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PubMed2003

InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes.

Advances in proteomics technology have enabled new proteins to be discovered at an unprecedented speed, and high throughput experimental methods have been developed to detect protein interactions and complexes en masse. Such bottom-up, data-driven approach has resulted in data that may be uninformative or potentially errorful, requiring further validation and annotation. The InterDom database focuses on providing supporting evidence for the detected protein interactions based on putative protein domain interactions. Using an integrative approach, InterDom derives potential domain interactions by combining data from multiple sources, ranging from domain fusions, protein interactions and complexes, to scientific literature. The InterDom database is available at http://InterDom.lit.org.sg.

Databases, Protein↗

PubMed2004

Two-hybrid Mpp10p interaction-defective Imp4 proteins are not interaction defective in vivo but do confer specific pre-rRNA processing defects in Saccharomyces cerevisiae.

The SSU processome is a large, evolutionarily conserved ribonucleoprotein (RNP), consisting of the U3 snoRNA and at least 28 protein components, that is required for biogenesis of the 18S rRNA. We tested the function of one protein-protein interaction in the SSU processome, Mpp10p-Imp4p, in ribosome biogenesis. Exploiting the reverse two-hybrid system, we screened for mutated Imp4 proteins that were conditionally defective for interaction with Mpp10p. Three different imp4 sequences were isolated that: (i) conferred conditional growth in the two-hybrid strain; (ii) complemented the disrupted imp4; (iii) conferred conditional growth in the context of their normal cellular function; and (iv) resulted in defective pre-rRNA processing at the non-permissive temperatures. Domain swapping revealed that mutations that conferred cold sensitivity resided in the N-terminal coiled-coil domain while mutations in the C-terminus conferred temperature sensitivity. Surprisingly, the mutated Imp4 proteins were not measurably defective for interaction with Mpp10p in the context of the SSU processome. This suggests that other members of the complex may contribute to maintaining the Mpp10p-Imp4p interaction in this large RNP. Since protein-protein interactions are critical for many different aspects of cellular metabolism, our work has implications for the study of other large protein complexes.

Amino Acid Sequence↗

PubMed1998

Early detection of social interaction problems: development of a social interaction instrument in young children.

Children with developmental or psychiatric disorders often have problems with social interaction. This study reports on the development of the Ghuman-Folstein Screen for Social Interaction (SSI), a parent/caregiver questionnaire designed to measure the capacity for basic social interaction skills across a variety of contexts in preschool children. The SSI was administered to 51 clinically referred children with a high probability of deficits in social interaction and 60 healthy control subjects to establish reliability and validity. The children were 24 to 61 months of age, with diverse ethnic and socioeconomic backgrounds. Strong internal consistency, significant correlation for test/retest reliability, moderate correlation for interrater reliability and support for external validity of the SSI was established. The SSI scores differentiated between the clinically referred subjects and healthy control subjects and between children with pervasive developmental disorder (PDD) of the autistic type and other non-PDD developmental disorders. The SSI is a relatively simple, efficient, reliable, and valid measure for the capacity for basic social interaction skills in children 24 months to 5 years of age. The SSI has a potential to be useful in primary health care settings to identify children at risk who may need tracking and/or further evaluation and treatment services.

Child Behavior↗

PubMed2003

Cell-cell interactions: leukocyte-endothelial interactions.

Interactions of leukocytes with endothelial cells are early events in acute and chronic inflammation, immune surveillance of tissues, and wound defense and repair. In contrast with their requisite roles in host defense, dysregulated leukocyte-endothelial interactions mediate inflammatory tissue injury, thrombosis, and other pathologic sequelae. Recent observations also identify dysregulated leukocyte-endothelial interactions in neoplasia and sickle cell vasculopathy. Leukocyte interactions with inflamed endothelial cells are mediated by selectins, signaling molecules that include lipids and chemokines, integrins and their ligands, and junctional molecules. They provide multiple checkpoints for regulation in physiologic inflammation and hemostasis and for dysregulation in pathologic syndromes. Neutrophil-endothelial encounters illustrate a multistep paradigm for inflammatory cell-cell interactions and provide the basis for multiple variations on the central themes.

Animals↗

PubMed1995

Measles virus phosphoprotein (P) requires the NH2- and COOH-terminal domains for interactions with the nucleoprotein (N) but only the COOH terminus for interactions with itself.

A mammalian two-hybrid system was used to characterize protein-protein interactions between the measles virus nucleoprotein (N) and phosphoprotein (P). Progressive deletions at both the amino- and carboxy-termini of P facilitated the mapping of two distinct domains on P that are important for interaction with N: (i) a domain mapping predominantly within the C-terminal 100 amino acids and (ii) a domain composed of the extreme amino-terminal residues. Using the same two-hybrid assay, we discovered that the P protein interacts strongly with itself. In contrast to the N-P interaction, only a single C-proximal domain of P was essential for P-P interaction.

Amino Acids↗

PubMed2001

Isolation and characterization of kinase interacting protein 1, a pollen protein that interacts with the kinase domain of PRK1, a receptor-like kinase of petunia.

Many receptor-like kinases have been identified in plants and have been shown by genetic or transgenic knockouts to play diverse physiological roles; however, to date, the cytosolic interacting proteins of relatively few of these kinases have been identified. We have previously identified a predominantly pollen-expressed receptor-like kinase of petunia (Petunia inflata), named PRK1, and we have shown by the antisense RNA approach that it is required for microspores to progress from the unicellular to bicellular stage. To investigate the PRK1-mediated signal transduction pathway, PRK1-K cDNA, encoding most of the cytoplasmic domain of PRK1, was used as bait in yeast (Saccharomyces cerevisiae) two-hybrid screens of pollen/pollen tube cDNA libraries of petunia. A protein named kinase interacting protein 1 (KIP1) was found to interact very strongly with PRK1-K. This interaction was greatly reduced when lysine-462 of PRK1-K, believed to be essential for kinase activity, was replaced with arginine (the resulting protein is named PRK1-K462R). The amino acid sequence of KIP1 deduced from full-length cDNA contains an EF-hand Ca(2+)-binding motif and nine predicted coiled-coil regions. The yeast two-hybrid assay and affinity chromatography showed that KIP1 interacts with itself to form a dimer or higher multimer. KIP1 is present in a single copy in the genome, and is expressed predominantly in pollen with a similar temporal pattern to PRK1. In situ hybridization showed that PRK1 and KIP1 transcripts were localized in the cytoplasm of pollen. PRK1-K phosphorylated KIP1-NT (amino acids 1--716), whereas PRK1-K462R only weakly phosphorylated KIP1-NT in vitro.

Amino Acid Sequence↗

PubMed2002

Nine isomeric nitrobenzylidene-iodoanilines: interplay of C-H...O hydrogen bonds, iodo...nitro interactions and aromatic pi...pi stacking interactions.

Nine isomeric nitrobenzylidene-iodoanilines, O(2)NC(6)H(4)CH= NC(6)H(4)I [(I)-(IX)], have been synthesized and the structures of all except 4-nitrobenzylidene-4'-iodoaniline (IX) have been analyzed. 2-Nitrobenzylidene-2'-iodoaniline (I) contains isolated molecules, while 3-nitrobenzylidene-2'-iodoaniline (II) and 2-nitrobenzylidene-3'-iodoaniline (IV) both contain chains of molecules linked by C-H...O hydrogen bonds: similar chains in 4-nitrobenzylidene-2'-iodoaniline (III) are further linked by aromatic pi...pi stacking interactions, forming sheets. In both 3-nitrobenzylidene-3'-iodoaniline and 4-nitrobenzylidene-3'-iodoaniline, (V) and (VI), a combination of C-H...O hydrogen bonds and iodo...nitro interactions generates molecular ladders that are linked into sheets by aromatic pi...pi stacking interactions, while in 2-nitrobenzylidene-4'-iodoaniline and 3-nitrobenzylidene-4'-iodoaniline, (VII) and (VIII), which both crystallize with Z' = 2 in C2/c and P1, respectively, the combination of C-H...O hydrogen bonds and iodo...nitro interactions generates sheets, which in (VIII) are further linked by pi...pi stacking interactions to form a three-dimensional structure. The 4,4'-isomer (IX) crystallizes in Fdd2 with Z' = 2, but both molecules are intractably disordered.

Journal Article↗

PubMed1985

Interaction of opiates with opioid binding sites in the bovine adrenal medulla: I. Interaction with delta and mu sites.

In the present study we examined the interaction of opiates with the delta and mu opioid binding sites in the bovine adrenal medulla. [3H][D-Ala2, D-Leu5]-enkephalin ( [3H]DADLE) in the presence of saturating concentrations of morphiceptin was used to analyze delta site interactions, whereas either [3H]DADLE in the presence of saturation concentrations of [D-Ser2, Leu5]-enkephalin-Thr6 (DSLET) or [3H][D-Ala2, Me-Phe4, Gly5-ol]-enkephalin ( [3H]DAGO) was used for the determination of mu sites. Both binding sites were found to interact stereoselectively with opiates. The binding was affected differentially by proteolytic enzymes (trypsin, alpha-chymotrypsin, pepsin), N-ethylmaleimide, and A2-phospholipase. Kinetic and equilibrium binding studies revealed that in each case radiolabeled opiates interact with one class of binding sites, following simple second-order bimolecular kinetics. Competition for binding by opiates and opioid peptides confirmed the delta and mu selectivity of these sites. Monovalent (Na+, Li+, K+) and divalent (Mg2+, Mn2+, Ca2+) ions interacted differentially with these two binding sites: In general, monovalent cations affected preferentially the apparent number of binding sites, whereas divalent ions modified the equilibrium dissociation constant. Furthermore, positive or negative cooperativity and an apparent heterogeneity of binding sites were detected under some ionic conditions.

Adrenal Medulla↗

PubMed1991

Identification of multiple nuclear factors that interact with cyclic adenosine 3',5'-monophosphate response element-binding protein and activating transcription factor-2 by protein-protein interactions.

Understanding the nature and importance of protein-protein interactions in the mechanisms of eukaryotic gene expression is essential to understanding the normal and aberrant regulation of gene transcription. Using 125I-labeled cAMP response element-binding protein (CREB) and activating transcription factor-2 (ATF-2) recombinant peptides to probe Western blots of HeLa nuclear extracts, we have identified multiple separate nuclear factors that form specific protein-protein interactions with these leucine zipper-containing transcriptional regulatory proteins. The interaction is specific because preincubation of blots with cold homologous protein blocks the binding of labeled protein, whereas preincubation of blots with cold heterologous protein has no effect on labeled protein interactions. Although these studies focus on two specific transactivators, CREB and ATF-2, the approach is of general use for the study of other leucine zipper-containing mammalian transcription factors. Furthermore, in addition to allowing the detection of protein-protein interactions of CREB and ATF-2 with nuclear factors, we have used this strategy to isolate cDNA clones expressing these nuclear proteins. We demonstrate that CREB will form heterodimers with ATF-1, but not ATF-2, Jun, Fos, or C/EBP whereas, ATF-2 will form heterodimers with Jun and Fos, but not with C/EBP or ATF-1. This strategy, therefore, allows a systematic approach to identifying, characterizing, and cloning proteins involved in the control of eukaryotic transcriptional regulation. The identification and characterization of the components of eukaryotic transcription complexes will allow studies that address the molecular mechanisms of normal and abnormal control of cellular gene expression.

Activating Transcription Factor 2↗

PubMed1999

The beta-subunit of human choriogonadotropin interacts with the exodomain of the luteinizing hormone/choriogonadotropin receptor and changes its interaction with the alpha-subunit.

Human CG (hCG) consists of a common alpha-subunit and a hormone-specific beta-subunit. Similarly, its receptor is also composed of two domains, an extracellular N-terminal half (exodomain) and a membrane-associated C-terminal half (endodomain). hCG initially binds the exodomain of the receptor after which the resulting hCG/exodomain complex is thought to interact with the endodomain. This secondary interaction is considered responsible for signal generation. Despite the importance, it is unclear which hormone subunit interacts with the exodomain or the endodomain. As a step to determine the mechanisms of the initial and secondary interactions and signal generation, we investigated the interaction of the hormone-specific beta-subunit in hCG with the receptor's exodomain. A photoactivable hCG derivative consisting of the wild-type alpha-subunit and a photoactivable beta-subunit derivative was prepared and used to label the exodomain. The analysis and immunoprecipitation of photoaffinity labeled exodomain demonstrate that the beta-subunit in hCG makes the direct contact with the exodomain.

Autoradiography↗

PubMed2005

FRET analyses of the U2AF complex localize the U2AF35/U2AF65 interaction in vivo and reveal a novel self-interaction of U2AF35.

We have analyzed the interaction between the U2AF subunits U2AF35 and U2AF65 in vivo using fluorescence resonance energy transfer (FRET) microscopy. U2 snRNP Auxiliary Factor (U2AF) is an essential pre-mRNA splicing factor complex, comprising 35-kDa (U2AF35) and 65-kDa (U2AF65) subunits. U2AF65 interacts directly with the polypyrimidine tract and promotes binding of U2 snRNP to the pre-mRNA branchpoint, while U2AF35 associates with the conserved AG dinucleotide at the 3' end of the intron and has multiple functions in the splicing process. Using two different approaches for measuring FRET, we have identified and spatially localized sites of direct interaction between U2AF35 and U2AF65 in vivo in live cell nuclei. While U2AF is thought to function as a heterodimeric complex, the FRET data have also revealed a novel U2AF35 self-interaction in vivo, which is confirmed in vitro using biochemical assays. These results suggest that the stoichiometry of the U2AF complex may, at least in part, differ in vivo from the expected heterodimeric complex. The data show that FRET studies offer a valuable approach for probing interactions between pre-mRNA splicing factors in vivo.

Bacterial Proteins↗

PubMed2000

Identification of a 14-3-3 protein from Lentinus edodes that interacts with CAP (adenylyl cyclase-associated protein), and conservation of this interaction in fission yeast.

We previously identified a gene encoding a CAP (adenylyl cyclase-associated protein) homologue from the edible Basidiomycete Lentinus edodes. To further discover the cellular functions of the CAP protein, we searched for CAP-interacting proteins using a yeast two-hybrid system. Among the candidates thus obtained, many clones encoded the C-terminal half of an L. edodes 14-3-3 homologue (designated cip3). Southern blot analysis indicated that L. edodes contains only one 14-3-3 gene. Overexpression of the L. edodes 14-3-3 protein in the fission yeast Schizosaccharomyces pombe rad24 null cells complemented the loss of endogenous 14-3-3 protein functions in cell morphology and UV sensitivity, suggesting functional conservation of 14-3-3 proteins between L. edodes and S. pombe. The interaction between L. edodes CAP and 14-3-3 protein was restricted to the N-terminal domain of CAP and was confirmed by in vitro co-precipitation. Results from both the two-hybrid system and in vivo co-precipitation experiments showed the conservation of this interaction in S. pombe. The observation that a 14-3-3 protein interacts with the N-terminal portion of CAP but not with full-length CAP in L. edodes and S. pombe suggests that the C-terminal region of CAP may have a negative effect on the interaction between CAP and 14-3-3 proteins, and 14-3-3 proteins may play a role in regulation of CAP function.

14-3-3 Proteins↗

PubMed1995

The effectiveness of an interactive instructional context. Principles from the parent-child interaction literature.

In the present study, the effectiveness of embedding a targeted linguistic structure within an interactive instructional context is examined. Ten subjects participated in a communication-games intervention which contained seven interactive elements drawn from the parent-child interaction literature. Ten subjects were assigned to a control group. A comparison of student performance before and after intervention supports the effectiveness of adopting instructional strategies that are consistent with a social-interaction perspective on language development. Qualitative results are presented that illustrate each of the interactional characteristics of the intervention. Implications for practice are discussed.

Child↗

PubMed1993

Interaction of unsaturated fatty acids with rat liver glucocorticoid receptors: studies to localize the site of interaction.

Polyunsaturated fatty acids have been shown to decrease the binding of [3H]dexamethasone to rat liver glucocorticoid receptors by mixed non-competitive inhibition, suggesting that these fatty acids interact at a site on the receptor different from the hormone binding site. The present study was undertaken to localize the site of interaction of polyunsaturated fatty acids on the receptor by comparing the differential effects of docosahexaenoic acid (a 22-carbon polyunsaturated fatty acid of the series n-3) on antagonist (RU486) and agonist binding, by covalent cross-linking of the hsp 90 and other proteins to the receptor to attempt to mask the site of interaction, by limited trypsinization to cleave the site and by using antibodies against specific epitopes to prevent fatty acid access by steric hindrance. Binding [3H]RU486 was not inhibited by docosahexaenoic acid at a concentration (60 mumol/l) that increases the dissociation constant of [3H]dexamethasone eightfold. Covalent stabilization of the hetero-oligomeric glucocorticoid receptor structure did not keep the fatty acid from inhibiting [3H]dexamethasone binding. The binding to the receptor of monoclonal and polyclonal antibodies against different domains of the receptor did not sterically hinder the fatty acid interaction with the receptor. After limited trypsinization of the receptor, the fatty acid still increased the dissociation rate constant of [3H]dexamethasone binding, indicating that the site of interaction of polyunsaturated fatty acids is on a fragment of the receptor containing the hormone-binding domain and some sequences C-terminal of the DNA-binding domain.

Animals↗

PubMed1998

Repression of basal transcription by vitamin D receptor: evidence for interaction of unliganded vitamin D receptor with two receptor interaction domains in RIP13delta1.

Repression of basal transcription of a 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3) responsive 25-hydroxyvitamin D3-24-hydroxylase (CYP24) promoter construct as observed in kidney cells in the absence of ligand and this repression was dependent on a functional vitamin D response element (VDRE). Basal repression was also seen with a construct where a consensus DR-3-type VDRE was fused to the thymidine kinase promoter. Expression of a dominant negative vitamin D receptor (VDR) isoform that strongly bound to the VDRE motif in the CYP24 promoter ablated basal repression. This VDR isoform lacked sequence in the hinge- and ligand-binding domains implicating one or both of these domains in basal repression. It is well known that thyroid hormone and retinoic acid receptors silence basal transcription of target genes in the absence of ligands and this repressor function can be mediated by the nuclear receptor corepressor N-CoR. Two variants of N-CoR have been described, RIP13a and RIP13delta1. N-CoR and the variants contain two receptor interaction domains, ID-I and ID-II, which are identical except region ID-II in RIP13delta1 has an internal deletion. We have used the mammalian two hybrid system to investigate whether VDR, in the absence of ligand 1,25-(OH)2D3, can interact with these domains. The data showed that unliganded VDR does not interact with either ID-I or ID-II from RIP13a and RIP13delta1, but does interact strongly with a composite domain of ID-I and ID-II from RIP13delta1 (but not from RIP13a) and this strong interaction is abrogated in the presence of ligand. This finding implicates RIP13delta1 in VDR-dependent basal repression of the promoter constructs under investigation. However, over-expression of RIP13delta1 in kidney cell lines did not alter basal expression of the CYP24 promoter construct. It is concluded that either the level of endogenous RIP13delta1 in these kidney cells permits maximal repression or that repression occurs by a mechanism that is independent of RIP13delta1. Alternatively, repression may be dependent on RIP13delta1 but requires an additional cofactor that is limiting in these cells.

Animals↗

PubMed1999

MIAX: A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 1) Description of the Interaction Model and Simulation Algorithm.

We describe a novel computer system directed to evaluate protein complex formation in a liquid environment. The relevant feature of the system is a potential function expressing the main thermodynamic and kinetic factors leading to protein interaction in solution. The protein interaction model expresses the interaction energy as basically composed of three forces: electrostatic (hydrogen bond), van der Waals, and hydrophobic. The latter is defined in function of the forces that the solvent molecules exert on the surface of the complex, and the van der Waals forces between the monomers and the solvent. The interaction model implemented in the system has proven a high discrimination ability between different protein dockings, scoring high those close to the observed crystal structures. These results have led to the establishment of the basic principles underlying protein interaction, which constitutes the main way of expression of the biological function of these macromolecules.

Journal Article↗

PubMed2001

In vitro synergistic interactions between the cisplatin analogue nedaplatin and the DNA topoisomerase I inhibitor irinotecan and the mechanism of this interaction.

Among the numerous clinical regimens used in combination chemotherapy, synergy is particularly marked in combinations containing cisplatin (CDDP). However, the clinical use of CDDP is sometimes limited due to its nephrotoxicity. Nedaplatin (NDP) is a second-generation platinum complex with reduced nephrotoxicity that may substitute for CDDP or even surpass it for use in combination with other drugs. We investigated the effects of combinations of NDP and other anticancer drugs on the growth of human small cell lung cancer cells (SBC-3) and non-small cell lung cancer cells (PC-14) using a three-dimensional analysis model. Among the combinations tested, the combination of NDP and irinotecan (CPT-11) showed the most marked synergistic interaction, and the synergism has also been observed against PC-14 cells. With regard to treatment schedule, a remarkable synergistic interaction was produced by concurrent exposure to NDP and CPT-11. On the other hand, sequential exposure to the two drugs led only to additivity. To analyze the interaction between the drugs, the effect of NDP on the 7-ethyl-1-hydroxy-CPT (the active form of CPT-11)-induced inhibitory effect on DNA topoisomerase I was examined. The topoisomerase I-inhibitory effect of 7-ethyl-1-hydroxy-CPT was enhanced 10-fold in the presence of NDP at microgram/milliliter concentrations. These biochemical interactions might be responsible for the synergistic interaction between NDP and CPT-11. These results suggest that the combination of NDP with CPT-11 may be clinically useful for the chemotherapy of lung cancer.

Antineoplastic Agents↗

PubMed1999

[Study on the interaction of copper-zinc superoxide dismutase with cobalt (II)-histidine by spectral analysis. II. Effects of pH, interaction time].

The direct interaction of Cu2Zn2SOD with organic metal compound (Cobalt (II)-Histidine) was studied by ICP, VIS and the measurement of enzyme activity, and also investigated the effect of pH values and different interaction times for this interaction. The results showed that with the increased in pH values and the more longer interaction times, the intensity of interaction were increased and the corresponding catalytic activity of enzyme were affected.

Cobalt↗