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PubMedDate not supplied

[Study of interactions between anti-retroviral agents and concomitant drugs].

UNLABELLED: Clinical efficacy of antiretroviral treatment requires drugs to maintain a plasma concentration over MIC90. One of the facts that can prevent drugs from reaching and maintaining required concentrations are pharmacological drug interactions. OBJECTIVE: The aim of this study is to identify the main interactions between antiretroviral medicines and concomitant treatment in a HIV positive group of patients in a general hospital. Clinical significance and the way to avoid or minimize these interactions is indicated. MATERIAL AND METHODS: from the computerized records of dispensation the Pharmacy Service and from the reports of the internal medicine deparment, demographic and epidemiological data were collected, as well as previous and current antirretroviral treatment and concomitant treatment. Interactions were identified after the Guide of Pharmacological Interactions for HIV. RESULTS AND DISCUSSION: the number of patients analysed was 189. Of these, in 153 (81%) 466 interactions were detected (2.46 interactions/patient). The classification according to its clinical significance was the following: no clinical relevancy (52.8%), potential interactions (45.5%) and co-administered drugs contraindicated or not recommended (1.7%, nA masculine = 8). This last one corresponded to the following medications: efavirenz/terfenadine, nelfinavir/terfenadine, ritonavir/diazepam and zidovudine/ribavirin (five cases). Zidovudine was the one with the highest number of interactions detected (129 patients) followed by indinavir while the co-administered drug was cotrimoxazole (93 cases). The remaining interactions detected for all the anti-retrovirals are shown. We conclude that thought the number of drug interactions is high, the number of contraindicated or not recommended ones is low. Finally the therapeutic alternatives for those interactions detected that show the highest clinical relevancy are described. General procedures to identify and prevent them are also described. CONCLUSION: We conclude that though the number of drug interactions is high, the number of contraindicated or not recommended ones is low. Finally the therapeutic alternatives for those interactions detected that show the highest clinical relevancy are described. General procedures to identify and prevent them are also described.

Adult↗
PubMed2026

Library-based, multiplexed strategy for mapping protein interaction networks via crosslinking.

BACKGROUND: Protein-protein interactions are fundamental to cellular function, yet resolving their interaction interfaces and dynamic behaviors in native biological contexts remains challenging, particularly for weak or transient interactions. Crosslinking strategies based on noncanonical amino acids offer an effective means to capture such interactions; however, traditional single-site incorporation provides limited coverage and may overlook critical interaction hotspots. RESULTS: By employing a mutagenesis library, multiple interaction partners and cross-linking sites of a target protein can be simultaneously screened in a single experiment, without prior knowledge of its precise structural or functional features, enabling effective and unbiased analysis of its interaction network. In this study, we constructed an amber codon-scanning mutagenesis library of PSMD10, facilitating independent incorporation of the photocrosslinking ncAA p-azido-phenylalanine at multiple distinct residues. This approach allowed us to systematically interrogate and precisely map potential interaction regions across the protein surface. Coupled with crosslinking mass spectrometry, we identified multiple residues involved in intermolecular interactions, as well as previously unreported interaction partners, including T2FA, TBA1C, and ATRIP. CONCLUSIONS: These findings expand our understanding of PSMD10-associated proteasome interactome, demonstrate a multiplexed strategy for in situ mapping of protein interaction interfaces with broad coverage, and offer a valuable platform for developing therapeutics that target protein-protein interactions.

Protein Interaction Mapping↗
PubMed1997

Effects of genotype-by-sex interaction on quantitative trait linkage analysis.

Genotype-by-sex (G x S) interaction refers to the interaction of autosomal genes with male or female physiological "environments." G x S interaction has been demonstrated in quantitative genetic analysis of a variety of traits including serum lipid concentrations and anthropometrics, and the importance of considering sex-specific major gene effects in segregation analyses also has been demonstrated. The goal of this study was to examine the effects of G x S interaction on the power to detect linkage. Trait Q3 in GAW10 Problem 2 was analyzed because it was modeled to have G x S interaction at the major gene locus MG3. All 200 nuclear family and 200 extended pedigree replicates were first screened for the presence of G x S interaction in Q3 using a quantitative genetic method. More than half of both the nuclear family and extended pedigree replicates evidenced significant G x S interaction. Variance components linkage analysis was then performed using all markers on GAW10 chromosome 4 in all 200 nuclear family and 200 extended pedigree replicates. A peak lod score of 1.92 at the correct chromosomal location was obtained using the extended pedigree data and incorporating G x S interaction effects. Not incorporating G x S interaction lowered the peak lod score from the analyses of the extended pedigrees to 1.53. Incorporation of G x S interaction effects also increased the power to detect linkage in the nuclear family replicates, although the nuclear families had considerably less power than the extended pedigrees to detect linkage, whether or not G x S interaction was modeled. Incorporation of G x S interaction effects can increase the power to detect linkage, even when the G x S interaction effects are modest.

Environment↗
PubMed2006

Direct versus mediated through-space magnetic interactions: A first principles, bottom-up reinvestigation of the magnetism of the pyridyl-verdazyl:hydroquinone molecular co-crystal.

The mechanism of the magnetic interaction in the pyridyl-verdazyl radical:hydroquinone (pyvd:hq) molecular co-crystal is important as it has been suggested to originate by a unique "mediated through-space" magnetic interaction. This interaction was proposed to magnetically connect two nonadjacent pyridyl-verdazyl radicals within a pi stack, where adjacent radicals pile up in a head-over-tail orientation. The connection is made through a third radical sitting between the previous two mediated radicals. Given the relevance of this proposal, we decided to reinvestigate the magnetic properties of this co-crystal by using our recently proposed first-principles "bottom-up" procedure. Based on B3LYP/6-31+G(d) and CASSCF(6,6)/6-31+G(d) calculations (the results of which are identical to those provided by CASSCF(10,10)/6-31+G(d) calculations), we have computed the microscopic J(AB) values for all direct through-space magnetic interactions between nearby pyridyl-verdazyl radicals. The magnetic interactions give rise to two dominant values of similar strength: -56 and -54 cm(-1) at the B3LYP level, which are calculated as -38 and -31 cm(-1) at the CASSCF(6,6) and CAS(10,10) levels (all other interactions being smaller than |1| cm(-1)). The dominant interactions correspond to the direct through-space interaction between two adjacent radicals of a pi stack. The crystal also exhibits a radical-mediated through-space interaction of -0.31 cm(-1) between two nonadjacent radicals of a pi stack. The direct through-space magnetic interactions are two orders of magnitude larger than the mediated through-space interaction. Thus, first-principles calculations do not support a mediated through-space mechanism to explain the magnetism of the pyvd:hq co-crystal. The magnetic topology generated by the two dominant antiferromagnetic interactions in the pyvd:hq co-crystal consists of one-dimensional (1D) alternating chains (interacting very weakly along the b and c axes). By using this topology, the computed macroscopic magnetic susceptibility curve reproduces the experimental one properly. This first-principles bottom-up description of the magnetism in the pyvd:hq co-crystal differs in some fundamental aspects from that previously proposed in the literature.

Journal Article↗
PubMed1993

Ionic interactions in the coiled-coil domain of laminin determine the specificity of chain assembly.

Laminins are a family of large (800 to 900 kDa) multidomain glycoproteins specifically found in basement membranes. They consist of one heavy A chain and two light chains B1 and B2, and several tissue-specific laminin isoforms exist. Chain assembly is mediated through the formation of a rod-like triple-stranded alpha-helical coiled-coil domain about 75 nm long. The interacting edges of the chains are mostly formed by hydrophobic residues in positions a and d of an (abcdefg)n heptad sequence repeat and by a distinct pattern of charged residues in positions e and g. Here, we have analyzed the sequences of known laminin chains in an effort to relate them to interaction potential. Initially, those sequences localized in the long arm were arranged in an optimum heptad-repeating scheme. The interacting edges between chains were then analyzed for interchain hydrophobic and ionic interactions. The short heptad blocks were allowed to shift axially with respect to each other to maximize the number of interactions. The number of hydrophobic interactions was very high and similar for all chain combinations, but especially so for homodimers. As these were not observed experimentally, it seems that hydrophobic interactions probably represent only a prerequisite for coiled-coil formation. The number of ionic interactions, however, directly resembles the interaction potential observed in in vitro experiments. In particular, the number of interchain ionic interactions is high for parallel heterodimer configurations of A and B chains, but low for homodimer arrangements. When the laminin isoform chains, rat s-laminin (B1s) and human merosin (Am), are included in the analysis, they show rather low numbers of mutual interactions but high ionic interaction potentials between them and distinct mouse laminin chains are predicted. For mouse laminin the analysis was extended to a full three-stranded coiled-coil structure. The highest number of interchain ionic interactions occurs for an anti-clockwise chain arrangement of A-->B1-->B2 when viewed from the N terminus. None of the laminin chains appears to be designed for the formation of homodimers, although such conformations are frequently found in other alpha-fibrous proteins.

Amino Acid Sequence↗
PubMed2001

C-H...pi-interactions in proteins.

A non-redundant set of 1154 protein structures from the Protein Data Bank was examined with respect to close interactions between C-H-donor and pi-acceptor groups. A total of 31,087 interactions were found to satisfy our selection criteria. Their geometric parameters suggest that these interactions can be classified as weak hydrogen bonds.A set of 12 interaction classes were defined based on the division of the donors into three groups and the acceptors into four groups. These classes were examined separately, and the respective interactions described in detail in each class. Most prominent were interactions between aliphatic C-H donors and aromatic pi-acceptors and interactions between aromatic C-H donors and aromatic pi-acceptors. About three-quarters of the Trp-rings, half of all Phe and Tyr-rings and a quarter of all His-rings were found to be involved as acceptors in C-H...pi-interactions. On the donor side, a preference for aromatic C-H groups was observed, but also for the aliphatic side-chains of the long, extended amino acid residues Lys, Arg and Met, and the Pro ring. The average distance between the C-donor and the center-of-mass of the pi-acceptor was observed to be significantly longer in the 174 protein structures determined at >2.5 A resolution. Also, the distribution is significantly wider. This resolution dependence suggests that the force fields commonly used for the refinement of protein structures may not be adequate. C-H...pi-interactions involving aromatic groups either as donor or as acceptor groups are found mostly in the interior of the protein. The more hydrophilic the participating groups are, the closer to the surface are the interactions located. About 40 % of all C-H...pi-interactions occur between amino acid residue side-chains that are separated by nine or less residues in sequence. Dependent on the interaction class, different preferences for secondary structure, residue type and side-chain conformation were observed. It is likely that the C-H...pi-interactions contribute significantly to the overall stability of a protein.

Databases, Factual↗
PubMed1989

Anatomical bases of binaural interaction in auditory brain-stem responses from guinea pig.

There is a non-linear interaction of binaural stimulation on auditory brain-stem potentials in both human and animals. The interaction takes the form of the binaurally evoked ABR being of smaller amplitude than the sum of the monaurally evoked ABRs. In the guinea pig this interaction occurs at the time of components P4, N4 and P5. In order to investigate the generator sites of binaural interaction in the ABR, various lesions were made in the brain-stem auditory system in 29 guinea pigs. The effects of those lesions on binaural interaction were as follows: (1) unilateral lesion of lateral lemniscus or bilateral lesions of the inferior colliculi had no significant effect on binaural interaction; (2) transection of the lateral lemnisci bilaterally was associated with a loss of the component of binaural interaction associated in time with N4; (3) a lesion just lateral to the lateral superior olivary complex resulted in an attenuation of the component of binaural interaction associated in time with P4; (4) complete section of the decussating fibers of the trapezoid body or a complete unilateral lesion of the superior olivary complex led to a loss of all components of binaural interaction. These results suggest that binaural interaction in the guinea pig ABR requires the integrity of several distinct portions of the brain-stem auditory pathway, i.e., both lateral lemnisci are required for the interaction occurring at the time of N4; the brain-stem just lateral to the lateral superior olive participates in the interaction at the time of P4. The trapezoid body and superior olivary nucleus are required for binaural interaction at P4, N4 and P5.

Animals↗
PubMed2004

Interparticle interactions in concentrate water-oil emulsions.

The present investigation is based on the description of electrostatic interaction in concentrated disperse systems proposed 45 years ago by Albers and Overbeek. Starting from their model, we developed a stability theory of concentrated Brownian W/O emulsions in which nondeformed droplets undergo electrostatic and Van der Waals interactions. While the droplets in dilute emulsion may be described by pair interaction, in dense emulsions, every droplet is closely surrounded by other droplets, and when two of them come together, not only the energy of their pair interaction, but also their interaction with surrounding droplets change. Unlike in dilute emulsion, for which the reference energy of the pair is the energy at infinity (taken equal to zero), in concentrate emulsion, the reference energy is not zero but is the energy of interaction with averaged ensemble of nearest droplets. The larger the volume fraction, the higher the reference energy and, thus, the lower the energy barrier between two coagulating droplets, which enhances the coagulation. In dense packing of drops, the energy of interaction and the reference energy coincide, therefore, the height of energy barrier vanishes. In contrast with dense emulsion, at medium volume fraction, when two coagulating droplets interact only with a few nearest neighbors, our analysis shows that the energy barrier may also increase, which extends thus the domain of stability. Because in W/O emulsion, the thickness of the electric double layer is of the same order or larger than the size of droplets, the electrostatic energy was calculated with a correction factor beta that accounts for the deviation of double layers from sphericity. A more complete van der Waals interaction with account of screening of interaction by electrolyte has been used. Both factors promote the decrease of energy barrier between coagulating droplets and enhance the coagulation. Our model introduces two critical volume fractions. The first one, phi(c1), is the volume fraction depending on the characteristics of system (size of drops, thickness of double layer, surface potential, dielectric permittivity of medium) that limits the validity of the pair interaction model. The second one, phi(c2), is a volume fraction that limits the applicability of the simplified model of interaction of three or more double layers. By comparing the energies of barrier height and of Brownian motion, a critical volume fraction phi(c3) is defined, which determines the starting point of rapid coagulation. Finally, the influence of drop interaction on gravitational coagulation is also briefly presented. It is shown that the probability of coagulation between fixed in space and sedimenting droplets is larger than with only Brownian coagulation. Unlike at free sedimentation of two identical drops, the gravitation cannot accelerate their aggregation. The surface potential, which leads to the equilibration of surface forces, gravitational and Archimedes forces for a given volume fraction, is then obtained.

Journal Article↗
PubMed2006

Clinically important drug-disease interactions and their prevalence in older adults.

BACKGROUND: Older adults may have decreased homeostatic reserve, have multiple chronic diseases, and take multiple medications. Therefore, they are at risk for adverse outcomes after receiving a drug that exacerbates a chronic disease. OBJECTIVES: The aims of this study were to compile a list of clinically important drug-disease interactions in older adults, obtain the consensus of a multidisciplinary panel of geriatric health care professionals on these interactions, and determine the prevalence of these interactions in a sample of outpatients. METHODS: This analysis included a 2-round modified Delphi survey and cross-sectional study. Possible drug-disease interactions in patients aged > or =65 years were identified through a search of the English-language literature indexed on MEDLINE and International Pharmaceutical Abstracts (1966-July 2004) using terms that included drug-disease interaction, medication errors, and inappropriate prescribing. Nine health care professionals with expertise in geriatrics (2 geriatricians, 7 geriatric clinical pharmacist specialists) were selected based on specialty training and continuing clinical work in geriatrics, academic appointments, and geographic location. The panel rated the importance of the potential drug-disease interactions using a 5-point Likert scale (from 1 = definitely not serious to 5 = definitely serious). Consensus on a drug-disease interaction was defined as a lower bound of the 95% CI > or =4.0. The prevalence of drug-disease interactions was determined by applying the consensus criteria to a convenience sample of frail older veterans at hospital discharge who were enrolled in a health services intervention trial. RESULTS: The panel reached consensus on 28 individual drug-disease interactions involving 14 diseases or conditions. Overall, 205 (15.3%) of the 1340 veterans in the sample had > or =1 drug-disease interaction. The 2 most common drug-disease interactions were use of first-generation calcium channel blockers in patients with congestive heart failure and use of aspirin in patients with peptic ulcer disease (both, 3.7%). CONCLUSIONS: A survey of multidisciplinary geriatric health care professionals resulted in a concise consensus list of clinically important drug-disease interactions in older adults. Further research is needed to examine the impact of these drug-disease interactions on health outcomes and their applicability as national measures for the prevention of drug-related problems.

Aged↗
PubMed2006

Intermolecular interaction between hexafluorobenzene and benzene: Ab initio calculations including CCSD(T) level electron correlation correction.

The intermolecular interaction energy of hexafluorobenzene-benzene has been calculated with the ARS-E model (a model chemistry for the evaluation of the intermolecular interaction energy between aromatic systems using extrapolation), which was formerly called the AIMI model. The CCSD(T) interaction energy at the basis-set limit has been estimated from the MP2 interaction energy at the basis-set limit and the CCSD(T) correction term obtained using a medium-sized basis set. The slipped-parallel (Cs) complex has the largest (most negative) interaction energy (-5.38 kcal/mol). The sandwich (C6v) complex is slightly less stable (-5.07 kcal/mol). The interaction energies of two T-shaped (C2v) complexes are very small (-1.74 and -0.88 kcal/mol). The calculated interaction energy of the slipped-parallel complex is about twice as large as that of the benzene dimer. The dispersion interaction is found to be the major source of attraction in the complex, although electrostatic interaction also contributes to the attraction. The dispersion interaction increases the relative stability of the slipped-parallel benzene dimer and the hexafluorobenzene-benzene complex compared to T-shaped ones. The electrostatic interaction is repulsive in the slipped-parallel benzene dimer, whereas it stabilizes the slipped-parallel hexafluorobenzene-benzene complex. Both electrostatic and dispersion interactions stabilize the slipped-parallel hexafluorobenzene-benzene complex, which is the cause of the preference of the slipped-parallel orientation and the larger interaction energy of the complex compared to the benzene dimer.

Benzene↗
PubMed2002

UCS15A, a novel small molecule, SH3 domain-mediated protein-protein interaction blocking drug.

Protein-protein interactions play critical regulatory roles in mediating signal transduction. Previous studies have identified an unconventional, small-molecule, Src signal transduction inhibitor, UCS15A. UCS15A differed from conventional Src-inhibitors in that it did not alter the levels or the tyrosine kinase activity of Src. Our studies suggested that UCS15A exerted its Src-inhibitory effects by a novel mechanism that involved the disruption of protein-protein interactions mediated by Src. In the present study we have examined the ability of UCS15A to disrupt the interaction of Src-SH3 with Sam68, both in vivo and in vitro. This ability of UCS15A was not restricted to Src-SH3 mediated protein-protein interactions, since the drug was capable of disrupting the in vivo interactions of Sam68 with other SH3 domain containing proteins such as Grb2 and PLCgamma. In addition, UCS15A was capable of disrupting other typical SH3-mediated protein-protein interactions such as Grb2-Sos1, cortactin-ZO1, as well as atypical SH3-mediated protein-protein interactions such as Grb2-Gab1. However, UCS15A was unable to disrupt the non-SH3-mediated protein-protein interactions of beta-catenin, with E-cadherin and alpha-catenin. In addition, UCS15A had no effect on the SH2-mediated interaction between Grb2 and activated Epidermal Growth Factor receptor. Thus, the ability of UCS15A, to disrupt protein-protein interactions appeared to be restricted to SH3-mediated protein-protein interactions. In this regard, UCS15A represents the first example of a non-peptide, small molecule agent capable of disrupting SH3-mediated protein-protein interactions. In vitro analyses suggested that UCS15A did not bind to the SH3 domain itself but rather may interact directly with the target proline-rich domains.

Adaptor Proteins, Signal Transducing↗
PubMed1995

Distinct modes of interaction of SHC and insulin receptor substrate-1 with the insulin receptor NPEY region via non-SH2 domains.

Insulin receptor substrate 1 (IRS-1) and src homology and collagen protein (SHC) are signaling proteins which are rapidly phosphorylated on tyrosines after insulin receptor (IR) activation. We have recently shown that both SHC and IRS-1 interact with the tyrosine-phosphorylated NPEY motif of the IR and insulin-like growth factor I receptor via non-SH2 domains (Gustafson, T. A., He, W., Craparo, A., Schaub, C. D., and O'Neill, T. J. (1995) Mol. Cell. Biol. 15, 2500-2508; O'Neill, T. J., Craparo, A., and Gustafson, T. A. (1994) Mol. Cell. Biol. 14, 6433-6442; Craparo, A., O'Neill, T. J., and Gustafson, T. A. (1995) J. Biol. Chem. 270, 15639-15643). In this study we characterize these interactions by examining the effects of 18 amino acid substitutions within and around the IR NPEY motif upon interaction with SHC and IRS-1. We confirm that Tyr-960 within the NPEY motif of the IR is essential for both IRS-1 and SHC interaction and that Asn-957 and Pro-958 are essential for IRS-1 interaction and important but not critical for SHC interaction. Additional mutations surrounding the NPEY motif revealed completely distinct patterns of interaction for SHC and IRS-1. Specifically, mutation of Leu-952 or Tyr-953 (at positions -7 and -8 from Tyr-960) markedly reduced IRS-1 interaction but had no effect upon SHC interaction. Likewise, mutation of Ala-963 (+3) reduced IRS-1 but not SHC interaction. Conversely, substitution of Leu-961 (+1) with either Ala or Arg reduced SHC interaction by 70 and 90%, respectively, yet had no effect upon interaction with IRS-1. Our data show that the sequences within and surrounding the NPEY contribute differentially to either SHC or IRS-1 recognition. Our findings suggest mechanisms by which the differential interaction of known receptors with IRS-1 and SHC may be mediated.

Amino Acid Sequence↗
PubMed2000

Evidence for simultaneous protein interactions between human Rad51 paralogs.

In yeast, the Rad51-related proteins include Rad55 and Rad57, which form a heterodimer that interacts with Rad51. Five human Rad51 paralogs have been identified (XRCC2, XRCC3, Rad51B/Rad51L1, Rad51C/Rad51L2, and Rad51D/Rad51L3), and each interacts with one or more of the others. Previously we reported that HsRad51 interacts with XRCC3, and Rad51C interacts with XRCC3, Rad51B, and HsRad51. Here we report that in the yeast two-hybrid system, Rad51D interacts with XRCC2 and Rad51C. No other interactions, including self-interactions, were found, indicating that the observed interactions are specific. The yeast Rad51 interacts with human Rad51 and XRCC3, suggesting Rad51 conservation since the human yeast divergence. Data from yeast three-hybrid experiments indicate that a number of the pairs of interactions between human Rad51 paralogs can occur simultaneously. For example, Rad51B expression enhances the binding of Rad51C to XRCC3 and to HsRad51D, and Rad51C expression allows the indirect interaction of Rad51B with Rad51D. Experiments using 6xHis-tagged proteins in the baculovirus system confirm several of our yeast results, including Rad51B interaction with Rad51D only when Rad51C is simultaneously expressed and Rad51C interaction with XRCC2 only when Rad51D is present. These results suggest that these proteins may participate in one complex or multiple smaller ones.

Baculoviridae↗
PubMed2000

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways.

MOTIVATION: Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein interactions in a cell and will eventually create more recorded biological information than the Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information. RESULTS: We have defined a complete data specification in ASN.1 that can describe information about biomolecular interactions, complexes and pathways. Our group is using this data specification in our database, the Biomolecular Interaction Network Database (BIND). An interaction record is based on the interaction between two objects. An object can be a protein, DNA, RNA, ligand, molecular complex or an interaction. Interaction description encompasses cellular location, experimental conditions used to observe the interaction, conserved sequence, molecular location, chemical action, kinetics, thermodynamics, and chemical state. Molecular complexes are defined as collections of more than two interactions that form a complex, with extra descriptive information such as complex topology. Pathways are defined as collections of more than two interactions that form a pathway, with additional descriptive information such as cell cycle stage. A request for proposal of a human readable flat-file format that mirrors the BIND data specification is also tendered for interested parties. AVAILABILITY: The ASN.1 data specification for biomolecular interaction, molecular complex and pathway data is available at ftp://bioinfo.mshri.on.ca/pub/BIND/Spec/bind.asn. An interactive browser for this document is available through our homepage at http://bioinfo.mshri.on.ca/BIND/asn-browser/.

DNA↗
PubMed2003

Whole-proteome interaction mining.

MOTIVATION: A major post-genomic scientific and technological pursuit is to describe the functions performed by the proteins encoded by the genome. One strategy is to first identify the protein-protein interactions in a proteome, then determine pathways and overall structure relating these interactions, and finally to statistically infer functional roles of individual proteins. Although huge amounts of genomic data are at hand, current experimental protein interaction assays must overcome technical problems to scale-up for high-throughput analysis. In the meantime, bioinformatics approaches may help bridge the information gap required for inference of protein function. In this paper, a previously described data mining approach to prediction of protein-protein interactions (Bock and Gough, 2001, Bioinformatics, 17, 455-460) is extended to interaction mining on a proteome-wide scale. An algorithm (the phylogenetic bootstrap) is introduced, which suggests traversal of a phenogram, interleaving rounds of computation and experiment, to develop a knowledge base of protein interactions in genetically-similar organisms. RESULTS: The interaction mining approach was demonstrated by building a learning system based on 1,039 experimentally validated protein-protein interactions in the human gastric bacterium Helicobacter pylori. An estimate of the generalization performance of the classifier was derived from 10-fold cross-validation, which indicated expected upper bounds on precision of 80% and sensitivity of 69% when applied to related organisms. One such organism is the enteric pathogen Campylobacter jejuni, in which comprehensive machine learning prediction of all possible pairwise protein-protein interactions was performed. The resulting network of interactions shares an average protein connectivity characteristic in common with previous investigations reported in the literature, offering strong evidence supporting the biological feasibility of the hypothesized map. For inferences about complete proteomes in which the number of pairwise non-interactions is expected to be much larger than the number of actual interactions, we anticipate that the sensitivity will remain the same but precision may decrease. We present specific biological examples of two subnetworks of protein-protein interactions in C. jejuni resulting from the application of this approach, including elements of a two-component signal transduction systems for thermoregulation, and a ferritin uptake network.

Algorithms↗
PubMed2003

Time-dependent interactions of oxidant-sensitive fluoroprobes with inhibitors of cellular metabolism.

SUMMARY: We tested three oxidant sensitive fluoroprobes (dihydrorhodamine [DHR], 2',7'-dichlorodihydrofluorescein [H(2)DCF], and dihydroethidium [DHE]) for interactions with three inhibitors of mitochondrial electron transport. DHR, H(2)DCF, and DHE produced large time-dependent increases in fluorescence in a cell-free medium that contained either of the site III inhibitors antimycin (A) and 2-heptyl-4-hydroxy-quinoline-N-oxide but minimal increases in medium that contained another site III inhibitor, myxothiazol (Mx). The interactions between A and each of the fluoroprobes occurred at concentrations of agent/probe that are frequently used in experiments designed to investigate cellular oxidant production. To define more effectively the nature of these agent/probe interactions, we determined the oxygen dependence of the interactions between A and each probe. The A/H(2)DCF and A/DHR interactions either were highly oxygen-dependent or exhibited a small degree of oxygen dependence, respectively, whereas the A/DHE interaction was oxygen-independent. Finally, we determined multiple ways to reduce the impact of the agent/probe interaction on data acquisition. The addition of either fetal bovine serum (10%) or albumin (5%) to the media abolished the A/DHR and A/H(2)DCF interactions. Shifting the excitation wavelength of DHE (from 470 to 530 nm) reduced measurement of the A/DHE interaction while preserving measurement of the intracellular signal. Collectively, these results emphasize the importance of testing for interactions between agents and probes, because these interactions can interfere with the accurate interpretation of experimental results. In addition, the methods presented for circumventing these interactions may be applicable to other experiments in which agent/probe interactions are an obstacle to accurate interpretation of the experimental results.

Antimycin A↗
PubMedDate not supplied

Frequency of spousal interaction and 3-year progression of carotid artery intima medial thickness: the Pittsburgh Healthy Heart Project.

OBJECTIVE: We employed Ecological Momentary Assessment (EMA) real-time recording in the natural setting to determine whether spousal interaction frequency predicts 3-year progression of carotid artery intima medial thickening (IMT). METHODS: Participants were 250 healthy, older adults (M age = 61, 48% female) who, at baseline, underwent 6 days of ambulatory monitoring using electronic diaries to collect data on mood, activity, and posture, as well as current or recent (past 10 minutes) social interactions. Participants also underwent ultrasound imaging of the carotid arteries at baseline and 3-year follow-up. Spousal interaction frequency was computed as the sum of total interactions with only the spouse during the 6 days of monitoring. RESULTS: Spousal interaction frequency did not predict IMT change in the sample as a whole (p = .87). However, a sex by spousal interaction by marital adjustment interaction (p = .02) indicated that more frequent spousal interaction was associated with less IMT progression among men with better marital adjustment (p = .03). In contrast, frequent spousal interaction predicted greater IMT progression among women with better martial adjustment (p < .01). This effect lost significance when women's total social interactions (sum of all interactions) were included in the model. Total social interaction frequency was an independent predictor of IMT among women but not men. CONCLUSIONS: These findings extend those of previous research by suggesting that frequent spousal interactions may be associated with long-term cardiovascular health among happily married older men and demonstrate how sampling daily experience may enhance our understanding of the possible health benefits of marriage.

Aged↗
PubMed1997

Analysis of hepatitis C virus core protein interaction domains.

Hepatitis C virus (HCV) core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. As the single capsid protein, core should be capable of multimerization but attempts to produce virus-like particles following expression of HCV structural proteins have not been successful. In this study, we have analysed the interaction capacity of full-length and truncated HCV core using the yeast two-hybrid system. Full-length core containing or lacking the translocation signal for the E1 glycoprotein did not interact with full-length or truncated core proteins. Truncation to the N-terminal 122 aa revealed an interaction domain which was mapped to the tryptophan-rich sequence from aa 82-102 and was termed the main homotypic interaction domain. The C-terminal hydrophobic fragment of core (aa 122-172) was incapable of interacting with itself but interacted with the main homotypic interaction domain in trans (the weak heterotypic interaction domain). Core proteins truncated at their N and C termini (aa 46-102) were trans-activating when fused to the DNA-binding domain of GAL4. Based on our results, we suggest that the C-terminal segment may interact in cis with the main homotypic interaction domain and thereby prevent multimerization. Core-core interaction was also observed for in vitro-translated proteins bound to truncated immobilized core 102. However, interaction was less specific in this system suggesting that protein interaction and possibly conformational alteration of core may be dependent on the experimental system.

Hepacivirus↗