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PubMed1978

Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions.

The effects of monovalent and divalent cations on the bimolecular rate constant of the reaction of a positively charged ligand with a nucleic acid polyanion are analyzed for two possible reaction mechanisms. One mechanism postulates that the association reaction occurs without intermediates, and that ion effects on the rate constant result entirely from the screening of the charged reactants by ionic atmospheres of low molecular weight ions (a screening-controlled mechanism). This mechanism is analyzed by analogy with the Bronsted-Bjerrum theory for the kinetics of interaction of low molecular weight ions. The second mechanism to be considered here postulates the existence of a ligand-DNA intermediate which is in rapid equilibrium with the reactants (pre-equilibrium mechanism). Ion concentration effects on the association rate constants for the pre-equilibrium mechanism result mainly from the release of counterions from the DNA upon formation of the intermediate. Both of the above mechanisms predict that the logarithm of the association rate constant, ka, will be a linear function of the logarithm of the monovalent cation concentration, [M+] (in the absence of competition by divalent cations or anions). Knowledge of the salt dependences of ka and of the observed equilibrium constance Kobs of the ligand-nucleic acid interaction should usually be sufficient to determine whether a screening controlled mechanism or a pre-equilibrium mechanism is suitable to describe the process. If the association reaction can be described by a pre-equilibrium mechanism, the number of ionic interactions involved in the ligand-nucleic acid intermediate can be estimated. This analysis, extended to include the effects of divalent cations on screening or on the pre-equilibrium step, is applied to literature data on the salt dependence of the kinetics of the interaction of lac repressor with lac operator DNA. When the operator is present on bacteriophage lambda DNA, the observed reaction kinetics are consistent with the formation of an intermediate repressor-DNA complex in a pre-equilibrium step. On the other hand, the kinetics of association of lac repressor with synthetic lac operator fragments may be an example of a screening-controlled reaction.

Binding Sites↗
PubMed2006

Interactions of hypocrellin B with hyaluronan and photo-induced interactions.

In the current work, the molecular recognition and interaction were studied by taking advantages of the environmentally sensitive fluorescence of hypocrellin B (HB) and the structural knowledge of hyaluronan (HYA), a polysaccharide over-expressed in tumor cells or tissues. Interestingly, it was found that, binding to HYA, the absorbance of HB would be greatly strengthened, suggesting HB fitting to a hydrophobic environment in HYA, while the fluorescence seriously quenched at pH 7.0, which was very distinct from the binding of HB to proteins, liposome, other polysaccharide molecules or HYA at pH 2.0. Synchronously, the particle size of HYA would become bigger after interaction with HB, suggesting an aggregation of HYA. Considering the spectral responses of HB and the particle size change of HYA, a specific interaction of HB with HYA was proposed, that is, an HB molecule would link two HYA molecules not only by hydrophobic interaction but also by formations of intermolecular hydrogen bonds at physiological pH values. Furthermore, the estimated binding constant suggests a quite high affinity of HB to HYA. Besides, an oxygen-dependent degradation of HYA and photobleaching of HB were observed via photosensitization of HB.

Hyaluronic Acid↗
PubMed2004

Thermodynamics of alpha-lactalbumin-DL-alpha-dipalmitoylphosphatidylcholine interactions and effect of the antioxidant nicotinamide on these interactions.

Differential scanning calorimetry has been used to understand the thermodynamics of the interactions of dl-alpha-dipalmitoylphosphatidylcholine (DPPC) with alpha-lactalbumin and the effect of the antioxidant nicotinamide on these interactions. Nicotinamide decreases the thermal transition temperature of both the lipid and the protein at high concentrations. The thermal unfolding transitions of the protein were two state and calorimetrically reversible. There was no significant change in the shape and thermodynamic parameters accompanying the lipid endotherms, suggesting that nicotinamide did not penetrate the lipid bilayer. The thermal unfoldings of alpha-lactalbumin in the presence of DPPC as cosolute also adhered to two-state reversible mechanism. The changes in the thermodynamic parameters accompanying the thermal transitions were small, indicating no significant interaction of alpha-lactalbumin with DPPC. The changes in the thermodynamic parameters indicate that the lipid bilayer organization, as well as the partitioning of the extrinsic protein alpha-lactalbumin into the bilayer, is not affected in the entire studied concentration range of the lipid. It is observed that the presence of increasing concentration of nicotinamide (as high as 1.0 mol dm(-3)) in the lipid-protein mixture does not affect its partitioning into the lipid bilayer, although nicotinamide preferentially interacts with alpha-lactalbumin. The change in the effect of nicotinamide on lipid transition temperature in the mixture and literature report suggests that nicotinamide may be forming a hydrogen-bonded complex with the protein through its amide functionality. The surface tension data of aqueous nicotinamide in combination with the thermal denaturation results of protein in presence of nicotinamide confirmed that surface tension effect does not have any significant contribution to the effect of nicotinamide on protein.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2005

Differential interactions of the homeodomain-interacting protein kinase 2 (HIPK2) by phosphorylation-dependent sumoylation.

Homeodomain-interacting protein kinase 2 (HIPK2) interacts with and phosphorylates various transcription factors that are critical regulators of cell fate decisions and apoptosis during development. Here we show that lysine 25 of HIPK2 is the major sumoylation site, both in vitro and in vivo, and that the sumoylation of this site occurs in a phosphorylation-dependent manner. This became clear with the finding that kinase-dead HIPK2 (K221R) could not be efficiently sumoylated in vitro. The sumoylation of HIPK2 resulted in the disruption of its interaction with a Groucho corepressor. Consequently, sumoylation inhibited the regulatory activity of HIPK2 on the Groucho-mediated repression of transcription, whereas not on p53-mediated transactivation. These results suggest that phosphorylation-dependent sumoylation enables HIPK2 to drive different target gene transcription by means of differential interactions with its binding partners.

Basic Helix-Loop-Helix Proteins↗
PubMed2004

Small interacting peptides. Part II: Interaction of cyclohexapeptides with immobilised model peptides. Comparison of infrared investigations, principal components analysis and force field calculations.

The interaction of cyclic peptides with surface-bound model peptides was investigated by ATR-FTIR spectroscopy, principal components analysis and force field calculations. Information about the interacting functional COOH, COO-, and NH3+ groups and the peptide backbone was gained through a set of cyclohexapeptides (seven of the type c(X1KX2KX3K) (K = L-lysine) and one of the type c(X1KX2KX3k) (k = D-lysine), which are interacting with L-arginine- or tripeptide-coated Si-ATR crystals. All measurements were performed in aqueous solutions. Spectra evaluation in the range 1800-1500 cm(-1) was done by band and principal components analysis (PCA). Only adsorbed molecules were present in these spectra. The coatings were investigated by ATR-FTIR spectroscopy too in order to characterise their functional groups. Based on this knowledge, the spectra of the interacting partners could be evaluated in relation to cyclohexapeptides and coatings. As a result, it was possible to identify the distinct differences in the bonding behaviour of the various peptides.

Amino Acid Sequence↗
PubMed1987

The insulin-receptor interaction: is the kinetic approach for inferring negative-cooperative site-site interactions valid?

The dissociation of insulin from its receptor is reportedly enhanced when the dissociation is induced by dilution in the presence of insulin. This experiment is frequently conducted when curvilinear Scatchard plots of insulin binding are observed in order to infer negative cooperative site-site interactions amongst insulin receptors. However, when insulin binding to purified liver plasma membranes was measured at 15 degrees C in 50 mM Tris, pH 7.5 containing 0.1% bovine serum albumin and 100 U/ml bacitracin, the insulin binding data was characterised by a linear Scatchard plot and a Hill plot with a slope equal to unity. Thus, under the conditions of this binding assay, insulin apparently bound to a single non-interacting class of homogeneous binding sites. But, despite the apparent absence of cooperative interactions under these specific conditions, the dissociation of receptor-bound insulin was still enhanced when the dissociation of insulin from its receptor was induced by dilution in the presence of insulin. This result cast serious doubt on the validity of inferring negative-cooperative site-site interactions amongst insulin receptors based solely on the observation that the dissociation of receptor-bound insulin is enhanced by dilution in the presence of insulin.

Allosteric Regulation↗
PubMed2001

Effects of social stimuli on sleep in mice: non-rapid-eye-movement (NREM) sleep is promoted by aggressive interaction but not by sexual interaction.

Sleep is generally considered to be a process of recovery from prior wakefulness. In addition to being affected by the duration of the waking period, sleep architecture and sleep EEG also depend on the quality of wakefulness. In the present experiment, we examined how sleep is affected by different social stimuli (social conflict and sexual interaction). Male C57BL/6J mice were placed in the cage of an aggressive dominant male or an estrous female for 1 h in the middle of the light phase. The conflict with an aggressive male had a pronounced NREM sleep-promoting effect. EEG slow wave activity, a measure of NREM sleep intensity, was increased for about 6 h and NREM sleep time was significantly increased for 12 h. REM sleep was strongly suppressed during the remainder of the light phase after the conflict, followed by a rebound later in the recovery phase. The sexual interaction, in contrast, had only mild effects. Both NREM sleep and REM sleep were somewhat suppressed shortly after the interaction. In a separate group of mice, blood samples were taken to measure prolactin and corticosterone. The results suggest that the temporary suppression of REM sleep following the social stimuli may be partly due to elevated corticosterone. The different effects of the social stimuli on NREM sleep are not easily explained by differences in the hormone responses. In conclusion, although both social conflict and sexual interaction induce a strong physiological activation, only social conflict has a strong stimulatory effect on NREM sleep mechanisms.

Aggression↗
PubMed2002

Interaction of ochratoxin A with human serum albumin. Binding sites localized by competitive interactions with the native protein and its recombinant fragments.

Competitive interactions of ochratoxin A (OTA) and several other acidic compounds were utilized to gain insight into the localization of binding sites and the nature of binding interactions between anionic species and human serum albumin (HSA). Depolarization of OTA fluorescence in the presence of a competing anion was used to quantify ligand-protein interactions. The results obtained were rationalized in terms of OTA displacement from its major binding site. Based on their ability to displace OTA, two distinct groups of the anionic ligands were revealed. The first group contained structurally diverse compounds that shared a common binding site in subdomain IIA (Sudlow Site I). The second group consisted of three non-steroidal anti-inflammatory drugs, which showed much lower affinity to Site I than the OTA dianion. The major site for these drugs was located in domain III. Fluorescence spectroscopy measurements of OTA, warfarin (WAR) and naproxen (NAP) complexes with recombinant proteins corresponding to the domains of HSA (D1-D3) revealed binding to all domains but with different affinities. The binding constants for OTA and WAR decreased in the series D2z.Gt;D3>D1. In contrast, NAP showed the most favorable interaction with D3 and comparable affinities to the two remaining domains. The OTA binding constant for D2, 7.9 x 10(5) M(-1), was smaller than the largest constant for HSA by a factor of approximately 7. The binding constant for OTA with D3, 1.1 x 10(5) M(-1), was very close to that of the secondary binding site for HSA.

Anions↗
PubMed1999

Calcium-dependent interaction of annexin I with annexin II and mapping of the interaction sites.

Annexins are multifunctional intracellular proteins with Ca2+- and phospholipid-binding properties. Their structures consist of four conserved repeat domains that form the core and a diverse N-terminal tail, from which their functional differences may arise. We searched for cellular proteins that interact with the N-terminal tail plus domain I of annexin I (ANX1) by using the yeast two-hybrid method. Screening of a HeLa cell cDNA library yielded annexin II (ANX2) cDNA. The interaction between ANX1 and ANX2 also occurred in vitro in a Ca2+-dependent manner. Mapping of the interaction sites revealed that interaction between domain I of ANX1 and domain IV of ANX2 was stronger than the other combinations.

Annexin A1↗
PubMed2003

Modeling of adsorption in hydrophobic interaction chromatography systems using a preferential interaction quadratic isotherm.

A preferential interaction quadratic isotherm model for hydrophobic interaction chromatographic systems is presented in this paper. In this isotherm, the nonlinear effect of salt on the capacity factor is described using the preferential interaction model developed by Perkins et al. [J. Chromatogr. A, 766 (1997) 1]. This is then coupled with a quadratic nonlinear isotherm to describe nonlinear adsorption behavior at high solute concentrations. The resulting preferential interaction quadratic isotherm is examined for its ability to describe solute adsorption behavior under both linear and nonlinear conditions over a wide range of salt concentrations in HIC systems. The results indicate that this isotherm is well suited for predicting nonlinear adsorption behavior in HIC systems for both proteins and low-molecular mass HIC displacers.

Adsorption↗
PubMed2003

False interaction of syntaxin 1A with a Ca(2+)-activated K(+) channel revealed by co-immunoprecipitation and pull-down assays: implications for identification of protein-protein interactions.

The techniques of co-immunoprecipitation and immunocytochemical co-labelling are classically used to identify protein-protein interactions. We have used an antibody to the rat small conductance calcium-activated potassium channel subtype 1 (rSK1) to immunoprecipitate proteins from rat brain. A 35 kDa protein was recognized by two monoclonal antibodies to syntaxin 1 and a polyclonal antibody to syntaxin 1A, but not by antibodies to syntaxins 2, 3 or 4. These data suggested that syntaxin 1A is specifically associated with rSK1 in rat brain. A GST construct of the carboxyl terminus of rSK1 was able to pull-down syntaxin 1A from rat brain. Immunocytochemistry showed somatic labelling for both rSK1 and syntaxin 1A in acutely dissociated hippocampal CA1 neurons, confirming that these proteins could interact in vivo. However, control immunoprecipitations showed that antibodies to eight potassium channels could also immunoprecipitate syntaxin, even though some of these channels would not be expected to reside in the same subcellular compartment. Mock immunoprecipitations and pull-down assays showed that syntaxin 1 could directly interact with sepharose and agarose resins. Hence immunoprecipitation and pull-down assays do not provide evidence that syntaxin is specifically associating with a protein, placing doubt on a number of reported interactions with syntaxin 1A.

Animals↗
PubMed2001

JAB1/CSN5 interacts with the GAL4 DNA binding domain: a note of caution about two-hybrid interactions.

The Jun activation domain binding protein 1 (JAB1) was first identified as an interaction partner and coactivator of c-Jun. Subsequently, it was found to be a subunit of the COP9 signalosome (CSN) and termed CSN subunit 5 (CSN5). This complex regulates light-mediated development in plants and plays an essential role in a variety of organisms. A striking feature of JAB1/CSN5 is its reported interaction with a wide range of proteins and its modulation of their activity or stability. We applied the yeast two-hybrid system to screen for proteins interacting with the DNA-binding domain of the transcription factor c-Myb and found JAB1/CSN5 among the double-positive clones. To our surprise JAB1/CSN5 was shown to interact with the DNA-binding domain of GAL4 alone and had to be rejected as a false positive in the GAL4-based two-hybrid system. This finding emphasizes the necessity of particular caution when JAB1/CSN5 is found in two-hybrid screenings.

Bone Marrow↗
PubMed2003

X-linked thrombocytopenia caused by a mutation in the Wiskott-Aldrich syndrome (WAS) gene that disrupts interaction with the WAS protein (WASP)-interacting protein (WIP).

OBJECTIVE: We studied two adult brothers with severe congenital thrombocytopenia in order to determine the genetic etiology of their inherited disorder. Despite the absence of eczema or immunodeficiency, a mutation of the Wiskott-Aldrich syndrome (WAS) gene was suspected because of the presence of microthrombocytes. MATERIALS AND METHODS: Peripheral blood was obtained for characterization of hematopoietic cells and megakaryocyte progenitors. The coding region of the WAS gene was fully sequenced, and expression of the Wiskott-Aldrich syndrome protein, WASP, was evaluated by immunoblotting. The ability of WASP to physically associate with the WASP-interacting protein, WIP, was tested by yeast and mammalian two-hybrid techniques. RESULTS: In addition to thrombocytopenia, our investigation revealed an increased frequency of peripheral megakaryocyte progenitors (CFU-Mk) and incomplete cytoplasmic maturation by electron microscopy. Sequencing the WAS gene revealed a single base mutation, resulting in substitution of proline for arginine 138 (i.e., Arg138Pro). Immunoblotting demonstrated reduced expression of the mutant WAS protein, and we showed that the Arg138Pro mutation significantly, but incompletely, disrupts WASP-WIP interaction. CONCLUSIONS: In this pedigree, X-linked thrombocytopenia is caused by a rare mutation in the fourth exon of the WAS gene. WASP levels are reduced in lymphocyte cell lines derived from the affected individuals. Furthermore, the mutation significantly but incompletely disrupts WASP-WIP interaction, whereas substitution of alanine or glutamic acid residues at the same position does not. This raises the possibility that protein-protein interaction and WASP stability are related properties.

Adaptor Proteins, Signal Transducing↗
PubMed2000

Identification of factors interacting with hMSH2 in the fetal liver utilizing the yeast two-hybrid system. In vivo interaction through the C-terminal domains of hEXO1 and hMSH2 and comparative expression analysis.

Mutations in DNA mismatch repair (MMR) genes have been shown to segregate with Hereditary Nonpolyposis Colorectal Cancer (HNPCC). However, because many HNPCC families fail to display mutations in known MMR genes, we argued that changes in other components of the MMR pathway may be responsible. The increasing number of proteins reported to interact in the MMR pathway suggests that larger complexes are formed, the composition of which may differ among cell types and tissues. In an attempt to identify tissue-specific MMR-associated factors, we employed the yeast two-hybrid system, using the human hMSH2 as bait and a human fetal liver library as prey. We demonstrate that hMSH2 interacts with a human 5'-3' exonuclease 1 (hEXO1/HEX1) and that this interaction is mediated through their C-terminal domains. The hMSH6 protein does not interact with hEXO1 in the two-hybrid system. Dot-blot analysis of multiple tissue RNA revealed that hMSH2 and hEXO1 are coexpressed at high levels in fetal liver as well as in adult testis and thymus. Northern blot analysis also revealed that hEXO1/HEX1 is highly expressed in several liver cancer cell lines as well as in colon and pancreas adenocarcinomas, but not in the corresponding non-neoplastic tissue.

14-3-3 Proteins↗
PubMed2001

Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments.

The study of protein--protein interactions is central to understanding the chemical machinery that makes up the living cell. Until recently, facile methods to study these processes in intact, living cells have not existed. Furthermore, the assignment of function to novel proteins relies on demonstrating interactions of these proteins with proteins of known function. This review describes an experimental strategy, devised to study protein--protein interactions in any intact living cells based on protein-fragment complementation assays. Applications to quantitative analysis of interactions, allosteric processes and cDNA library screening are discussed. Recently, the feasibility of employing this strategy in genome-wide biochemical pathway mapping efforts has been demonstrated.

Animals↗
PubMed1996

Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design.

BACKGROUND: The explosive growth in the rate of X-ray determination of protein structures is fuelled largely by the expectation that structural information will be useful for pharmacological and biotechnological applications. For example, there have been intensive efforts to develop orally administrable antithrombotic drugs using information about the crystal structures of blood coagulation factors, including thrombin. Most of the low molecular weight thrombin inhibitors studied so far are based on arginine and benzamidine. We sought to expand the database of information on thrombin-inhibitor binding by studying new classes of inhibitors. RESULTS: We report the structures of three new inhibitors complexed with thrombin, two based on 4-aminopyridine and one based on naphthamidine. We observe several geometry changes in the protein main chain and side chains which accompany inhibitor binding. The two inhibitors based on 4-aminopyridine bind in notably different ways: one forms a water-mediated hydrogen bond to the active site Ser195, the other induces a rotation of the Ser214-Trp215 peptide plane that is unprecedented in thrombin structures. These binding modes also differ in their 'weak' interactions, including CH-O hydrogen bonds and interactions between water molecules and aromatic pi-clouds. Induced-fit structural changes were also seen in the structure of the naphthamidine inhibitor complex. CONCLUSIONS: Protein flexibility and variable water structures are essential elements in protein-ligand interactions. Ligand design strategies that fail to take this into account may overlook or underestimate the potential of lead structures. Further, the significance of 'weak' interactions must be considered both in crystallographic refinement and in analysis of binding mechanisms.

4-Aminopyridine↗
PubMed1975

Molecular interactions between ribosomal proteins. Evidence for specificity of interaction between isolated proteins.

The proteins S2, S3, S5, and S10 from the 30S ribosomal subunit of Escherichia coli was studied by analytical ultracentrifugation to characterize them in solution and to determine whether isolated protein-protein interactions exist. Such interactions, if specific, may therefore bear some relationship to the spatial organization of the subunit structure. It was found that protein S2 self-associates to a slight extent and that solution mixtures of S2 and S3 contain only enough dimeric species to account for the S2 dimer. Hence, no observable interaction was detected between S2 and S3. Solution mixtures of proteins S5 and S10 revealed a species of molecular weight greater than either protein. The proposal is that S5 and S10 interact with an association equilibrium constant of 7.6 X 10(-5) M-1 at 3 degrees in a Tris buffer at pH 7.4. It was also shown that solution with a 1:1:1 mixture by mass, of S2, S5, and S10 contained a species possessing a molecular weight consistent with a simple ternary complex of the three proteins.

Bacterial Proteins↗
PubMedDate not supplied

Analysis of the spin exchange interactions in the three phases of vanadium pyrophosphate, (VO)2P2O7, in terms of spin-orbital interaction energy.

The spin exchange interactions in the ambient-pressure orthorhombic (APO), high-pressure orthorhombic (HPO), and ambient-pressure monoclinic (APM) phases of the vanadium pyrophosphate, (VO)2P2O7, were analyzed by calculating the spin-orbital interaction energies delta e-delta e0 of their spin dimers. The anisotropy of the spin exchange interactions in the HPO phase is well explained by the delta e-delta e0 values. For the APO phase, the reported crystal structure does not provide accurate enough delta e-delta e0 values to conclude unambiguously which of the V1-V2 and V3-V4 chains has a larger spin gap and which of the bridged and edge-sharing spin dimers has a stronger spin exchange interaction in the V1-V2 and V3-V4 chains. The APM phase is predicted to exhibit essentially two spin gaps, with a large spin gap for the V8-V5-V7-V6 chain and a very small one for the V4-V2-V3-V1 chain.

Journal Article↗