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PubMed2001

Interaction of caveolin with 7-ketocholesterol.

Caveolin is an integral membrane protein that interacts with cholesterol in glycosphingolipid-rich rafts at the cell surface. We have examined the interaction of recombinant His-tagged caveolin-1 with cholesterol and 7-keto cholesterol, the most abundant non-enzymatically formed oxysterol found in oxidised LDL and atheromatous plaque. Our data show that caveolin-1 is able to interact with both sterols. This might have consequences for sterol transport and the signalling properties of cells during atherosclerosis.

Blotting, Western↗

PubMed1996

Lymphocyte homing and homeostasis.

The integration and control of systemic immune responses depends on the regulated trafficking of lymphocytes. This lymphocyte "homing" process disperses the immunologic repertoire, directs lymphocyte subsets to the specialized microenvironments that control their differentiation and regulate their survival, and targets immune effector cells to sites of antigenic or microbial invasion. Recent advances reveal that the exquisite specificity of lymphocyte homing is determined by combinatorial "decision processes" involving multistep sequential engagement of adhesion and signaling receptors. These homing-related interactions are seamlessly integrated into the overall interaction of the lymphocyte with its environment and participate directly in the control of lymphocyte function, life-span, and population dynamics. In this article a review of the molecular basis of lymphocyte homing is presented, and mechanisms by which homing physiology regulated the homeostasis of immunologic resources are proposed.

Animals↗

PubMed2006

Escherichia coli TolA tolerates multiple amino-acid substitutions as revealed by screening randomized variants for membrane integrity and phage receptor function.

Escherichia coli TolA is a cytoplasmic membrane protein required for outer membrane integrity and the translocation of F-specific filamentous (Ff) bacteriophage DNA. Both phage infection and membrane integrity depend on several TolA interactions, e.g. those of the TolA C-terminal domain (TolAIII). Membrane integrity involves interaction with two host proteins and phage translocation requires direct interaction with the N-terminal domain (N1) of Ff phage protein g3p. Although cocrystallization of TolAIII and N1g3p has identified several contact points, it is still uncertain which residues are selectively involved in the different TolA functions. Thus, four different limited substitution libraries of TolA were created, targeting contacts at positions 415-420. These libraries were introduced into the tolA strain K17DE3tolA/F(+) and several variants, containing complementing, multiple amino-acid substitutions, were identified. However, most randomized variants did not complement the tolA strain K17DE3tolA/F(+). The TolA variants that restored sensitivity to phage infection displayed a considerable sequence variation, while the few variants that restored tolerance to detergent were from the same library. A comparison of the generated residue variation and natural variation, suggests that structural dependence overrides contact residue dependence. Thus, library screening can be efficient in identifying TolA variants with different functionally associated characteristics.

Amino Acid Sequence↗

PubMed1984

A cell surface integral membrane glycoprotein of 85,000 mol wt (gp85) associated with triton X-100-insoluble cell skeleton.

The Triton X-100-insoluble skeleton of baby hamster kidney BHK cells consists of the nucleus, intermediate-size filaments, and actin fibers. By transmission electron microscopy, membrane fragments were found to be associated with these insoluble structures. When radioiodinated or [3H]glucosamine-labeled cells were extracted with 0.5% Triton, most plasma membrane glycoproteins were solubilized except for a glycoprotein with a molecular weight of 85,000 (gp85) that remained associated with the insoluble skeletons. Immunoprecipitation with a specific antiserum indicated that the gp85 is not a proteolytic degradation product of fibronectin, an extracellular matrix glycoprotein insoluble in detergent. A monoclonal antibody of BHK cells specific for gp85 was produced. Immunofluorescence analysis with this monoclonal antibody indicated that gp85 is not associated with the extracellular matrix, but is confined to the cell membrane. Both in fixed and unfixed intact cells, fluorescence was concentrated in dots preferentially aligned in streaks on the cell surface. Gp85 was found to behave as an integral membrane protein interacting with the hydrophobic core of the lipid bilayer since it was extracted from membrane preparations by ionic detergents such as SDS, but not by 0.1 N NaOH (pH 12) in the absence of detergents, a condition known to release peripheral molecules. Association of gp85 with the cell skeleton was unaffected by increasing the Triton concentration up to 5%, but it was affected when actin filaments were dissociated or when a protein-denaturing agent (6 M urea) was used in the presence of Triton, suggesting that protein-protein interactions are involved in the association of gp85 with the cell skeleton. We conclude that gp85 is an integral plasma membrane glycoprotein that might have a role in cell surface-cytoskeleton interaction.

Animals↗

PubMed1985

Mobilization and aggregation of integral membrane proteins in erythrocytes induced by interaction with influenza virus at acidic pH.

Effect of influenza virus on erythrocyte membranes was investigated by electron microscopy and fluorescence photobleaching recovery measurements. The virus induced mobilization of integral proteins in erythrocyte membrane at acidic pH, where it fused with the cell membrane to cause hemolysis and also cell fusions but not at neutral pH. At lower temperatures (e.g., 4 degrees C), the proteins aggregated in the membrane and, consequently, large protein-free lipid bilayer area was produced. At higher temperatures (e.g., 37 degrees C) the protein distribution became randomized. Spectrin meshwork underneath the erythrocyte membrane was also markedly modified by the virus at acidic pH. Diffuse fibril structure was converted into dense spots and the membrane area lacking the fibril structure was produced. Isolated hemagglutinin rosettes also caused mobilization and aggregation of the integral proteins at acidic pH but to smaller extent than that induced by virus. The membrane perturbation detected as the protein mobilization by the action of hemagglutinin was assigned to be the cause for envelope fusion.

Blood Proteins↗

PubMed2001

Towards integration of clinical decision support in commercial hospital information systems using distributed, reusable software and knowledge components.

PROBLEM: Clinicians' acceptance of clinical decision support depends on its workflow-oriented, context-sensitive accessibility and availability at the point of care, integrated into the Electronic Patient Record (EPR). Commercially available Hospital Information Systems (HIS) often focus on administrative tasks and mostly do not provide additional knowledge based functionality. Their traditionally monolithic and closed software architecture encumbers integration of and interaction with external software modules. Our aim was to develop methods and interfaces to integrate knowledge sources into two different commercial hospital information systems to provide the best decision support possible within the context of available patient data. METHODS: An existing, proven standalone scoring system for acute abdominal pain was supplemented by a communication interface. In both HIS we defined data entry forms and developed individual and reusable mechanisms for data exchange with external software modules. We designed an additional knowledge support frontend which controls data exchange between HIS and the knowledge modules. Finally, we added guidelines and algorithms to the knowledge library. RESULTS: Despite some major drawbacks which resulted mainly from the HIS' closed software architectures we showed exemplary, how external knowledge support can be integrated almost seamlessly into different commercial HIS. This paper describes the prototypical design and current implementation and discusses our experiences.

Abdominal Pain↗

PubMed1997

Alteration of interendothelial adherens junctions following tumor cell-endothelial cell interaction in vitro.

The integrity of the vascular endothelium is mainly dependent upon the organization of interendothelial adherens junctions (AJ). These junctions are formed by the homotypic interaction of a transmembrane protein, vascular endothelial cadherin (VE-cadherin), which is complexed to an intracellular protein network including alpha-, beta-, and gamma-catenin. Additional proteins such as vinculin and alpha-actinin have been suggested to link the VE-cadherin/catenin complex to the actin-based cytoskeleton. During the process of hematogenous metastasis, circulating tumor cells must disrupt these intercellular junctions in order to extravasate. In the present study, we have investigated the influence of tumor cell-endothelial cell interaction upon interendothelial AJ. We show that human breast adenocarcinoma cells (MCF-7), but not normal human mammary epithelial cells, induce a rapid endothelial cell (EC) dissociation which correlates with the loss of VE-cadherin expression at the site of tumor cell-EC contact and with profound changes in vinculin distribution and organization. This process could not be inhibited by metalloproteinase nor serine protease inhibitors. Immunoprecipitations and Western blot analysis demonstrate that the overall expression of VE-cadherin and vinculin as well as the composition of the VE-cadherin/catenins complex are not affected by tumor cells while the tyrosine phosphorylation status of proteins within the complex is significantly altered. Our data suggest that tumor cells modulate AJ protein distribution and phosphorylation in EC and may, thereby, facilitate EC dissociation.

Adenocarcinoma↗

PubMed1997

Involvement of the rfp tripartite motif in protein-protein interactions and subcellular distribution.

The ret finger protein (rfp) is a member of the B box zinc finger gene family which possesses a tripartite motif consisting of a RING finger, B box finger, and a coiled-coil domain. Rfp is expressed at specific stages of spermatogenesis and in various adult mouse and human tissues. It becomes oncogenic when the tripartite domain is recombined with the tyrosine kinase domain of the ret protooncogene. Many of the B box family proteins function as homodimers, although the role of the individual components of the tripartite motif in this process remains unclear. We demonstrate that rfp homomultimerization occurs through the coiled-coil domains; however, while the B box is not an interacting interface itself, its structural integrity is necessary for this interaction to occur. This is the first evidence that the B box zinc finger domain is involved in regulating protein-protein interactions. Interestingly, we find that mutations of the RING finger and B box affect the subcellular compartmentalization of rfp in various cell lines. These results demonstrate that the interactions of rfp with itself and its association with specific subcellular compartments is dependent upon the function of all of the components of the tripartite motif. It is likely that these domains play a crucial role in the function of the rfp protein in normal cell differentiation and in its transformation potential in the recombined state.

3T3 Cells↗

PubMed1999

Potential interactions of zinc in the neuroendocrine-endocrine disturbances of diabetes mellitus type 2.

An accumulation of evidence implicates leptin, insulin, glucocorticoids, proopiomelanocortin (POMC), and neuropeptide Y (NPY) interactions as being integral to metabolic control associated with neuroendocrine-endocrine functioning. Dysfunction of neuroendocrine-endocrine interactions contributes to the metabolic disturbances of diabetes mellitus type 2 (DM-2). Since Zn has a direct impact on the healthy functioning of hormonal and neuropeptide balance, it is possible that altered Zn status and metabolism in DM-2 are involved in some of the metabolic dysfunctions of DM-2.

Animals↗

PubMed1991

A switch in the formation of alternative DNA loops modulates lambda site-specific recombination.

The virally encoded Xis protein is one of the components in the site-specific recombination reactions of bacteriophage lambda. It is required for excisive recombination and inhibits integrative recombination. The mechanism of Xis inhibition of the integration reaction was investigated by methylation protection assays (footprinting analyses) in conjunction with recombination assays. Xis is shown to mediate the formation of a specific attP looped structure involving cooperative and competitive long-range interactions among integrase, integration host factor, and Xis proteins. This higher-order structure precludes supercoiled attP from engaging in the productive partner interactions that lead to execution of the first strand exchange in integrative recombination. In addition to its previously characterized role in excision, Xis-induced DNA bending is postulated to act as a regulatory switch (in an alternative loop mechanism) that converts the attP intasome from an integrative-competent complex to a nonreactive one.

Bacterial Proteins↗

PubMed2005

An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network.

We developed an integrated proteomic approach to decipher in vivo protein-protein interactions and applied this strategy to globally map the 26 S proteasome interaction network in yeast. We termed this approach QTAX for quantitative analysis of tandem affinity purified in vivo cross-linked (X) protein complexes. For this work, in vivo formaldehyde cross-linking was used to freeze both stable and transient interactions occurring in intact cells prior to lysis. To isolate cross-linked protein complexes with high purification efficiency under fully denaturing conditions, a new tandem affinity tag consisting of a hexahistidine sequence and an in vivo biotinylation signal was adopted for affinity-based purification. Tandem affinity purification after in vivo cross-linking was combined with tandem mass spectrometry coupled with a quantitative SILAC (stable isotope labeling of amino acids in cell culture) strategy to carry out unambiguous protein identification and quantification of specific protein interactions. Using this method, we captured and identified the full composition of yeast 26 S proteasome complex as well as the two known ubiquitin receptors, Rad23 and Dsk2. Quantitative mass spectrometry analysis allowed us to distinguish specific proteasome-interacting proteins (PIPs) from background proteins and led to the identification of a total of 64 potential PIPs of which 42 are novel interactions. Among the 64 putative specific PIPs, there are ubiquitin pathway components, ubiquitinated substrates, chaperones, and transcription and translation regulators, demonstrating the efficacy of the developed approach in capturing in vivo protein interactions. The method offers an advanced technical approach to elucidate the dynamic protein interaction networks of the proteasome and can find a wide range of applications in the studies of other macromolecular protein complex interaction networks.

Amino Acid Sequence↗

PubMed2002

Interaction of FGF, Ihh/Pthlh, and BMP signaling integrates chondrocyte proliferation and hypertrophic differentiation.

Mutations in fibroblast growth factor (FGF) receptor 3 lead to the human dwarfism syndrome achondroplasia. Using a limb culture system, we have analyzed the role of FGF signaling and its interaction with the Ihh/Pthlh and BMP pathways in regulating chondrocyte differentiation. In contrast to previous suggestions, we demonstrate that FGF signaling accelerates both the onset and the pace of hypertrophic differentiation. We furthermore found that FGF and BMP signaling act in an antagonistic relationship regulating chondrocyte proliferation, Ihh expression, and the process of hypertrophic differentiation. Importantly, BMP signaling rescues the reduced domains of proliferating and hypertrophic chondrocytes in a mouse model for achondroplasia. We propose a model in which the balance of BMP and FGF signaling adjusts the pace of the differentiation process to the proliferation rate.

Animals↗

PubMed2005

An integrative approach to the biomechanical function and neuromuscular control of the fingers.

The exquisite mechanical functionality and versatility of the human hand emerges from complex neuro-musculo-skeletal interactions that are not completely understood. I have found it useful to work within a theoretical/experimental paradigm that outlines the fundamental neuro-musculo-skeletal components and their interactions. In this integrative paradigm, the laws of mechanics, the specifications of the manipulation task, and the sensorimotor signals define the interactions among hand anatomy, the nervous system, and manipulation function. Thus, our collaborative research activities emphasize a firm grounding in the mechanics of finger function, insistence on anatomical detail, and meticulous characterization of muscle activity. This overview of our work on precision pinch (i.e., the ability to produce and control fingertip forces) presents some of our findings around three Research Themes: Mechanics-based quantification of manipulation ability; Anatomically realistic musculoskeletal finger models; and Neural control of finger muscles. I conclude that (i) driving the fingers to some limit of sensorimotor performance is instrumental to elucidating motor control strategies; (ii) that the cross-over of tendons from flexors to extensors in the extensor mechanism is needed to produce force in every direction, and (iii) the anatomical routing of multiarticular muscles makes co-contraction unavoidable for many tasks. Moreover, creating realistic and clinically useful finger models still requires developing new computational means to simulate the viscoelastic tendinous networks of the extensor mechanism, and the muscle-bone-ligament interactions in complex articulations. Building upon this neuromuscular biomechanics paradigm is of immense clinical relevance: it will be instrumental to the development of clinical treatments to preserve and restore manual ability in people suffering from neurological and orthopedic conditions. This understanding will also advance the design and control of robotic hands whose performance lags far behind that of their biological counterparts.

Biomechanical Phenomena↗

PubMed2004

A path integral influence functional for excess electron in fluids: Density-functional formulation.

In this paper, we propose a path integral influence functional from a solvent to determine a self-correlation function of a quantum particle in classical simple fluid. It is shown that the influence functional is related to a grand potential functional of the pure solvent under a three-dimensional external field arising from a classical isomorphic polymer, on which the quantum particle is mapped. The influence functional can be calculated from the self-correlation function, the solute-solvent and the solvent-solvent pair correlation function. The obtained equation of the self-correlation function is applied to an excess electron problem in fluid helium. The Fourier path-integral Monte Carlo method is employed to perform the path integral of the electron. The solute-solvent pair correlation function is estimated from a reference interaction site model integral equation. These results obtained form our proposed influence functional and from that proposed by Chandler, Singh, and Richardson are compared with those provided by a path integral Monte Carlo simulation with the explicit helium solvent.

Journal Article↗

PubMed2004

A computational approach for ordering signal transduction pathway components from genomics and proteomics Data.

BACKGROUND: Signal transduction is one of the most important biological processes by which cells convert an external signal into a response. Novel computational approaches to mapping proteins onto signaling pathways are needed to fully take advantage of the rapid accumulation of genomic and proteomics information. However, despite their importance, research on signaling pathways reconstruction utilizing large-scale genomics and proteomics information has been limited. RESULTS: We have developed an approach for predicting the order of signaling pathway components, assuming all the components on the pathways are known. Our method is built on a score function that integrates protein-protein interaction data and microarray gene expression data. Compared to the individual datasets, either protein interactions or gene transcript abundance measurements, the integrated approach leads to better identification of the order of the pathway components. CONCLUSIONS: As demonstrated in our study on the yeast MAPK signaling pathways, the integration analysis of high-throughput genomics and proteomics data can be a powerful means to infer the order of pathway components, enabling the transformation from molecular data into knowledge of cellular mechanisms.

Computational Biology↗

PubMed2003

Sequence-specific binding of prePhoD to soluble TatAd indicates protein-mediated targeting of the Tat export in Bacillus subtilis.

The Tat (twin-arginine protein translocation) system initially discovered in the thylakoid membrane of chloroplasts has been described recently for a variety of eubacterial organisms. Although in Escherichia coli four Tat proteins with calculated membrane spanning domains have been demonstrated to mediate Tat-dependent transport, a specific transport system for twin-arginine signal peptide containing phosphodiesterase PhoD of Bacillus subtilis consists of one TatA/TatC (TatAd/TatCd) pair of proteins. Here, we show that TatAd was found beside its membrane-integrated localization in the cytosol were it interacted with prePhoD. prePhoD was efficiently co-immunoprecipitated by TatAd. Inefficient co-immunoprecipitation of mature PhoD and missing interaction to Sec-dependent and cytosolic peptides by TatAd demonstrated a particular role of the twin-arginine signal peptide for this interaction. Affinity of prePhoD to TatAd was interfered by peptides containing the twin-arginine motif but remained active when the arginine residues were substituted. The selective binding of TatAd to peptides derived from the signal peptide of PhoD elucidated the function of the twin-arginine motif as a target site for pre-protein TatAd interaction. Substitution of the binding motif demonstrated the pivotal role of basic amino acid residues for TatA binding. These features suggest that TatA interacts prior to membrane integration with its pre-protein substrate and could therefore assist targeting of twin-arginine pre-proteins.

Amino Acid Motifs↗

PubMed2006

Stable evolutionary signal in a yeast protein interaction network.

BACKGROUND: The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-protein interaction data casts doubt on the broader usefulness of these interaction sets. Approaches focusing on one-protein-at-a-time have been powerfully employed to demonstrate the high degree of conservation of proteins participating in numerous interactions; here, we expand his 'node' focused paradigm to investigate the relative persistence of 'link' based evolutionary signals in a protein interaction network of S. cerevisiae and point out the value of this relatively untapped source of information. RESULTS: The trend for highly connected proteins to be preferably conserved in evolution is stable, even in the context of tremendous noise in the underlying protein interactions as well as in the assignment of orthology among five higher eukaryotes. We find that local clustering around interactions correlates with preferred evolutionary conservation of the participating proteins; furthermore the correlation between high local clustering and evolutionary conservation is accompanied by a stable elevated degree of coexpression of the interacting proteins. We use this conserved interaction data, combined with P. falciparum/Yeast orthologs, as proof-of-principle that high-order network topology can be used comparatively to deduce local network structure in non-model organisms. CONCLUSION: High local clustering is a criterion for the reliability of an interaction and coincides with preferred evolutionary conservation and significant coexpression. These strong and stable correlations indicate that evolutionary units go beyond a single protein to include the interactions among them. In particular, the stability of these signals in the face of extreme noise suggests that empirical protein interaction data can be integrated with orthologous clustering around these protein interactions to reliably infer local network structures in non-model organisms.

Evolution, Molecular↗

PubMed1999

Late maturation of visual spatial integration in humans.

Visual development is thought to be completed at an early age. We suggest that the maturation of the visual brain is not homogeneous: functions with greater need for early availability, such as visuomotor control, mature earlier, and the development of other visual functions may extend well into childhood. We found significant improvement in children between 5 and 14 years in visual spatial integration by using a contour-detection task. The data show that long-range spatial interactions-subserving the integration of orientational information across the visual field-span a shorter spatial range in children than in adults. Performance in the task improves in a cue-specific manner with practice, which indicates the participation of fairly low-level perceptual mechanisms. We interpret our findings in terms of a protracted development of ventral visual-stream function in humans.

Adolescent↗