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PubMed1998

Identification and characterization of a novel corepressor interaction region in RVR and Rev-erbA alpha.

Rev-erbA alpha and RVR are orphan nuclear receptors that function as dominant transcriptional silencers. Ligand-independent repression of transcription by Rev-erbA alpha and RVR is mediated by the nuclear receptor corepressors, N-CoR and its variants RIP (RXR interacting protein) 13a and RIP13 delta 1. The physical association between the corepressors and Rev-erbA alpha and RVR is dependent on the presence of a receptor interaction domain (RID) in the N-CoR family. Our previous study demonstrated that the E region of RVR and Rev-erbA alpha is necessary and sufficient for the in vivo interaction with the nuclear receptor corepressor, RIP13 delta 1. The present investigation demonstrates that two corepressor interaction regions, CIR-1 and CIR-2, separated by approximately 150 amino acids in the E region of RVR, are required for the interaction with N-CoR, RIP13a, and RIP13 delta A. The D region is not required for the physical interaction. In contrast, the D and E regions of Rev-erbA alpha were necessary for the interaction with the N-CoR and RIP13a-RIDs in vivo, suggesting that RIP13 delta 1 and N-CoR/RIP13a differentially interact with Rev-erbA alpha. Mutagenesis of CIR-1, a novel domain that is highly conserved between RVR and Rev-erbA alpha, demonstrated that the N-terminal portion of helix 3 plays a key role and is absolutely necessary for the interaction with RIP13 delta 1, RIP13a, and N-CoR. The phenylalanine residues, F402 and F441, in RVR and Rev-erbA alpha, respectively, were critical residues in supporting corepressor interaction. Cotransfection studies demonstrated that repression of a physiological target, the human Rev-erbA alpha promoter, by RVR was significantly impaired by mutation of CIR-1 or deletion of CIR-2. Furthermore, overexpression of either the N-CoR/RIP13a or RIP13 delta 1-RIDs alleviated RVR-mediated repression of the Rev-erbA alpha promoter, demonstrating that corepressor binding mediates the repression of a native target gene by RVR. A minimal region containing juxtapositioned CIR-1 and CIR-2 was sufficient for corepressor binding and transcriptional repression. In conclusion, our study has identified a new corepressor interaction region, CIR-1, in the N terminus of helix 3 in the E region of RVR and Rev-erbA alpha, that is required for transcriptional silencing. Furthermore, we provide evidence that CIR-1 and CIR-2 may form a single corepressor interaction interface.

Amino Acid Sequence↗

PubMed2003

Computational analyses of high-throughput protein-protein interaction data.

Protein-protein interactions play important roles in nearly all events that take place in a cell. High-throughput experimental techniques enable the study of protein-protein interactions at the proteome scale through systematic identification of physical interactions among all proteins in an organism. High-throughput protein-protein interaction data, with ever-increasing volume, are becoming the foundation for new biological discoveries. A great challenge to bioinformatics is to manage, analyze, and model these data. In this review, we describe several databases that store, query, and visualize protein-protein interaction data. Comparison between experimental techniques shows that each high-throughput technique such as yeast two-hybrid assay or protein complex identification through mass spectrometry has its limitations in detecting certain types of interactions and they are complementary to each other. In silico methods using protein/DNA sequences, domain and structure information to predict protein-protein interaction can expand the scope of experimental data and increase the confidence of certain protein-protein interaction pairs. Protein-protein interaction data correlate with other types of data, including protein function, subcellular location, and gene expression profile. Highly connected proteins are more likely to be essential based on the analyses of the global architecture of large-scale interaction network in yeast. Use of protein-protein interaction networks, preferably in conjunction with other types of data, allows assignment of cellular functions to novel proteins and derivation of new biological pathways. As demonstrated in our study on the yeast signal transduction pathway for amino acid transport, integration of high-throughput data with traditional biology resources can transform the protein-protein interaction data from noisy information into knowledge of cellular mechanisms.

Animals↗

PubMed2002

Population response to toxicants is altered by intraspecific interaction.

Negative interaction between individuals is a distinctive feature of populations. The question is addressed whether the population response to toxicants (e.g., the pyrethroid pesticide fenvalerate) is altered by the strength of negative intraspecific interaction. Larvae of the trichopteran Limnephilus lunatus Curtis were exposed for 1 h to fenvalerate, then larval survival and adult emergence were monitored in outdoor stream microcosms over eight months. Degree of interaction was varied by changing larval densities. No survival was observed after 15 d at 100 microg/L. Survival decreased slightly at 10 microg/L when strong interaction was present. Survival in the range of 0.001 to 1 microg/L was similar to that in the control, regardless of the strength of interaction. In contrast, chronic effects differed widely according to the degree of interaction. Weak interaction resulted in high survival of controls, a lowest-observed-effect concentration (LOEC) (mortality) of 0.1 microg/L, a delay in development at 0.001 to 0.01 microg/L, and reduced weight of adults from 0.01 microg/L on. Strong interaction resulted in low survival of controls, a LOEC (mortality) of 100 microg/L, and a delay in development at 0.1 microg/L. The suggestion was made that these differences in chronic effects are caused by a toxicant-induced reduction of negative intraspecific interaction at high concentrations (> or =1 microg/L). Hence, direct effects of the toxicant are partly compensated because of indirect reduction of negative interaction compared to the control. Interaction is not decreased at low concentrations (< or =0.1 microg/L) and, thus, effects of the toxicant are not compensated. Accordingly, the response to toxicants at the population level when negative interaction is present differs from the response at individual level.

Animals↗

PubMed2001

A surface plasmon resonance study of the interactions between the component subunits of protein kinase CK2 and two protein substrates, casein and calmodulin.

Surface plasmon resonance has been used to study the interaction between the subunits composing protein kinase CK2 (two catalytic, alpha-subunits, and two regulatory, beta-subunits), as well as the interaction of each subunit with two types of protein substrates, casein, the phosphorylation of which is activated by the regulatory subunit, and calmodulin, which belongs to the kind of substrates on which the catalytic subunit is downregulated by the regulatory subunit. The interaction of casein with the catalytic subunit differs from the interaction with the holoenzyme. Similarly to the interaction with the regulatory subunit, the catalytic subunit interacts with the protein substrate forming a very stable, irreversible complex. The reconstituted holoenzyme, however, binds casein reversibly, displaying a binding mode similar to that displayed by the regulatory subunit. The interaction of calmodulin with the catalytic subunit gives place, like in the case of casein, to an irreversible complex. The interactions with the regulatory subunit and with the holoenzyme were practically negligible, and the interaction with the regulatory subunit disappeared upon increasing the temperature value to close to 30 degrees C. The presence of polylysine induced a high increase in the extent of calmodulin binding to the holoenzyme. The results obtained suggest that CK2beta subunit and protein substrates share a common, or at least an overlapping, site of interaction on the catalytic subunit. The interaction between both subunits would prevent substrates from binding irreversibly to alpha subunit, and, at the same time, it would generate a new and milder site of interaction between the whole holoenzyme and the protein substrate. The main difference between casein and calmodulin would consist in the lower affinity display by the last for the new site generated upon the binding of the regulatory subunit, in the absence of polycations like polylysine.

Binding Sites↗

PubMed2003

A domain combination based probabilistic framework for protein-protein interaction prediction.

In this paper, we propose a probabilistic framework to predict the interaction probability of proteins. The notion of domain combination and domain combination pair is newly introduced and the prediction model in the framework takes domain combination pair as a basic unit of protein interactions to overcome the limitations of the conventional domain pair based prediction systems. The framework largely consists of prediction preparation and service stages. In the prediction preparation stage, two appearance probability matrices are constructed. Each matrix holds information on appearance frequencies of domain combination pairs in the interacting and non-interacting sets of protein pairs, respectively. Based on the appearance probability matrix, a probability equation is devised. The equation maps a protein pair to a real number in the range of 0 to 1. Two distributions of interacting and non-interacting sets of protein pairs are obtained using the equation. In the prediction service stage, the interaction probability of a protein pair is predicted using the distributions and the equation. The validity of the prediction model is evaluated for the interacting set of protein pairs in a Yeast organism and artificially generated non-interacting set of protein pairs. When 80% of the set of interacting protein pairs in DIP (Database of Interacting Proteins) is used as a learning set of interacting protein pairs, very high sensitivity (86%) and moderate specificity (56%) are achieved within our framework.

Amino Acid Sequence↗

PubMed1989

Specific interaction between gangliotriaosylceramide (Gg3) and sialosyllactosylceramide (GM3) as a basis for specific cellular recognition between lymphoma and melanoma cells.

In view of the possible role of glycosphingolipids in defining the specificity of cell-cell interactions, the key molecules for recognition of cell surface glycosphingolipids have been studied. In addition to previously suggested recognition mechanisms involving endogenous lectins and glycosyltransferases, an alternative possibility, based on carbohydrate-carbohydrate (Lex-Lex) interaction, has been raised (Eggens, I., Fenderson, B., Toyokuni, T., Dean, B., Stroud, M., and Hakomori, S. (1989) J. Biol. Chem. 264, 9476-9484). We now report a highly specific interaction between gangliotriaosylceramide (Gg3, GalNAc beta 1----4Gal beta 1----4Glc beta 1----Cer) and sialosyllactosylceramide (GM3, NeuAc alpha 2----3Gal beta 1----4Glc beta 1----Cer). The interaction requires a bivalent cation (Ca2+ or Mg2+) and can be inhibited by sialosyl 2----3 lactose, anti-GM3 antibody (DH2), anti-Gg3 antibody (2D4), or EDTA. The strength of interaction between GM3 liposome and the Gg3-coated plastic surface was highly density-dependent. The mouse lymphoma L5178 AA12 cell line (high expressor of Gg3) interacted specifically with the mouse B16 melanoma cell line (high expressor of GM3). The interaction was inhibited by 5 mM sialosyllactose, anti-GM3 antibody, anti-Gg3 antibody, and EDTA in analogy to GM3-Gg3 interaction. L5178 AV27, a genetically related variant clone which does not express Gg3, showed no interaction with B16 cells. Untreated AA12 cells, but not 2D4-treated AA12 cells or AV27 cells, interacted with GM3 coated on the plastic surface. These findings suggest a specific interaction between AA12 cells and B16 cells based on Gg3-GM3 interaction.

Animals↗

PubMed1986

Cellular interactions in tissue and organ development.

Developmental patterns result from combinations of interactions and intracellular programmes. The purpose here is to define the roles of interactions wherever possible and to consider their major parameters, such as the timing of their action, their specificity and the distances over which they occur. The approach is one of a board survey, attempting to outline major interaction systems on the basis of information from different sources. The evidence concerning interactions that control development must come primarily from development itself. Both disturbed, as during regeneration and grafts, and normal development are relevant. Growing apices interact over relatively long distances. They reduce the development of similar apices and induce the development of axial tissues that connect them to the plant. Young shoot tissues also induce the development of root apices and vice versa. These various effects can be understood on the basis of a hormonal feedback involving auxins and cytokinins. Vascular differentiation, furthermore, is a cellular expression of these interactions. It occurs along the flow of auxin from the young tissues of the shoot towards the root apices. This flow is canalized by a positive feedback between cell polarization and the polar flow that both controls and results from this polarization. Structural relations between pholem and xylem, limitations of regeneration and the formation of rays all indicate the existence of additional, radial interactions. The fate of individual cells in development is varied and often follows no recognizable rules. This indicates interactions that operate on the size of a tissue or organ rather than on its precise cellular development. On the other hand, the continuity of plasmodesmata, wall thickenings and cytoplasmic strands demonstrate local interactions between neighbouring cells. It is concluded that, though the possibilities of developmental interactions may be bewildering, the list, when known, may not be all that long. The interactions specify orientation and quantity rather than the precise fate of cells. Their effects are gradual and they involve feedback loops. Growth factors, even known growth factors, play surprisingly large roles in cellular interactions. Such controls whose effect is gradual and general could provide a basis for developmental plasticity.

Cell Communication↗

PubMed2006

Reducing warfarin medication interactions: an interrupted time series evaluation.

BACKGROUND: Computerized decision support reduces medication errors in inpatients, but limited evidence supports its effectiveness in reducing the coprescribing of interacting medications, especially in the outpatient setting. The usefulness of academic detailing to enhance the effectiveness of medication interaction alerts also is uncertain. METHODS: This study used an interrupted time series design. In a health maintenance organization with an electronic medical record, we evaluated the effectiveness of electronic medical record alerts and group academic detailing to reduce the coprescribing of warfarin and interacting medications. Participants were 239 primary care providers at 15 primary care clinics and 9910 patients taking warfarin. All 15 clinics received electronic medical record alerts for the coprescription of warfarin and 5 interacting medications: acetaminophen, nonsteroidal anti-inflammatory medications, fluconazole, metronidazole, and sulfamethoxazole. Seven clinics were randomly assigned to receive group academic detailing. The primary outcome, the interacting prescription rate (ie, the number of coprescriptions of warfarin-interacting medications per 10 000 warfarin users per month), was analyzed with segmented regression models, controlling for preintervention trends. RESULTS: At baseline, nearly a third of patients had an interacting prescription. Coinciding with the alerts, there was an immediate and continued reduction in the warfarin-interacting medication prescription rate (from 3294.0 to 2804.2), resulting in a 14.9% relative reduction (95% confidence interval, -19.5 to -10.2) at 12 months. Group academic detailing did not enhance alert effectiveness. CONCLUSIONS: This study, using a strong and quasi-experimental design in ambulatory care, found that medication interaction alerts modestly reduced the frequency of coprescribing of interacting medications. Additional efforts will be required to further reduce rates of inappropriate prescribing of warfarin with interacting drugs.

Acetaminophen↗

PubMed2005

Food-drug interactions in the summary of product characteristics of proprietary medicinal products.

BACKGROUND: Food-drug interactions can produce negative effects in the safety and efficacy of drug therapy, as well as in the nutritional status of the patient. However, the data commonly provided to the prescriber about possible nutrient-pharmacological compound interactions and the recommendations for their prevention are often scarce. The summary of product characteristics (SmPC) of a proprietary medicinal product, as authorised by the health authorities in Europe, is usually the main source of information for the health professional. Therefore, the SmPC can be a useful tool to prevent or reduce food-drug interactions and, as a consequence, improve the therapeutical approach. OBJECTIVE: The aim of this study was to assess the information about food-drug interactions with potential clinical relevance as it is described in the SmPCs of the authorised medicinal products in a European Union country (Spain). METHODS: A bibliographical search of food-drug interactions, including nutrients and alcohol, was carried out. The adequate information to be included in the SmPC was defined in accordance with the European Recommendations in this field. The SmPCs of the medicinal products containing selected active substances were examined with emphasis on food-drug interactions. RESULTS: It was found that, frequently, the information concerning food-drug interactions as is mentioned in the SmPC of the authorised medicinal products in Spain does not fulfil the current recommendations, both in quantity and quality. Indeed, the available data reveal that the food-drug information is only mentioned in 72.7% of all SmPC where it should be and it was only found in the specific section for interactions in 36.0% of all cases. The description and agreement with recommendations for each SmPC item ranged between 4.2% and 36.0% and between 31.8% and 49.0%, respectively. Some related factors, such as the clinical relevance of the interaction, the existence of an authorised SmPC and the registration procedure followed, influence the information characteristics concerning food-drug interactions. CONCLUSION: The SmPC is a suboptimal source of information for food-drug interactions.

Beverages↗

PubMed2007

Management of potential drug interactions in community pharmacies: a questionnaire-based survey in Switzerland.

OBJECTIVE: To analyze the current drug-interaction management in Swiss community pharmacies, with a particular focus on electronic systems, and to compare the results with those expressed by German general practitioners in a recent survey. METHODS: Data were collected with a postal questionnaire which was randomly sent to 500 out of 833 community pharmacies in the German part of Switzerland. RESULTS: The response rate was 57.4%, and only 24.7% pharmacists reported that they were confronted less than daily with potential drug interactions. Use of computer software to identify potential drug interactions was widespread in community pharmacies (90.2%), and the software was the primary source of information (81.2 +/- 29.6%). The quality of the interaction software was judged sensitive (identifying all dangerous interactions) by 80.5 +/- 21.5%, but specific (identifying only relevant interactions) by only 38.3 +/- 32%. Pharmacists declared a low override rate (14%) of drug interaction alerts, although unjustified alerts were reported by 60.6 +/- 33.1%. In contrast to general practitioners, pharmacists opted less often for information on the mechanism of the interaction, and more frequently for details for dose adjustment. Both groups complained about deficient information on non-interacting alternatives. CONCLUSION: The information needs of community pharmacists differed considerably from general practitioners, and pharmacists were overwhelmed by inappropriate alerts because of a lack of specificity of their drug-interaction systems. Substantial improvement of drug-interaction software systems is thus required at least in two important aspects, the suppression of inappropriate alerts and the tailoring to the needs of the user.

Adult↗

PubMed2003

A general test of the interactive-isolationist continuum in gastrointestinal parasite communities of fish.

Parasite communities are generally believed to lie somewhere along the interactive-to-isolationist continuum, i.e. from rich assemblages of species with high colonisation rates in which interspecific interactions play an important structuring role, to species-poor assemblages where interactions are unlikely. This framework has become one of the paradigms of parasite community ecology. There is, however, no objective way of ranking a set of parasite communities in terms of the extent of interactivity among their constituent species. Here, we propose a simple index of interactivity based on the general likelihood of species co-occurrence, and thus on the potential for interactions, and we apply it to component communities of gastrointestinal helminth parasites from 37 species of marine fish hosts. The index essentially collapses several features of parasite communities thought to influence the degree of interactivity into a single number independent of the number of hosts examined or the total number of species in a component community. The range of values obtained here suggests that the potential interactivity in helminth communities of fish covers almost the full spectrum of possibilities, i.e. from isolationist to highly interactive communities. Although derived from presence/absence data only, the index correlates relatively strongly with the total parasite abundance per host, as well as the total prevalence of infection and the mean infracommunity richness. In other words, it captures properties of the community that influence interactivity. The use of the index in comparative studies may help in determining whether interactive helminth communities are, as widely believed, more common in endothermic vertebrate hosts than in fish hosts.

Animals↗

PubMed2003

Opioid receptor interactions: local and nonlocal, symmetric and asymmetric, physical and functional.

The pharmacological effects of opioid drugs and endogenous opioid peptides are mediated by several kinds of receptors, the major ones being mu, delta and kappa. Though classically it has been thought that a particular effect mediated by a drug or other ligand results from its interaction with a single type of receptor, accumulating evidence demonstrates that interactions between receptors play a major role in opioid actions. These interactions may be either local, involving receptors within the same tissue, or nonlocal, between receptors located in different tissues. Nonlocal interactions always involve intercellular mechanisms, whereas local interactions may involve either intercellular or intracellular interactions, the latter including physical association of receptors. Both local and nonlocal interactions, moreover, may be either symmetric, with ligand interaction at one receptor affecting interaction at the other, or asymmetric; and either potentiating or inhibitory. In this article we discuss major examples of these kinds of interactions, and their role in the acute and chronic effects of opioids. Knowledge of these interactions may have important implications for the design of opioids with more specific actions, and for eliminating the addictive liability of these drugs.

Animals↗

PubMed2003

Interaction of nuclear receptor zinc finger DNA binding domains with histone deacetylase.

A direct interaction between the nuclear receptor TR2 and histone deacetylases (HDACs) 3 and 4 is mediated by the DNA binding domain (DBD) of TR2. To test if this interaction is common to members of the nuclear receptor family, the Cys2-Cys2 type zinc finger (ZF) DBDs were subcloned from several nuclear receptors (mRARalpha, mRXRbeta, mTR2, mTR4, RAR, mPPARdelta, and mPPARgamma2). Using GST pull-downs, both HDACs 3 and 4 were found to interact directly with the core DBD from each receptor. The three-dimensional structure of the ZF domains was essential for this interaction as disruption by zinc chelation precluded interaction with HDACs. The results suggest that the ZFs of nuclear receptors provide a general interaction interface for HDACs 3 and 4. Functional significance of this interaction was demonstrated using ChIP assays where a truncated TR2 protein (lacking the LBD) recruited HDACs 3 and 4 to the target DNA causing demonstrable histone deacetylation. GST pull-downs and mammalian two-hybrid interaction tests were then used to define the interaction domains of HDAC3 with TR2. Both the N- and C-terminal portions of HDAC3 showed interaction with the TR2 DBD. Thus, multiple domains of HDAC3 form the interaction surface for the DBD of nuclear receptors.

Animals↗

PubMed2002

The extent of potential antihypertensive drug interactions in a Medicaid population.

BACKGROUND: Drug interactions are a frequent cause of adverse drug events and these might be avoided by computer alerts to physicians or pharmacists. We evaluated the frequency of potential drug-drug interactions in patients receiving medications commonly used for hypertension. METHODS: Patients more than 30 years of age with hypertension who were receiving Medicaid and who were enrolled in the Iowa Pharmaceutical Case Management (PCM) program were evaluated. All prescription claims for patients were obtained on their date of eligibility. A drug interaction database was developed to examine potential drug interactions in each patient's regimen. RESULTS: There were 1574 patients who received a drug typically used for hypertension. Depending on age and sex, 23% to 48% of patients had a potential interaction of high significance and 55% to 84% had at least one potential interaction. Both increasing age (P =.0007, odds ratio [OR] 1.012 [1.005,1.019]) and number of drugs (P <.0001, OR 1.120 [1.092,1.150]) were significantly associated with the potential for a highly significant drug interaction in the univariable models. Female sex was not significant (P =.56, OR 1.074 [0.845,1.364]). The multivariable model found that there was a significant interaction between age and the number of drugs in the regimen (P <.0001). CONCLUSIONS: This study found a very high frequency of potential drug interactions with agents typically used for hypertension. Because of the large volume of potential interactions, these data raise the concern that any attempt to provide physicians and pharmacists with computer alerts about these interactions will result in alerts for the vast majority of patients.

Adult↗

PubMed2004

Architecture of basic building blocks in protein and domain structural interaction networks.

MOTIVATION: The structural interaction of proteins and their domains in networks is one of the most basic molecular mechanisms for biological cells. Topological analysis of such networks can provide an understanding of and solutions for predicting properties of proteins and their evolution in terms of domains. A single paradigm for the analysis of interactions at different layers, such as domain and protein layers, is needed. RESULTS: Applying a colored vertex graph model, we integrated two basic interaction layers under a unified model: (1) structural domains and (2) their protein/complex networks. We identified four basic and distinct elements in the model that explains protein interactions at the domain level. We searched for motifs in the networks to detect their topological characteristics using a pruning strategy and a hash table for rapid detection. We obtained the following results: first, compared with a random distribution, a substantial part of the protein interactions could be explained by domain-level structural interaction information. Second, there were distinct kinds of protein interaction patterns classified by specific and distinguishable numbers of domains. The intermolecular domain interaction was the most dominant protein interaction pattern. Third, despite the coverage of the protein interaction information differing among species, the similarity of their networks indicated shared architectures of protein interaction network in living organisms. Remarkably, there were only a few basic architectures in the model (>10 for a 4-node network topology), and we propose that most biological combinations of domains into proteins and complexes can be explained by a small number of key topological motifs. CONTACT: doheon@kaist.ac.kr.

Animals↗

PubMed2005

Correlation between gene expression profiles and protein-protein interactions within and across genomes.

MOTIVATION: Function annotation of an unclassified protein on the basis of its interaction partners is well documented in the literature. Reliable predictions of interactions from other data sources such as gene expression measurements would provide a useful route to function annotation. We investigate the global relationship of protein-protein interactions with gene expression. This relationship is studied in four evolutionarily diverse species, for which substantial information regarding their interactions and expression is available: human, mouse, yeast and Escherichia coli. RESULTS: In E.coli the expression of interacting pairs is highly correlated in comparison to random pairs, while in the other three species, the correlation of expression of interacting pairs is only slightly stronger than that of random pairs. To strengthen the correlation, we developed a protocol to integrate ortholog information into the interaction and expression datasets. In all four genomes, the likelihood of predicting protein interactions from highly correlated expression data is increased using our protocol. In yeast, for example, the likelihood of predicting a true interaction, when the correlation is > 0.9, increases from 1.4 to 9.4. The improvement demonstrates that protein interactions are reflected in gene expression and the correlation between the two is strengthened by evolution information. The results establish that co-expression of interacting protein pairs is more conserved than that of random ones.

Animals↗

PubMed2004

PreSPI: a domain combination based prediction system for protein-protein interaction.

With the accumulation of protein and its related data on the Internet, many domain-based computational techniques to predict protein interactions have been developed. However, most techniques still have many limitations when used in real fields. They usually suffer from low accuracy in prediction and do not provide any interaction possibility ranking method for multiple protein pairs. In this paper, we propose a probabilistic framework to predict the interaction probability of proteins and develop an interaction possibility ranking method for multiple protein pairs. Using the ranking method, one can discern the protein pairs that are more likely to interact with each other in multiple protein pairs. The validity of the prediction model was evaluated using an interacting set of protein pairs in yeast and an artificially generated non-interacting set of protein pairs. When 80% of the set of interacting protein pairs in the DIP (Database of Interacting Proteins) was used as a learning set of interacting protein pairs, high sensitivity (77%) and specificity (95%) were achieved for the test groups containing common domains with the learning set of proteins within our framework. The stability of the prediction model was also evident when tested over DIP CORE, HMS-PCI and TAP data. In the validation of the ranking method, we reveal that some correlations exist between the interacting probability and the accuracy of the prediction.

Computational Biology↗

PubMed2004

Investigation of the nature of the methionine-pi interaction in beta-hairpin peptide model systems.

There are frequent contacts between aromatic rings and sulfur atoms in proteins. However, it is unclear to what degree this putative interaction is stabilizing and what the nature of the interaction is. We have investigated the aryl-sulfur interaction by placing a methionine residue diagonal to an aromatic ring on the same face of a beta-hairpin, which places the methionine side chain in close proximity to the aryl side chain. The methionine (Met)-aryl interaction was compared with an equivalent hydrophobic and cation-pi interaction in the context of the beta-hairpin. The interaction between phenylalanine (Phe), tryptophan (Trp), or cyclohexylalanine (Cha) and Met stabilized the beta-hairpin by -0.3 to -0.5 kcal mole(-1), as determined by double-mutant cycles. The peptides were subjected to thermal denaturations that suggest a hydrophobic driving force for the interactions between Met and Trp or Cha. The observed interaction of Met or norleucine (Nle) with Trp or Cha are quite similar, implying a hydrophobic driving force for the Met-pi interaction. However, the thermodynamic data suggest that there may be some differences between the interaction of Met with Trp and Phe and that there may be a small thermodynamic component to the Met...Phe interaction.

Amides↗