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PubMed2006

Interaction of spatial and temporal integration in global form processing.

The mechanisms by which global structure is extracted from local orientation information are not well understood. Sensitivity to global structure can be investigated using coherence thresholds for detection of global forms of varying complexity, such as parallel and concentric arrays of oriented line elements. In this study, we investigated temporal integration in the detection of these forms and its interaction with spatial integration. We find that for concentric patterns, integration times drop as region size increases from 3 degrees to 10.9 degrees , while for parallel patterns, the reverse is true. The same spatiotemporal relationship was found for Glass patterns as for line element arrays. The two types of organization therefore show quite different spatiotemporal relations, supporting previous arguments that different types of neural mechanism underlie their detection.

Form Perception↗

PubMed2005

The integral inner nuclear membrane protein MAN1 physically interacts with the R-Smad proteins to repress signaling by the transforming growth factor-{beta} superfamily of cytokines.

Smad proteins are critical intracellular mediators of the transforming growth factor-beta, bone morphogenic proteins (BMPs), and activin signaling. Upon ligand binding, the receptor-associated R-Smads are phosphorylated by the active type I receptor serine/threonine kinases. The phosphorylated R-Smads then form heteromeric complexes with Smad4, translocate into the nucleus, and interact with various transcription factors to regulate the expression of downstream genes. Interaction of Smad proteins with cellular partners in the cytoplasm and nucleus is a critical mechanism by which the activities and expression of the Smad proteins are modulated. Here we report a novel step of regulation of the R-Smad function at the inner nuclear membrane through a physical interaction between the integral inner nuclear membrane protein MAN1 and R-Smads. MAN1, through the RNA recognition motif, associates with R-Smads but not Smad4 at the inner nuclear membrane in a ligand-independent manner. Overexpression of MAN1 results in inhibition of R-Smad phosphorylation, heterodimerization with Smad4 and nuclear translocation, and repression of transcriptional activation of the TGFbeta, BMP2, and activin-responsive promoters. This repression of TGFbeta, BMP2, and activin signaling is dependent on the MAN1-Smad interaction because a point mutation that disrupts this interaction abolishes the transcriptional repression by MAN1. Thus, MAN1 represents a new class of R-Smad regulators and defines a previously unrecognized regulatory step at the nuclear periphery.

Bone Morphogenetic Protein 2↗

PubMed1997

Neuronal pentraxin receptor, a novel putative integral membrane pentraxin that interacts with neuronal pentraxin 1 and 2 and taipoxin-associated calcium-binding protein 49.

We have identified the first putative integral membrane pentraxin and named it neuronal pentraxin receptor (NPR). NPR is enriched by affinity chromatography on columns of a snake venom toxin, taipoxin, and columns of the taipoxin-binding proteins neuronal pentraxin 1 (NP1), neuronal pentraxin 2 (NP2), and taipoxin-associated calcium-binding protein 49 (TCBP49). The predominant form of NPR contains an putative NH2-terminal transmembrane domain and all forms of NPR are glycosylated. NPR has 49 and 48% amino acid identity to NP1 and NP2, respectively, and NPR message is expressed in neuronal regions that express NP1 and NP2. We suggest that NPR, NP1, NP2, and TCBP49 are involved in a pathway responsible for the transport of taipoxin into synapses and that this may represent a novel neuronal uptake pathway involved in the clearance of synaptic debris.

Amino Acid Sequence↗

PubMed1985

The phi 80 and P22 attachment sites. Primary structure and interaction with Escherichia coli integration host factor.

Although the lambdoid bacteriophage phi 80 and P22 possess site-specific recombination systems analogous to bacteriophage lambda, they have different attachment (att) site specificities. We have identified and determined the nucleotide sequences of the att sites of phi 80 and P22 and have examined the interaction of these sites with purified Escherichia coli integration host factor (IHF). The sizes of the homologous core regions of the att sites vary greatly: P22 has a 46-base pair core, while phi 80 and lambda have 17- and 15-base pair cores, respectively. The core sequences of the three phage show no significant homology, although dispersed regions of homology in arm sequences indicate that the three phage att sites are related. All three att sites have a high A + T composition, and restriction fragments carrying these sites migrate anomalously upon polyacrylamide gel electrophoresis. IHF binds to a site to the left of the common core in the phi 80 and P22 phage att sites (attP) and to a site to the right of the core in P22 attP and attB (the bacterial att site). In the lambda system, IHF interacts with three regions on attP (designated H1, H2, and H') and none on attB (Craig N., and Nash, H.A. (1984) Cell 39, 707-716). Alignment of the IHF sites of all three phage results in a consensus sequence for IHF binding, Pyr-AANNNNTTGATAT. Among the three phage, the number of IHF sites differs; however, the location and orientation of the binding sites in relation to the respective core regions are well conserved. An IHF site analogous to lambda H2 is present in both phi 80 and P22 attP, while a site analogous to lambda H' is present in P22 attP. This conservation suggests that IHF plays a very similar role in the site-specific recombination pathways of all three phage, and that the flanking arm sequences are necessary for phi 80 and P22 attP function, as is the case for lambda attP function. These structural similarities presumably reflect a conservation of the mechanism of site-specific recombination for the three phage.

Bacteriophage lambda↗

PubMed1991

Use of monoacetyl-4-hydroxyaminoquinoline 1-oxide to probe contacts between guanines and protein in the minor and major grooves of DNA. Interaction of Escherichia coli integration host factor with its recognition site in the early promoter and transposition enhancer of bacteriophage Mu.

Monoacetyl-4-hydroxyaminoquinoline 1-oxide (Ac-HAQO) reacts with DNA to form adducts at the C8- and N2-positions of guanine and with the N6-position of adenine. Only the N2-guanine adduct blocks the 3'-5' exonuclease action of phage T4 DNA polymerase. Piperidine treatment cleaves the DNA at sites bearing C8-guanine adducts. The N2-position of guanine lies in the minor groove of DNA, whereas the C8-position of guanine occupies the major groove. We have taken advantage of these characteristics to employ Ac-HAQO in conjunction with either T4 DNA polymerase or piperidine in a footprinting technique to probe the interaction of the Escherichia coli integration host factor (IHF) with its binding site. We show that when IHF binds to its recognition site both the N2- and C8-positions of guanines are protected from modification by AcHAQO. In addition, the binding of IHF to DNA was prevented when either an N2- or a C8-AQO adduct was present in the binding site. When dimethylsulfate was used as the footprinting reagent, IHF protected against methylation of the N3 position of adenine in the minor groove but not the N7 position of guanine in the major groove. The difference in results obtained with the two reagents is ascribed to their relative sizes. Both DMS and AcHAQO are excluded by IHF from the minor groove, but only the larger AcHAQO molecule is excluded from the major groove.

Aminoquinolines↗

PubMed1994

Integrated psychotherapy for the elderly.

The complexity of interacting variables in the geriatric patient imposes the therapeutic necessity to employ all effective therapeutic modalities in an interactive and integrated fashion. This paper examines the efficacy data on brief and longer term therapies as applied to the elderly, most particularly for treatment of depression and bereavement. In determining the development of an integrated psychotherapy treatment plan, the author suggests a decision pathway which incorporates concurrent utilization of theoretical principles derived from psychodynamic, interpersonal and cognitive behavioural theory. This tripartite approach informs the assessment and diagnosis of the patient as well as the specific choice of therapy. Directions for further research are suggested.

Aged↗

PubMedDate not supplied

Microtubule-actin interactions may regulate endothelial integrity and repair.

An important mechanism for the initiation and progression of atherosclerosis is the loss of endothelial integrity, which is required for normal blood vessel function. The important components of the endothelial cell cytoskeleton system that regulate endothelial integrity include actin microfilaments and microtubules, which are both associated with protein complexes that regulate cell-cell and cell-substratum adhesion. To date, studies have shown that microfilaments are essential in maintaining the structural integrity of the endothelium while microtubules regulate the directional cell migration during repair. When microtubules are disrupted at the onset of wounding, neither centrosome reorientation, which is essential for efficient endothelial cell wound repair, nor cell migration occurs. Disruption of microfilaments is also associated with inefficient endothelial cell migration and repair. How then might these systems be associated with one another? Linker proteins, which may facilitate interaction between microtubules and actin microfilaments, have recently been identified in nonendothelial systems. It is likely that microtubule-microfilament interactions are important in the complex regulation of endothelial integrity and repair especially as they relate to atherosclerotic plaque formation.

Actin Cytoskeleton↗

PubMed2002

In silico two-hybrid system for the selection of physically interacting protein pairs.

Deciphering the interaction links between proteins has become one of the main tasks of experimental and bioinformatic methodologies. Reconstruction of complex networks of interactions in simple cellular systems by integrating predicted interaction networks with available experimental data is becoming one of the most demanding needs in the postgenomic era. On the basis of the study of correlated mutations in multiple sequence alignments, we propose a new method (in silico two-hybrid, i2h) that directly addresses the detection of physically interacting protein pairs and identifies the most likely sequence regions involved in the interactions. We have applied the system to several test sets, showing that it can discriminate between true and false interactions in a significant number of cases. We have also analyzed a large collection of E. coli protein pairs as a first step toward the virtual reconstruction of its complete interaction network.

Animals↗

PubMed1998

Identification of a novel ankyrin isoform (AnkG190) in kidney and lung that associates with the plasma membrane and binds alpha-Na, K-ATPase.

Ankyrins are a family of adapter molecules that mediate linkages between integral membrane and cytoskeletal proteins. Such interactions are crucial to the polarized distribution of membrane proteins in transporting epithelia. We have cloned and characterized a novel 190-kDa member of this family from a rat kidney cDNA library, which we term AnkG190 based on the predicted size and homology with the larger neuronal AnkG isoform. AnkG190 displays a unique 31-residue amino terminus, a repeats domain consisting of 24 repetitive 33-residue motifs, a spectrin binding domain, and a truncated regulatory domain. Probes derived from the unique amino terminus hybridize to an 8-kilobase message exclusively in kidney and lung and specifically to the kidney outer medullary collecting ducts by in situ hybridization. Transfections of Madin-Darby canine kidney and COS-7 epithelial cell lines with a full-length AnkG190 construct result in (a) expression at the lateral plasma membrane, (b) functional assembly with the cytoskeleton, and (c) interaction with at least one membrane protein, the Na,K-ATPase. Two independent Na,K-ATPase binding domains on AnkG190 are demonstrated as follows: one within the distal 12 ankyrin repeats, and a second site within the spectrin binding domain. Thus, ankyrins may interact with integral membrane proteins in a pleiotropic manner that may involve complex tertiary structural determinants.

Amino Acid Sequence↗

PubMed1992

Honeybee colony integration: worker-worker interactions mediate hormonally regulated plasticity in division of labor.

Adult workers in honeybee (Apis mellifera) colonies exhibit plasticity in hormonally regulated, age-based division of labor by altering their pattern of behavioral development in response to changes in colony conditions. One form of this plasticity is precocious development: levels of juvenile hormone increase prematurely and bees begin foraging as much as 2 weeks earlier than average. We used two experimental paradigms inspired by developmental biology to study how bees obtain information on changing colony needs that results in precocious foraging. An analog of "cell culture," with bees reared outside of colonies in different sized groups, revealed that worker-worker interactions exert quantitative effects on endocrine and behavioral development. "Transplants" of older bees to colonies otherwise lacking foragers demonstrated that worker-worker interactions also affect behavioral development in whole colonies. These results provide insights to a long-standing problem in the biology of social insects and further highlight similarities in the integration of activity that exist between individuals in insect colonies and cells in metazoans.

Age Factors↗

PubMed2005

Ladder-shaped polyether compound, desulfated yessotoxin, interacts with membrane-integral alpha-helix peptides.

Ladder-shaped polyether compounds, represented by brevetoxins, ciguatoxins, maitotoxin, and prymnesins, are thought to possess the high affinity to transmembrane proteins. As a model compound of ladder-shaped polyethers, we adopted desulfated yessotoxin (2) and examined its interaction with glycopholin A, a membrane protein known to form a dimer or oligomer. Desulfated yessotoxin turned out to interact with the alpha-helix so as to induce the dissociation of glycopholin oligomers when examined by SDS and PFO gel electrophoresis. The results provided the first evidence that ladder-shaped polyethers interact with transmembrane helix domains.

Amino Acid Sequence↗

PubMed1990

The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons.

The regulatory protein NIFA activates transcription of nitrogen fixation (nif) operons by the sigma 54 holoenzyme form of RNA polymerase. NIFA from Klebsiella pneumoniae activates transcription from the nifH promoter in vitro; in addition, the integration host factor, IHF, binds between the nifH promoter and an upstream binding site for NIFA. We demonstrate here that IHF greatly stimulates NIFA-mediated activation of nifH transcription in vitro and thus that the two factors are functionally synergistic. Electron micrographs indicate that IHF bends the DNA in the nifH promoter regulatory region. Although IHF binds close to the nifH promoter, it does not directly stimulate binding of sigma 54 holoenzyme. Rather, the IHF-induced bend may facilitate productive contacts between NIFA and sigma 54 holoenzyme that lead to the formation of open complexes. IHF binds to nif promoter regulatory regions from a variety of organisms within the phylum "purple bacteria," suggesting a general ability to stimulate NIFA-mediated activation of nif transcription.

Bacterial Proteins↗

PubMed1995

Characterization of a microsomal retinol dehydrogenase: a short-chain alcohol dehydrogenase with integral and peripheral membrane forms that interacts with holo-CRBP (type I).

Integral and peripheral forms of a microsomal retinol dehydrogenase (RoDH) have been distinguished in rat liver through differences in solubility, behavior toward affinity resins, and phase partitioning with Triton X-114. Despite physical differences, polyclonal antibodies raised against integral RoDH recognized peripheral RoDH. No obvious differences were observed in substrate specificity between the two forms. Integral and peripheral RoDH catalyzed retinal synthesis from all-trans-retinol bound to cellular retinol-binding protein, type I (CRBP), with similar Km values of 0.6 and 0.4 microM, respectively. Both also discriminated against CRBP-bound all-trans-3,4-didehydroretinol and against 9-cis-retinol. Phenylarsine oxide inhibited both forms with IC50 values of 5 microM (integral) and 15 microM (peripheral). The more stable peripheral form has been reduced to two major polypeptides that migrate as 34 and 54 kDa bands on SDS-PAGE. The active site of this form has been associated with the 34 kDa polypeptide by covalent binding and inactivation with phenylarsine oxide and by cross-linking to holo-CRBP. Cross-linking required cofactor and was maximum with NADP, consistent with the ordered bisubstrate reaction mechanism of an NADP-supported dehydrogenase. The 34 kDa polypeptide has a subunit molecular weight and other attributes typical of short-chain alcohol dehydrogenases (SCAD) including the highly-conserved SCAD sequence WXLVNNAG, Zn2+ independence; inhibition by carbenoxolone (IC50 = 55 microM), and insensitivity to inhibition by ethanol and 4-methylpyrazole. Tight association between the 34 and 54 kDa polypeptides was demonstrated by their coelution through several columns and the precipitation of RoDH activity with either anti-34 kDa or anti-54 kDa antisera. Because SCAD normally occur as homomultimers, however, the 54 kDa polypeptide is not likely to be a subunit of the peripheral form. This work provides new evidence that the retinol-CRBP "cassette" serves as a substrate for a microsomal RoDH and further characterizes the RoDH.

Alcohol Oxidoreductases↗

PubMed1999

Yeast Dam1p is required to maintain spindle integrity during mitosis and interacts with the Mps1p kinase.

We have identified a mutant allele of the DAM1 gene in a screen for mutations that are lethal in combination with the mps1-1 mutation. MPS1 encodes an essential protein kinase that is required for duplication of the spindle pole body and for the spindle assembly checkpoint. Mutations in six different genes were found to be lethal in combination with mps1-1, of which only DAM1 was novel. The remaining genes encode a checkpoint protein, Bub1p, and four chaperone proteins, Sti1p, Hsc82p, Cdc37p, and Ydj1p. DAM1 is an essential gene that encodes a protein recently described as a member of a microtubule binding complex. We report here that cells harboring the dam1-1 mutation fail to maintain spindle integrity during anaphase at the restrictive temperature. Consistent with this phenotype, DAM1 displays genetic interactions with STU1, CIN8, and KAR3, genes encoding proteins involved in spindle function. We have observed that a Dam1p-Myc fusion protein expressed at endogenous levels and localized by immunofluorescence microscopy, appears to be evenly distributed along short mitotic spindles but is found at the spindle poles at later times in mitosis.

Carrier Proteins↗

PubMed1999

Effects of chromosomal integration site upon p53 interactions with DNA consensus sequence homologies.

In the present study, we report that, despite the presence of one perfect p53 consensus sequence homology (designated SCL CS) and four half-sites within the 3'-untranslated region of the stem cell leukemia (SCL) gene, the native endogenous gene is not regulated by p53. We employ a tet-repressible system to show that, under conditions in which the WAF1 mRNA steady-state level is upregulated fourfold by p53, the SCL mRNA level is not altered. In a previous report, we demonstrated that p53 interactions with the SCL CS can upregulate downstream reporter gene activity 43-fold in transient reporter assays. This disparity prompted us to explore the differences between p53 regulation of SCL CS activity in organized (chromosomally integrated) and disorganized (non-replicating episomal plasmid) chromatin. We show that p53 can increase (between 3-80-fold), decrease (between 5-33-fold) or have no effect upon transactivation of an SCL CS/reporter fusion gene depending upon chromosomal integration site. Most studies used to characterize p53 binding sites employ transient transfection assays. Our results suggest that characterization of consensus sequence homologies by assay of transiently transfected cells may be inaccurate.

3' Untranslated Regions↗

PubMed1993

Interaction of nitric oxide and salivary gland epidermal growth factor in the modulation of rat gastric mucosal integrity.

1. The interaction between endogenous nitric oxide (NO) and factors from the rat submandibular salivary gland such as epidermal growth factor (EGF) on gastric mucosal integrity in the rat has been investigated. 2. Bolus administration of the NO synthase inhibitor, NG nitro-L-arginine methyl ester (L-NAME; 6.25-50 mg kg-1, i.v.) to animals treated intraluminally with 0.15 N HCl resulted in a significant increase in the area of mucosal haemorrhagic damage at doses 12.5 and 50 mg kg-1. Concurrent administration of indomethacin (5 mg kg-1, i.v.) resulted in a significant haemorrhagic mucosal damage in response to L-NAME (12.5-50 mg kg-1). Administration of the highest dose of L-NAME resulted in an increase in histological damage to the rat gastric mucosa. 3. When compared to control animals, the extent of damage produced by L-NAME or L-NAME in combination with indomethacin was significantly exacerbated in rats which had been sialoadenectomized (SALX) by removal of the submandibular salivary glands. The mucosal damage in SALX rats was ameliorated by treatment with EGF (5 and 10 micrograms kg-1, i.v.). 4. L-NAME administration resulted in a small reduction of gastric mucosal blood flow as assessed by laser Doppler flowmetry (LDF). The reduction in LDF by 25 and 50 mg kg-1 L-NAME was significantly greater in SALX rats than in rats with intact salivary glands. Pretreatment of SALX rats with indomethacin did not augment this large decrease in LDF suggesting that endogenous prostanoids do not interact with NO and salivary factors in regulating mucosal microcirculation. 5. Mucosal NO biosynthesis as assessed by ['4C]-citrulline formation was reduced in SALX rats when compared to control animals. Pretreatment of SALX animals with parenterally-administered EGF(10 microg kg-1) was associated with an increase in [14C]-citrulline formation in the gastric mucosa to levels observed in control SALX rats.6. These data suggest that factors which originate from the salivary gland such as EGF interact with NO in the maintenance of mucosal integrity. The effects may be mediated at least in part by changes in gastric mucosal blood flow. Salivary glands and EGF may mediate these effects to some extent via changes in mucosal NO biosynthesis.

Amino Acid Oxidoreductases↗

PubMed1993

Detergent binding as a measure of hydrophobic surface area of integral membrane proteins.

The mode by which four nonionic detergents interact with integral membrane proteins was studied by relating detergent binding to characteristic detergent monolayer and micellar dimensions and to the surface area of the hydrophobic sector of the proteins. The detergents used (C12E8, Triton X-100, dodecyl-beta-D-maltoside, and dodecyldimethylamineoxide) are efficient membrane solubilizers, which, according to our hydrodynamic analysis, form small approximately spherical micelles. Their binding by protomeric forms of bacteriorhodopsin, photosynthetic reaction center, sarcoplasmic reticulum Ca(2+)-ATPase, and cytochrome oxidase was measured after equilibration and delipidation, both by the use of successive chromatographies on silica gel and the use of agarose gel columns in combination with DEAE-cellulose chromatography. It was found that, despite detergent binding by silica gel, both chromatographic procedures gave equivalent and consistent results. The data obtained show systematic trends; thus dodecyldimethylamineoxide exhibited the highest binding levels, followed by dodecylmaltoside, whereas the polyethylene glycol detergents C12E8 and Triton X-100 had the lowest degree of binding. This ranking order is inversely related to the cross-sectional areas of these detergents in monolayers at an air-water interface and in micelles. Binding was reduced by aggregation of protomers, whereas the presence of strongly bound residual lipid slightly increased it. Among the membrane proteins with a high molecular mass (reaction center, Ca(2+)-ATPase, and cytochrome oxidase), relative binding could be related to the size of their hydrophobic sectors. On the other hand, bacteriorhodopsin bound somewhat more detergent per transmembrane helix, probably because of less steric hindrance, caused by the absence of a sizable hydrophilic domain in this protein. Theoretical calculations indicated monolayer binding of detergent to the hydrophobic surface of membrane proteins to be a better model for interaction with membrane proteins than binding of the detergents in micellar form.

Animals↗

PubMed1999

The van der Waals Interaction between a Spherical Particle and a Cylinder.

Based on the Hamaker approach, this paper presents a general method to compute the retarded van der Waals (vdW) interaction potential and force between a spherical particle and a cylinder. The effects of the relative dimensions of the cylinder to the sphere were examined by this general method. First, the unretarded vdW interaction potential between these two bodies is obtained by pairwise summation of all the relevant intermolecular interactions and evaluated by accurate multiple numerical integrations. The interaction potential is then modified to account for the retardation effect by incorporating a correction factor which depends on the separation distance and the characteristic wavelength of the interactions. The numerical predictions indicate that the vdW interaction between a sphere and a finitely long cylinder can be approximated as the interaction between a sphere and an infinitely long cylinder only if the ratio of the cylinder length to its radius, B = L/R, is greater than a certain lower limit, say, B > 10. At smaller dimensionless separation distances, H = D/a </= 1, the vdW interaction between a sphere and a cylinder can be approximated by that between a sphere and a flat plate. However, such a commonly used flat plate approximation is found to be acceptable only if the ratio of the cylinder radius to the sphere radius, A = R/a, is larger than 10, regardless of the B value. Otherwise, it will seriously overestimate the vdW interaction for the sphere-cylinder system. Copyright 1999 Academic Press.

Journal Article↗