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PubMed1997

Surface Element Integration: A Novel Technique for Evaluation of DLVO Interaction between a Particle and a Flat Plate

A novel method, the surface element integration (SEI), is developed to determine the van der Waals and electrostatic double layer interactions between a particle and an infinite flat plate from the corresponding interactions per unit area between two infinite flat plates. Comparison with the Hamaker expression for nonretarded van der Waals interaction reveals that the new technique gives the exact interaction energy between a spherical particle and a flat plate. Available analytical expressions for the electrostatic double layer interaction energy between two infinite flat plates, based on the linearized Poisson-Boltzmann equation, are used in SEI to obtain the sphere-flat plate interaction energy. These sphere-flat plate interaction energies determined using SEI are compared with the corresponding interaction energies obtained from a detailed numerical solution of the Poisson-Boltzmann equation based on finite element analysis. The comparisons reveal that SEI scales the flat plate interaction to the corresponding sphere-flat plate geometry exactly, while the scaling based on the conventional Derjaguin approximation technique grossly overpredicts the interaction energy for small particles and low electrolyte concentrations. Copyright 1997 Academic Press. Copyright 1997Academic Press

Journal Article↗

PubMed2003

Detection of regulatory circuits by integrating the cellular networks of protein-protein interactions and transcription regulation.

The post-genomic era is marked by huge amounts of data generated by large-scale functional genomic and proteomic experiments. A major challenge is to integrate the various types of genome-scale information in order to reveal the intra- and inter- relationships between genes and proteins that constitute a living cell. Here we present a novel application of classical graph algorithms to integrate the cellular networks of protein-protein interactions and transcription regulation. We demonstrate how integration of these two networks enables the discovery of simple as well as complex regulatory circuits that involve both protein-protein and protein-DNA interactions. These circuits may serve for positive or negative feedback mechanisms. By applying our approach to data from the yeast Saccharomyces cerevisiae, we were able to identify known simple and complex regulatory circuits and to discover many putative circuits, whose biological relevance has been assessed using various types of experimental data. The newly identified relations provide new insight into the processes that take place in the cell, insight that could not be gained by analyzing each type of data independently. The computational scheme that we propose may be used to integrate additional functional genomic and proteomic data and to reveal other types of relations, in yeast as well as in higher organisms.

DNA, Fungal↗

PubMed2005

Uncharted ground: patterns of professional interaction among complementary/alternative and biomedical practitioners in integrative health care settings.

The development of "integrative health care" (IHC) settings combining various aspects of Western biomedicine and complementary/alternative medicine (CAM) is a relatively recent phenomenon among biomedical and CAM professions. While IHC is recognised internationally and occurs in many different contexts (e.g. clinic or hospital), patterns of interaction between biomedical and CAM practitioners, and the nature of IHC settings, are largely unknown. This paper presents findings from a research study of two newly established IHC settings in Canada. The main research question was: how are biomedical and CAM practitioners integrating or not integrating with each other at the level of professional interaction in IHC settings? Using a case study design, in-depth interviews were conducted with 13 biomedical and eight CAM practitioners during 2002-2003, and ethnographic observation and document analysis was conducted at each site. Drawing from closure theory of the professions, comparative analysis of the sites revealed that biomedical practitioners enact patterns of exclusionary and demarcationary closure, in addition to the use of "esoteric knowledge", by: (a) dominating patient charting, referrals and diagnostic tests; (b) regulating CAM practitioners to a specific "sphere of competence"; (c) appropriating certain CAM techniques from less powerful CAM professions; and (d) using biomedical language as the primary mode of communication. CAM practitioners, in turn, perform usurpationary closure strategies, by: (a) employing their own "esoteric knowledge" in relation to biomedicine and other CAM professions; (b) appropriating biomedical language and terminology; (c) increasing their professional status by working with biomedicine; and (d) referring among CAM practitioners to increase patient flow. The findings suggest that when attempts are made to integrate biomedicine and CAM, dominant biomedical patterns of professional interaction continue to exist. Despite continued patterns of social closure, biomedical and CAM practitioners continue to provide a certain form of integrative care that may be of benefit to patients, albeit not as integrative as current models of integration would prefer.

Anthropology, Cultural↗

PubMed2004

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.

Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of interactions that may shed light on basic cellular mechanisms. Previous studies have analyzed aspects of this network, concentrating on either transcription-regulation or protein-protein interactions. Here we search for composite network motifs: characteristic network patterns consisting of both transcription-regulation and protein-protein interactions that recur significantly more often than in random networks. To this end we developed algorithms for detecting motifs in networks with two or more types of interactions and applied them to an integrated data set of protein-protein interactions and transcription regulation in Saccharomyces cerevisiae. We found a two-protein mixed-feedback loop motif, five types of three-protein motifs exhibiting coregulation and complex formation, and many motifs involving four proteins. Virtually all four-protein motifs consisted of combinations of smaller motifs. This study presents a basic framework for detecting the building blocks of networks with multiple types of interactions.

Amino Acid Motifs↗

PubMed2003

Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.

Bioactive compounds can be valuable research tools and drug leads, but it is often difficult to identify their mechanism of action or cellular target. Here we investigate the potential for integration of chemical-genetic and genetic interaction data to reveal information about the pathways and targets of inhibitory compounds. Taking advantage of the existing complete set of yeast haploid deletion mutants, we generated drug-hypersensitivity (chemical-genetic) profiles for 12 compounds. In addition to a set of compound-specific interactions, the chemical-genetic profiles identified a large group of genes required for multidrug resistance. In particular, yeast mutants lacking a functional vacuolar H(+)-ATPase show multidrug sensitivity, a phenomenon that may be conserved in mammalian cells. By filtering chemical-genetic profiles for the multidrug-resistant genes and then clustering the compound-specific profiles with a compendium of large-scale genetic interaction profiles, we were able to identify target pathways or proteins. This method thus provides a powerful means for inferring mechanism of action.

Biotechnology↗

PubMed2004

Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model.

A new efficient method is developed for solving integral equations based on the reference interaction site model (RISM) of molecular liquids. The method proposes the expansion of site-site correlation functions into the wavelet series and further calculations of the approximating coefficients. To solve the integral equations we have applied the hybrid scheme in which the coarse part of the solution is calculated by wavelets with the use of the Newton-Raphson procedure, while the fine part is evaluated by the direct iterations. The Coifman 2 basis set is employed for the wavelet treatment of the coarse solution. This wavelet basis set provides compact and accurate approximation of site-site correlation functions so that the number of basis functions and the amplitude of the fine part of solution decrease sufficiently with respect to those obtained by the conventional scheme. The efficiency of the method is tested by calculations of SPC/E model of water. The results indicated that the total CPU time to obtain solution by the proposed procedure reduces to 20% of that required for the conventional hybrid method.

Journal Article↗

PubMed2003

Visual context integration is not fully developed in 4-year-old children.

Long-range horizontal interactions supporting contour integration were found to be weaker in children than in adults (Kovács et al, 1999 Proceedings of the National Academy of Sciences of the USA 96 12204-12209). In the present study, integration on a larger scale, between a target and its context was investigated. Contextual modulation of the percept of a local target can be directly measured in the case of geometric illusions. We compared the magnitude of a size contrast illusion (Ebbinghaus illusion or Titchener circles) in children and adults. 4-year-old children and adults performed 2AFC size comparisons between two target disks in the classical Ebbinghaus illusion display and in two other modified versions. We found that the magnitude of the illusion effect was significantly smaller in children than in adults. Our interpretation is that context integration is not fully developed in 4-year-old children. Closer-to-veridical-size estimations by children demonstrate that the perception of the local target is less affected by stimulus context in their case. We suggest that immature cortical connectivity is behind the reduced contextual sensitivity in children.

Adult↗

PubMed1991

Direct effects of ionizing radiation on integral membrane proteins. Noncovalent energy transfer requires specific interpeptide interactions.

The 12 transmembrane alpha helices (TMHs) of human erythrocyte glucose transporter were individually cut by pepsin digestion as membrane-bound 2.5-3.5-kDa peptide fragments. Radiation-induced chemical degradation of these fragments showed an average target size of 34 kDa. This is 10-12 x larger than the average size of an individual TMH, demonstrating that a significant energy transfer occurs among these TMHs in the absence of covalent linkage. Heating this TMH preparation at 100 degrees C for 15 min reduced the target size to 5 kDa or less, suggesting that the noncovalent energy transfer requires specific helix-helix interactions. Purified phospholamban, a small (6-kDa) integral membrane protein containing a single TMH, formed a pentameric assembly in sodium dodecyl sulfate. The chemical degradation target size of this phospholamban pentamer was 5-6 kDa, illustrating that not all integral membrane protein assemblies permit intersubunit energy transfer. These findings together with other published observations suggest strongly that significant noncovalent energy transfer can occur within the tertiary and quaternary structure of membrane proteins and that as yet undefined proper molecular interactions are required for such covalent energy transfer. Our results with pepsin-digested glucose transporter also illustrate the importance of the interhelical interaction as a predominating force in maintaining the tertiary structure of a transmembrane protein.

Blotting, Western↗

PubMed2000

Specific interaction between 14-3-3 isoforms and the human CDC25B phosphatase.

CDC25 dual-specificity phosphatases are essential regulators that activate cyclin-dependent kinases (CDKs) at critical stages of the cell cycle. In human cells, CDC25A and C are involved in the control of G1/S and G2/M respectively, whereas CDC25B is proposed to act both in S phase and G2/M. Evidence for an interaction between CDC25 phosphatases and members of the 14-3-3 protein family has been obtained in vitro and in vivo in several organisms. On the basis of the work performed with CDC25C, it has been proposed that phosphorylation is required to mediate the interaction with 14-3-3. Here we have examined the molecular basis of the interaction between CDC25B phosphatases and 14-3-3 proteins. We show that in the two-hybrid assay all three splice variants of CDC25B interact similarly and strongly with 14-3-3eta, beta and zeta proteins, but poorly with epsilon and Theta. In vitro, CDC25B interacts at a low level with 14-3-3beta, epsilon, zeta, eta, and Theta isoforms. This interaction is not increased upon phosphorylation of CDC25B by CHK1 and is not abolished by dephosphorylation. In contrast, a specific, strong interaction between CDC25B and 14-3-3zeta and eta isoforms is revealed by a deletion of 288 residues in the amino-terminal region of CDC25B. This interaction requires the integrity of Ser 323, although it is independent of phosphorylation. Thus, interaction between 14-3-3 proteins and CDC25B is regulated in a manner that is different from that with CDC25C. We propose that, in addition to a low affinity binding site that is available for all 14-3-3 isoforms, post-translational modification of CDC25B in vivo exposes a high-affinity binding site that is specific for the zeta and eta14-3-3 isoforms.

14-3-3 Proteins↗

PubMed1998

Effect of replacement of His-118, His-125 and Trp-143 by alanine on the catalytic activity and subunit assembly of inorganic pyrophosphatase from thermophilic bacterium PS-3.

Each of two histidine residues and one tryptophan residue in thermophilic bacterium PS-3 inorganic pyrophosphatase (PPase) was replaced by alanine. The activities of the H125A and W143A variants decreased to one-fifth, whereas the activity of H118A remained unaltered. CD spectra in the near-UV region indicated that the conformations of the first two variants changed with the substitution. In contrast with wild-type PPase, which is hexameric beyond an enzyme concentration of 0.1 microM in the presence of Mg2+, the H118A and H125A variants cannot be assembled from trimers into hexamers at less than an enzyme concentration of 10 microM even at a higher concentration of Mg2+. In particular, H118A was irreversibly inactivated in a diluted state. In contrast, the enzyme concentration dependence of W143A PPase activity was almost the same as that of wild-type PPase. These results indicated that His-118 and His-125 are important for both trimer-trimer interaction and structural integrity, whereas Trp-143 is important structurally. The trimer-trimer interaction is absolutely necessary for the thermostability of the PS-3 enzyme.

Alanine↗

PubMed2003

Top-down modulation of lateral interactions in early vision: does attention affect integration of the whole or just perception of the parts?

Attention can modulate sensitivity to local stimuli in early vision. But, can attention also modulate integration of local stimuli into global visual patterns? We recently measured effects of attention on the phenomenon of lateral interactions between collinear elements, commonly thought to reflect long-range mechanisms in early visual cortex underlying contour integration. We showed improved detection of low-contrast central Gabor targets in the context of collinear flankers, but only when the collinear flankers were attended for a secondary task rather than ignored in favor of an orthogonal flanker pair. Here, we contrast two hypotheses for how attention might modulate flanker influences on the target: by changing just local sensitivity to the flankers themselves (flanker-modulation-only hypothesis), or by weighting integrative connections between flanker and target (connection-weighting hypothesis). Modeled on the known nonlinear dependence of target visibility on collinear flanker contrast, the first hypothesis predicts that an increase in physical flanker contrast should readily offset any reduction in their effective contrast when ignored, thus eliminating attentional modulation. Conversely, the second hypothesis predicts that attentional modulation should persist even for the highest flanker contrasts. Our results showed the latter outcome and indicated that attention modulates flanker-target integration, rather than just processing of local flanker elements.

Attention↗

PubMed2005

A genomic-scale search for regulatory binding sites in the integration host factor regulon of Escherichia coli K12.

We examined general aspects of the DNA-protein interaction between the integration host factor (IHF) global regulator and its regulatory binding sites in the Escherichia coli K12 genome. Two models were developed with distinct weight matrices for the regulatory binding sites recognized by IHF. Using these matrices we performed a genome scale scan and built a set of computationally predicted binding sites for each of the models. The sites found by the model associated with repetitive sequences had a higher score in the sequence to matrix alignment. They were also more rare than the other sites. The sites not associated with repeats rapidly tended to become undistinguishable from the background as statistical stringency was relaxed. We compared our results to the known sites documented in RegulonDB and found new members of the IHF Regulon. The two models exhibit clearly distinct affinity patterns (scores in the sequence to matrix alignments and in the number of regulatory sites), as we vary the stringency of the statistical confidence parameters. We suggest that these differences may play an important role in the dynamics of the network. We concluded that IHF may regulate two genes encoding ATP-dependent RNA helicases. This interaction is not described in RegulonDB, even as a computational prediction. IHF may also regulate RNA modification processes.

Binding Sites↗

PubMed2004

Predicting co-complexed protein pairs using genomic and proteomic data integration.

BACKGROUND: Identifying all protein-protein interactions in an organism is a major objective of proteomics. A related goal is to know which protein pairs are present in the same protein complex. High-throughput methods such as yeast two-hybrid (Y2H) and affinity purification coupled with mass spectrometry (APMS) have been used to detect interacting proteins on a genomic scale. However, both Y2H and APMS methods have substantial false-positive rates. Aside from high-throughput interaction screens, other gene- or protein-pair characteristics may also be informative of physical interaction. Therefore it is desirable to integrate multiple datasets and utilize their different predictive value for more accurate prediction of co-complexed relationship. RESULTS: Using a supervised machine learning approach--probabilistic decision tree, we integrated high-throughput protein interaction datasets and other gene- and protein-pair characteristics to predict co-complexed pairs (CCP) of proteins. Our predictions proved more sensitive and specific than predictions based on Y2H or APMS methods alone or in combination. Among the top predictions not annotated as CCPs in our reference set (obtained from the MIPS complex catalogue), a significant fraction was found to physically interact according to a separate database (YPD, Yeast Proteome Database), and the remaining predictions may potentially represent unknown CCPs. CONCLUSIONS: We demonstrated that the probabilistic decision tree approach can be successfully used to predict co-complexed protein (CCP) pairs from other characteristics. Our top-scoring CCP predictions provide testable hypotheses for experimental validation.

Computational Biology↗

PubMedDate not supplied

The interaction between human Fc gamma RI and the gamma-chain is mediated solely via the 21 amino acid transmembrane domain of Fc gamma RI.

We have established a biological assay to investigate the nature of the non-covalent interaction between two integral type I membrane proteins, Fc gamma RI and gamma-chain. Fc gamma RI, the human high affinity receptor for immunoglobulin G (IgG), is expressed on the surface of macrophages and monocytes and mediates a broad range of important immunological functions. Fc gamma RI relies on a functional interaction with a second integral type I membrane protein, gamma-chain, to mediate many of these functions. For example, Fc gamma RI can only mediate phagocytosis of IgG-coated particles in COS cells when co-expressed with gamma-chain. We have previously shown that the cytoplasmic domain of Fc gamma RI is not necessary for this functional interaction. In this study we have used the phagocytosis assay to investigate the role of the transmembrane region of Fc gamma RI in mediating this functional interaction with gamma-chain by using mutant and chimeric forms of the receptor. Three mutants, which introduce or remove charged residues from a conserved 10 amino acid stretch of amino acids in the proximal transmembrane region of Fc gamma RI, were able to mediate phagocytosis of IgG-coated particles. In contrast, two chimeric receptors, In which 21 of the amino acids in the distal transmembrane region of Fc gamma RI were replaced with the transmembrane region of the related receptors CD2 or LFA3, were expressed but failed to interact functionally with gamma-chain to mediate phagocytosis. Thus, these mutants demonstrate that the interaction between human Fc gamma RI and gamma-chain is mediated solely via these 21 amino acids in the transmembrane domain of Fc gamma RI.

Amino Acid Sequence↗

PubMed1993

Integral membrane proteins of the nuclear envelope interact with lamins and chromosomes, and binding is modulated by mitotic phosphorylation.

Lamina-associated polypeptides (LAPs) 1A, 1B, 1C, and 2 are integral membrane proteins of the nuclear envelope associated with the nuclear lamina. Using in vitro assays, we show that LAPs 1A and 1B specifically bind to both lamins A and C and lamin B1, while LAP 2 associates only with lamin B1. LAP 2 also binds to mitotic chromosomes. The LAPs are phosphorylated during mitosis, and phosphorylation of LAP 2 by mitotic cytosol inhibits its binding to both lamin B1 and chromosomes. During late anaphase, LAP 2 associates with chromosomes prior to assembly of most lamins. Together, these data suggest that LAP 2 may have a key role in initial events of nuclear envelope reassembly, and that both LAP 2 and LAP 1 may be involved in attaching lamins to the nuclear envelope.

Animals↗

PubMed2025

Integrated transcriptomic, transcriptional factors, and protein interaction reveal the regulatory mechanisms of flowering time in rice (Oryza sativa L.).

Appropriate flowering time is important for rice regional adaptation and optimum rice production, but little is known about the omics of heading date in rice. Here, we studied omics including transcriptome, proteome and transcriptional factors to identify regulatory genes related to flowering time. A total of 1402 differentially expressed genes (DEGs, 721 up-regulated and 681 down-regulated) were detected in wild and mutant. These transcripts are classified according to biological processes, cellular components, and molecular functions. Among these differentially expressed genes, many transcription factor genes demonstrated multiple regulatory pathways involved in flowering time. Gene expression analysis showed that Os03g0122600 (OsMADS50), Os08g0105000 (Ehd3), Os06g0275000 (Hd1) were expressed higher and Os06g0199500 (OsHAL3), Os06g0498800 (OsMFT1), Os08g0105000 (Ehd3), Os06g0157700 (Hd3a), and Os02g0731700 (Ghd2), were expressed lower in wild compared to mutant, which are the key genes that regulate the flowering in rice. In addition, Ghd7 interacted with Os10g30860 and Os12g08260 using yeast two-hybrid assay. We identified 28 potential Ghd7 transcriptional regulators using the transcription factor-centered yeast one hybrid (TF-Centered Y1H) assay. Taken together, this study developed a new set of genomic resources to identify and characterize genes, proteins, and motifs associated with flowering time.

Oryza↗

PubMed2005

Navigating the chaperone network: an integrative map of physical and genetic interactions mediated by the hsp90 chaperone.

Physical, genetic, and chemical-genetic interactions centered on the conserved chaperone Hsp90 were mapped at high resolution in yeast using systematic proteomic and genomic methods. Physical interactions were identified using genome-wide two hybrid screens combined with large-scale affinity purification of Hsp90-containing protein complexes. Genetic interactions were uncovered using synthetic genetic array technology and by a microarray-based chemical-genetic screen of a set of about 4700 viable yeast gene deletion mutants for hypersensitivity to the Hsp90 inhibitor geldanamycin. An extended network, consisting of 198 putative physical interactions and 451 putative genetic and chemical-genetic interactions, was found to connect Hsp90 to cofactors and substrates involved in a wide range of cellular functions. Two novel Hsp90 cofactors, Tah1 (YCR060W) and Pih1 (YHR034C), were also identified. These cofactors interact physically and functionally with the conserved AAA(+)-type DNA helicases Rvb1/Rvb2, which are key components of several chromatin remodeling factors, thereby linking Hsp90 to epigenetic gene regulation.

Adenosine Triphosphatases↗

PubMed2005

Bridging emotion theory and neurobiology through dynamic systems modeling.

Efforts to bridge emotion theory with neurobiology can be facilitated by dynamic systems (DS) modeling. DS principles stipulate higher-order wholes emerging from lower-order constituents through bidirectional causal processes--offering a common language for psychological and neurobiological models. After identifying some limitations of mainstream emotion theory, I apply DS principles to emotion-cognition relations. I then present a psychological model based on this reconceptualization, identifying trigger, self-amplification, and self-stabilization phases of emotion-appraisal states, leading to consolidating traits. The article goes on to describe neural structures and functions involved in appraisal and emotion, as well as DS mechanisms of integration by which they interact. These mechanisms include nested feedback interactions, global effects of neuromodulation, vertical integration, action-monitoring, and synaptic plasticity, and they are modeled in terms of both functional integration and temporal synchronization. I end by elaborating the psychological model of emotion-appraisal states with reference to neural processes.

Adaptation, Psychological↗