcription assays performed with T4 late modified RNA polymerase on restriction fragments harbouring a T4 late promoter region prove that gene product DsbA enhances transcription from these promoter regions in the presence of gene product 33. Gene dsbA is distinct from gene das which maps close to this genomic region.

Base Sequence↗

PubMed2006

Visual arrestin binding to microtubules involves a distinct conformational change.

Recently we found that visual arrestin binds microtubules and that this interaction plays an important role in arrestin localization in photoreceptor cells. Here we use site-directed mutagenesis and spin labeling to explore the molecular mechanism of this novel regulatory interaction. The microtubule binding site maps to the concave sides of the two arrestin domains, overlapping with the rhodopsin binding site, which makes arrestin interactions with rhodopsin and microtubules mutually exclusive. Arrestin interaction with microtubules is enhanced by several "activating mutations" and involves multiple positive charges and hydrophobic elements. The comparable affinity of visual arrestin for microtubules and unpolymerized tubulin (K(D) > 40 mum and >65 mum, respectively) suggests that the arrestin binding site is largely localized on the individual alphabeta-dimer. The changes in the spin-spin interaction of a double-labeled arrestin indicate that the conformation of microtubule-bound arrestin differs from that of free arrestin in solution. In sharp contrast to rhodopsin, where tight binding requires an extended interdomain hinge, arrestin binding to microtubules is enhanced by deletions in this region, suggesting that in the process of microtubule binding the domains may move in the opposite direction. Thus, microtubule and rhodopsin binding induce different conformational changes in arrestin, suggesting that arrestin assumes three distinct conformations in the cell, likely with different functional properties.

Arrestin↗

PubMed2005

Subcellular localization of the dopamine D2 receptor and coexistence with the calcium-binding protein neuronal calcium sensor-1 in the primate prefrontal cortex.

Structures of the cerebral cortex expressing the D2 dopamine receptor subtype (D2) are important sites of action of antipsychotic drugs. It has also been repeatedly suggested that the prefrontal cortex plays a significant role in neuropsychiatric disorders, including schizophrenia. Here, by using single and double immunohistochemical techniques with electron microscopy, we investigated in the primate prefrontal cortex the ultrastructural localization of D2 and we compared it with that of the neuronal calcium sensor-1 (NCS-1), a neuron-specific calcium-binding and D2-interacting protein. D2 immunoreactivity, revealed with preembedding immunoperoxidase in single labeling and with preembedding immunogold for double labeling, was localized in cell bodies with ultrastructural characteristics of both neurons and astroglia. D2 was localized in pre- and postsynaptic structures, including spines and dendrites, and in both excitatory- and inhibitory-like axon terminals. Immunogold labeling revealed peri- and extrasynaptic localization of D2 in postsynaptic structures, whereas extrasynaptic labeling was typically found in boutons. NSC-1 immunoreactivity was abundant in pre- and postsynaptic structures, in which it was also colocalized with D2. With the present strategy (that has high resolution but relatively limited sensitivity), NSC-1 was observed in about 10% of the D2-immunopositive spines and in a lower proportion of D2-immunopositive dendrites and boutons. The data demonstrate the localization of D2 in pre- and postsynaptic as well as extra- and perisynaptic structures of the primate prefrontal cortex. The data also show the coexistence of NCS-1 and D2 at the ultrastructural level. The latter finding suggests a role for NCS-1 in desensitization of D2 in the prefrontal cortex.

Animals↗

PubMed2003

Binding studies on aluminum(III)-albumin interaction.

The present paper reports a quantitative investigation on the binding of aluminum to human serum albumin. Equilibrium dialysis and a general thermodynamic approach have been used to determine the binding parameters. Two aluminum binding sites have been identified on the albumin molecule, involving sites with single and double occupancy modes. The binding properties of these two distinct sites appear to undergo reciprocal influences, suggesting a possible interaction between the corresponding protein moieties. Both coordination modes proceed from weak interactions, as shown by the binding energies calculated.

Aluminum↗

PubMed2004

Interaction between dissimilar double layers with like signs under charge regulation on the basis of the Gouy-Chapman-Stern-Grahame model.

The force of interaction between two flat double layers with dissimilar surface potentials but of the same signs, in contact with 1-1 electrolyte solutions (0.001, 0.01, and 0.1 M), was calculated as a function of the surface separation. The calculation was carried out on the basis of the Gouy-Chapman-Stern-Grahame double-layer model, incorporating the site-dissociation and site-binding model used previously for many oxide studies. The results demonstrated that the interaction force under surface charge regulation was always repulsive, increasing progressively with decreasing surface separation. This result is in contrast to the predictions of previous theories that are based on the Gouy-Chapman (GC) double-layer model. Dependence of surface potentials and surface charge densities on the surface separation is also presented.

Journal Article↗

PubMed2005

Functional analysis of the GAF domain of NifA in Azospirillum brasilense: effects of Tyr-->Phe mutations on NifA and its interaction with GlnB.

Regulation of NifA activity in Azospirillum brasilense depends on GlnB (a PII protein), and it was previously reported that the target of GlnB activity is the N-terminal domain of NifA. Furthermore, mutation of the Tyr residue at position 18 in the N-terminal domain resulted in a NifA protein that did not require GlnB for activity under nitrogen fixation conditions. We report here that a NifA double mutant in which the Tyr residues at positions 18 and 53 of NifA N-were simultaneously replaced by Phe (NifA-Y1853F) displays high nitrogenase activity, which is still regulatable by ammonia, but not by GlnB. The yeast two-hybrid technique was used to investigate whether GlnB can physically interact with wild-type and mutant NifA proteins. GlnB was found to interact directly with the N-terminal GAF domain of wild-type NifA, but not with its central or C-terminal domain. GlnB could still bind to the single NifA mutants Y18F and Y53F. In contrast, no interaction was detected between GlnB and the double mutant NifA-Y18/53F or between GlnB and NifA-Y43.

Azospirillum↗

PubMed1997

Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP.

Serum amyloid P component (SAP) is a glycoprotein that binds in a calcium-dependent fashion to a variety of ligands including other proteins, glycosaminoglycans and DNA. SAP is universally associated with the amyloid deposits in all forms of amyloidoses including Alzheimer's disease. Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. We have carried out a screen for novel SAP ligands and have identified 2'-deoxyadenosine-5'-monophosphate (dAMP) as a ligand. The crystal structure of the SAP-dAMP complex determined at 2.8 A resolution (R = 0.232, R(free) = 0.252) reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The stability of the decamer in solution has been demonstrated by gel filtration chromatography. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. This mode of dAMP binding is not compatible with the nucleotide being part of double-helical DNA. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups; decamerization buries 1000 A2 (2.6%) of the pentamer solvent-accessible surface. Ligand-induced decamerization of SAP, which utilizes the high cooperativity of a multiple-site interaction, may be a strategy to overcome the problems for drug design associated with the rather modest affinities of SAP for small-molecule ligands.

Computer Graphics↗

PubMed2001

Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p.

Box H/ACA small nucleolar ribonucleoprotein particles (H/ACA snoRNPs) play key roles in the synthesis of eukaryotic ribosomes. How box H/ACA snoRNPs are assembled remains unknown. Here we show that yeast Nhp2p, a core component of these particles, directly binds RNA. In vitro, Nhp2p interacts with high affinity with RNAs containing irregular stem-loop structures but shows weak affinity for poly(A), poly(C) or for double-stranded RNAs. The central region of Nhp2p is believed to function as an RNA-binding domain, since it is related to motifs found in various RNA-binding proteins. Removal of two amino acids that shortens a putative beta-strand element within Nhp2p central domain impairs the ability of the protein to interact with H/ACA snoRNAs in cell extracts. In vivo, this deletion prevents cell viability and leads to a strong defect in the accumulation of H/ACA snoRNAs and Gar1p. These data suggest that proper direct binding of Nhp2p to H/ACA snoRNAs is required for the assembly of H/ACA snoRNPs and hence for the stability of some of their components. In addition, we show that converting a highly conserved glycine residue (G(59)) within Nhp2p central domain to glutamate significantly reduces cell growth at 30 and 37 degrees C. Remarkably, this modification affects the steady-state levels of H/ACA snoRNAs and the strength of Nhp2p association with these RNAs to varying degrees, depending on the nature of the H/ACA snoRNA. Finally, we show that the modified Nhp2p protein whose interaction with H/ACA snoRNAs is impaired cannot accumulate in the nucleolus, suggesting that only the assembled H/ACA snoRNP particles can be efficiently retained in the nucleolus.

Amino Acid Substitution↗

PubMed1998

Identification of pairwise interactions in the alpha-neurotoxin-nicotinic acetylcholine receptor complex through double mutant cycles.

alpha-Neurotoxins are potent inhibitors of the nicotinic acetylcholine receptor (nAChR), binding with high affinity to the two agonist sites located on the extracellular domain. Previous site-directed mutagenesis had identified three residues on the alpha-neurotoxin from Naja mossambica mossambica (Lys27, Arg33, and Lys47) and four residues on the mouse muscle nAChR alpha-subunit (Val188, Tyr190, Pro197, and Asp200) as contributing to binding. In this study, thermodynamic mutant cycle analysis was applied to these sets of residues to identify specific pairwise interactions. Amino acid variants of alpha-neurotoxin from N. mossambica mossambica at position 33 and of the nAChR at position 188 showed strong energetic couplings of 2-3 kcal/mol at both binding sites. Consistently smaller yet significant linkages of 1.6-2.1 kcal/mol were also observed between variants at position 27 on the toxin and position 188 on the receptor. Additionally, toxin residue 27 coupled to the receptor residues 190, 197, and 200 at the alphadelta binding site with observed coupling energies of 1.5-1.9 kcal/mol. No linkages were found between toxin residue Lys47 and the receptor residues studied here. These results provide direct evidence that the two conserved cationic residues Arg33 and Lys27, located on loop II of the toxin structure, are binding in close proximity to the alpha-subunit region between residues 188-200. The toxin residue Arg33 is closer to Val188, where it is likely stabilized by adjacent negative or aromatic residues on the receptor structure. Lys27 is positioned closer to Tyr190, Pro197, and Asp200, where it is likely stabilized through electrostatic interaction with Asp200 and/or cation/pi interactions with Tyr190.

Amino Acid Sequence↗

PubMed2006

Ligand-independent orphan receptor TR2 activation by phosphorylation at the DNA-binding domain.

In a previous report we demonstrated protein kinase C (PKC)-mediated phosphorylation of the ligand-binding domain (LBD) of orphan nuclear receptor TR2. In this report, we provide the evidence of PKC-mediated phosphorylation of the DNA-binding domain (DBD) of TR2. Two PKC target sites were predicted within the DBD, at Ser-170 and Ser-185, but only Ser-185 was confirmed by MS. Phosphorylation of DBD facilitated DNA binding of the TR2 receptor and its recruiting of coactivator p300/CBP-associated factor (P/CAF). Ser-185 was required for DNA binding, whereas both Ser-170 and Ser-185 were necessary for receptor interaction with P/CAF. The P/CAF-interacting domain of TR2 was located in its DBD. A double mutant (Ser-170 and Ser-185) of TR2 significantly lowered the activation of its target gene RARbeta2. This study provides the first evidence for ligand-independent activation of TR2 orphan receptor through PTM at the DBD, which enhanced its DNA-binding ability and interaction with coactivator P/CAF.

Base Sequence↗

PubMed2005

The interaction of LEDGF/p75 with integrase is lentivirus-specific and promotes DNA binding.

We have previously shown that the p75 isoform of the transcriptional co-activator lens epithelium-derived growth factor (LEDGF) interacts tightly with human immunodeficiency virus (HIV)-1 integrase (IN) and is essential for nuclear targeting of this protein in human cells (Cherepanov, P., Maertens, G., Proost, P., Devreese, B., Van Beeumen, J., Engelborghs, Y., De Clercq, E., and Debyser, Z. (2003) J. Biol. Chem. 278, 372-381; Maertens, G., Cherepanov, P., Pluymers, W., Busschots, K., De Clercq, E., Debyser, Z., and Engelborghs, Y. (2003) J. Biol. Chem. 278, 33528-33539). Here the interaction between recombinant LEDGF/p75 and HIV-1 IN was examined in a pull-down binding test. LEDGF/p75 was shown to increase the solubility of HIV-1 IN. Next, fluorescent correlation spectroscopy was used to measure the interaction of LEDGF/p75 or the complex of HIV-1 IN and LEDGF/p75 with a specific double-stranded DNA oligonucleotide. Whereas LEDGF/p75 displayed only a moderate affinity for DNA, it strongly promoted the binding of HIV-1 IN to DNA. This effect was specific for the p75 isoform of LEDGF and was not seen with p52. In the pull-down assay LEDGF/p75 interacted with HIV-1, HIV-2, and feline immunodeficiency virus IN, but not with the IN of human T-cell lymphotropic virus type 2, Moloney murine leukemia virus, or Rous sarcoma virus. These results strongly suggest that the interaction of LEDGF/p75 with IN is specific to lentiviridae. LEDGF/p75 stimulated the binding of HIV-1 and HIV-2 IN, but not Moloney murine leukemia virus or Rous sarcoma virus IN, to an aspecific DNA. These results provide supporting evidence for our hypothesis that LEDGF/p75 plays a role in the tethering of lentiviral IN to the chromosomal DNA.

Binding Sites↗

PubMed1999

Structure of acetylcholinesterase complexed with (-)-galanthamine at 2.3 A resolution.

(-)-Galanthamine (GAL), an alkaloid from the flower, the common snowdrop (Galanthus nivalis), shows anticholinesterase activity. This property has made GAL the target of research as to its effectiveness in the treatment of Alzheimer's disease. We have solved the X-ray crystal structure of GAL bound in the active site of Torpedo californica acetylcholinesterase (TcAChE) to 2.3 A resolution. The inhibitor binds at the base of the active site gorge of TcAChE, interacting with both the choline-binding site (Trp-84) and the acyl-binding pocket (Phe-288, Phe-290). The tertiary amine group of GAL does not interact closely with Trp-84; rather, the double bond of its cyclohexene ring stacks against the indole ring. The tertiary amine appears to make a non-conventional hydrogen bond, via its N-methyl group, to Asp-72, near the top of the gorge. The hydroxyl group of the inhibitor makes a strong hydrogen bond (2.7 A) with Glu-199. The relatively tight binding of GAL to TcAChE appears to arise from a number of moderate to weak interactions with the protein, coupled to a low entropy cost for binding due to the rigid nature of the inhibitor.

Acetylcholinesterase↗

PubMed1984

Trp holorepressor-trp operator interaction studied by protein distribution analysis.

Trp repressor protein of Escherichia coli (Mr 24,700) undergoes a conformational change upon interaction with L-tryptophan that enables the resulting binary complex to bind with high specificity to several operator targets in double-stranded DNA. By protein distribution analysis it was shown that a significant fraction of Trp repressor is inert in operator binding. The equilibrium dissociation constant for Trp holorepressor-Trp operator interaction is 6.7 nM at 20 degrees in 0.05M NaCl, pH 7.4. The Trp holorepressor-trp operator complex consists of one molecule of each of the participating species, even at high molar ratios of protein to DNA.

Bacterial Proteins↗

PubMed2002

Synthesis of adamantyl naphthalene diimide and its interaction with double stranded DNA.

An adamantyl naphthalene diimide derivative (AND) was synthesized as a highly selective double stranded DNA binding reagent. The binding studies with sonicated calf thymus DNA revealed that AND can bind to double stranded DNA by the threading mode, where the two adamantyl moieties are located in the major and minor grooves of DNA duplex separately. In the presence of beta-cyclodextrin (beta-CD), the complex of AND with DNA duplex was stabilized by capping of the adamantyl moieties of AND by beta-CD. In other words, beta-CD serves as a stabilizer for the complex of AND with DNA duplex to result in an enhanced selectivity of AND for double stranded DNA over single stranded DNA.

Adamantane↗

PubMed2004

Involvement of colicin in the limited protection of the colicin producing cells against bacteriophage.

The restriction/modification system is considered to be the most common machinery of microorganisms for protection against bacteriophage infection. However, we found that mitomycin C induced Escherichia coli containing ColE7-K317 can confer limited protection against bacteriophage M13K07 and lambda infection. Our study showed that degree of protection is correlated with the expression level of the ColE7 operon, indicating that colicin E7 alone or the colicin E7-immunity protein complex is directly involved in this protection mechanism. It was also noted that the degree of protection is greater against the single-strand DNA bacteriophage M13K07 than the double-strand bacteriophage(lambda). Coincidently, the K(A) value of ColE7-Im either interacting with single-strand DNA (2.94x10(5)M(-1)) or double-strand DNA (1.75x10(5)M(-1)) reveals that the binding affinity of ColE7-Im with ssDNA is 1.68-fold stronger than that of the protein complex interacting with dsDNA. Interaction between colicin and the DNA may play a central role in this limited protection of the colicin-producing cell against bacteriophages. Based on these observations, we suggest that the colicin exporting pathway may interact to some extent with the bacteriophage infection pathway leading to a limited selective advantage for and limited protection of colicin-producing cells against different bacteriophages.

Bacteriocin Plasmids↗