Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Origin Recognition Complex”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 541 records · Page 30Linked to original sources
PubMed1998

Differential requirements for conserved E2 binding sites in the life cycle of oncogenic human papillomavirus type 31.

Human papillomavirus (HPV) E2 proteins regulate viral replication by binding to sites in the upstream regulatory region (URR) and by complex formation with the E1 origin recognition protein. In the genital HPV types, the distribution and location of four E2 binding sites (BS1 to BS4) which flank a single E1 binding site are highly conserved. We have examined the roles of these four E2 sites in the viral life cycle of HPV type 31 (HPV31) by using recently developed methods for the biosynthesis of papillomaviruses from transfected DNA templates (M. G. Frattini et al., Proc. Natl. Acad. Sci. USA 93:3062-3067, 1996). In transient assays, no single site was found to be necessary for replication, and mutation of the early promoter-proximal site (BS4) led to a fourfold increase in replication. Cotransfection of the HPV31 wild-type (HPV-wt) and mutant genomes with expression vectors revealed that E1 stimulated replication of HPV31-wt as well as the HPV31-BS1, -BS2, and -BS3 mutants. In contrast, increased expression of E2 decreased replication of these genomes. Replication of the HPV31-BS4 mutant genome was not further increased by cotransfection of E1 expression vectors but was stimulated by E2 coexpression. In stably transfected normal human keratinocytes, mutation of either BS1, BS3, or BS4 resulted in integration of viral genomes into host chromosomes. In contrast, mutation of BS2 had no effect on stable maintenance of episomes or copy number. Following growth of stably transfected lines in organotypic raft cultures, the differentiation-dependent induction of late gene expression and amplification of viral DNA of the BS2 mutant was found to be similar to that of HPV31-wt. We were unable to find a role for BS2 in our assays for viral functions. We conclude that at least three of the four E2 binding sites in the URRs of HPVs are essential for the productive viral life cycle. The specific arrangement of E2 binding sites within the URR appears to be more important for viral replication than merely the number of sites.

Adenovirus E2 Proteins↗
PubMed1999

Mechanism of DNA replication in eukaryotic cells: cellular host factors stimulating adenovirus DNA replication.

Replication of adenovirus (Ad) DNA depends on interactions between three viral and three cellular proteins. Human transcription factors NFI and Oct-1 recruit the Ad DNA polymerase to the origin of DNA replication as a complex with the Ad protein primer pTP. High affinity and specificity DNA binding to recognition sites in this origin by the transcription factors stimulate and stabilize pre-initiation complex formation to compensate for the low binding specificity of the pTP/pol complex. In this review, we discuss the properties of NFI and Oct-1 and the mechanism by which they enhance initiation of DNA replication. We propose a model that describes the dynamics of initiation and elongation as well as the assembly and disassembly of the pre-initiation complex.

Adenoviridae↗
PubMed2002

Stereoselective recognition of an aziridine with a Co(III) complex: a potential transition-state analogue for catalytic epoxidation.

Reversible and stereoselective coordination of 1-(R)-phenyl-2-(S)-methylaziridine to (S,S)L-Co(III) and (R,R)L-Co(III) (where L represents a salen ligand obtained from diamino cyclohexane and 2,4-di-tert-butyl salicylaldehyde) has been investigated. 1H NMR data indicate that the aziridine binds about three times more tightly to (S,S)L-Co(III) than to (R,R)L-Co(III). Crystal structures of two molecules of the aziridine coordinated to the Co(III) complexes have been determined. These structures together with molecular mechanics computation provide insight into the origin of stereoselective recognition of the aziridine to the Co(III) complexes.

Journal Article↗
PubMed2004

T antigen origin-binding domain of simian virus 40: determinants of specific DNA binding.

To better understand origin recognition and initiation of DNA replication, we have examined by NMR complexes formed between the origin-binding domain of SV40 T antigen (T-ag-obd), the initiator protein of the SV40 virus, and cognate and noncognate DNA oligomers. The results reveal two structural effects associated with "origin-specific" binding that are absent in nonspecific DNA binding. The first is the formation of a hydrogen bond (H-bond) involving His 203, a residue that genetic studies have previously identified as crucial to both specific and nonspecific DNA binding in full-length T antigen. In free T-ag-obd, the side chain of His 203 has a pK(a) value of approximately 5, titrating to the N(epsilon)(1)H tautomer at neutral pH (Sudmeier, J. L., et al. (1996) J. Magn. Reson., Ser. B 113, 236-247). In complexes with origin DNA, His 203 N(delta)(1) becomes protonated and remains nontitrating as the imidazolium cation at all pH values from 4 to 8. The H-bonded N(delta1)H resonates at 15.9 ppm, an unusually large N-H proton chemical shift, of a magnitude previously observed only in the catalytic triad of serine proteases at low pH. The formation of this H-bond requires the middle G/C base pair of the recognition pentanucleotide, GAGGC. The second structural effect is a selective distortion of the A/T base pair characterized by a large (0.6 ppm) upfield chemical-shift change of its Watson-Crick proton, while nearby H-bonded protons remain relatively unaffected. The results indicate that T antigen, like many other DNA-binding proteins, may employ "catalytic" or "transition-state-like" interactions in binding its cognate DNA (Jen-Jacobson, L. (1997) Biopolymers 44, 153-180), which may be the solution to the well-known paradox between the relatively modest DNA-binding specificity exhibited by initiator proteins and the high specificity of initiation.

Antigens, Polyomavirus Transforming↗
PubMed1988

The T-cell receptor for antigen.

There are two important questions concerning the T-cell antigen receptor. Firstly, what is the structural basis of major histocompatibility complex (MHC)-restricted recognition? Secondly, what is the origin of tolerance to self-MHC and the 'learning' of MHC-restricted recognition during thymus development? These central questions are discussed here in the context of our current knowledge of the structures of the genes encoding T-cell receptor proteins, their expression during thymocyte development and the mechanisms by which the T-cell receptor repertoire is generated.

Animals↗
PubMed2003

Bioactive recognition sites may not be energetically preferred in protein-carbohydrate complexes in the gas phase.

Arrhenius parameters, obtained with the blackbody infrared radiative dissociation technique, are reported for the dissociation of a gaseous protonated complex of an antibody single chain fragment and its native trisaccharide antigen originating from nonspecific interactions during the nanoelectrospray process. It is shown that the nonspecific complex is kinetically more stable and, at the +10 charge state, energetically more stable than the corresponding specific complex originating from interactions in solution. This is the first demonstration that a bioactive recognition site is not energetically preferred in a protein-ligand complex in the gas phase.

Antibodies, Monoclonal↗
PubMed2004

[The electrocardiogram in ventricular tachycardias].

The electrocardiogram, as much as the clinical examination, is a basic tool for the cardiologist. Technological advances have led to a certain lack of interest in learning to read the electrocardiogram, for which close analysis can allow precise diagnosis, notably in the field of cardiac rhythm disorders. This article concerns the electrocardiogram in ventricular tachycardias with two themes: differential diagnosis of wide QRS complex tachycardias and recognition of the site of origin of a ventricular tachycardia. "Fine" analysis of the electrocardiogram is not an intellectual "game". Actually, careful analysis of the 12 lead ECG allows exact and rapid diagnosis in a large majority of cases, distinguishing a ventricular tachycardia from a supraventricular tachycardia with conduction defect; the appropriate management can be selected without delay. At the same time, close reading of the electrocardiogram also allows the site of origin of a ventricular tachycardia to be recognised. Combining this information with elements of the patient's record can allow the arrhythmia to be related to a known pathology or to prompt a targeted aetiological investigation.

Bundle-Branch Block↗
PubMed1993

Tandem binding in crystals of a trp repressor/operator half-site complex.

The crystal structure of trp repressor tandemly bound in a 2:1 complex to a 16-base-pair palindromic DNA containing a central trp operator half-site has been determined and refined to 2.4 A resolution. Despite dramatically different DNA sequence contexts and crystallization conditions, the protein/DNA interface is essentially identical to that seen in the original trp repressor/operator complex structure. Water-mediated sequence recognition by trp repressor is likely to be related to the unusual end-on approach of the recognition helix (E), which allows sharing of the major groove by tandem dimers. The tandem complex model accounts for the mutational sensitivity of all trp operator base pairs. The structure also provides the first detailed view of the tandem interaction, revealing a key role for the amino-terminal arms.

Bacterial Proteins↗
PubMed2004

Multiple roles of T7 RNA polymerase and T7 lysozyme during bacteriophage T7 infection.

T7 RNA polymerase selectively transcribes T7 genes during infection but is also involved in DNA replication, maturation and packaging. T7 lysozyme is an amidase that cuts a bond in the peptidoglycan layer of the cell wall, but it also binds T7 RNA polymerase and inhibits transcription, and it stimulates replication and packaging of T7 DNA. To better understand the roles of these two proteins during T7 infection, mutants of each were constructed or selected and their biochemical and physiological behavior analyzed. The amidase activity of lysozyme is needed for abrupt lysis and release of phage particles but appears to have no role in replication and packaging. The interaction between polymerase and lysozyme stimulates both replication and packaging. Polymerase mutants that gain the ability to grow normally in the absence of an interaction with lysozyme still fail to shut down late transcription and, remarkably, have become hypersensitive to inhibition when lysozyme is able to bind. These lysozyme-hypersensitive polymerases behave without lysozyme similarly to wild-type polymerase with lysozyme: both remain longer at the promoter before establishing a lysozyme-resistant elongation complex and both increase the length of pausing when elongation complexes encounter an eight-base recognition sequence involved in DNA packaging. Replication origins contain T7 promoters, but the role of T7 RNA polymerase in initiating replication is not understood well enough to more than speculate how the lysozyme-polymerase interaction stimulates replication. Maturation and packaging is apparently initiated through interaction between prohead-terminase complexes and transcription elongation complexes paused at the sequence TATCTGT(T/A), well conserved at the right-end of the concatemer junction of T7-like phages. A model that is consistent with the structure of an elongation complex and a large body of mutational and biochemical data is proposed to explain sequence-specific pausing and potential termination at the consensus recognition sequence (C/T)ATCTGT(T/A).

Amidohydrolases↗
PubMed1990

The computational measurement of apparent motion: a recurrent pattern recognition strategy as an approach to solve the correspondence problem.

In short, the model consists of a two-dimensional set of edge detecting units, modelled according to the zero-crossing detectors introduced first by Marr and Ullman (1981). These detectors are located peripherally in our synthetic vision system and are the input elements for an intelligent recurrent network. The purpose of that network is to recognize and categorize the previously detected contrast changes in a multi-resolution representation of the original image in such a manner that the original information will be decomposed into a relatively small number N of well-defined edge primitives. The advantage of such a construction is that time-consuming pattern recognition has no longer to be done on the originally complex motion-blurred images of moving objects, but on a limited number of categorized forms. Based on a number M of elementary feature attributes for each individual edge primitive, the model is then able to decompose each edge pattern into certain features. In this way an M-dimensional vector can be constructed for each edge. For each sequence of two successive frames a tensor can be calculated containing the distances (measured in M-dimensional feature space) between all features in both images. This procedure yields a set of K-1 tensors for a sequence of K images. After cross-correlation of all N x M feature attributes from image (i) with those from image (i + 1), where i = 1,...,K-1, probability distributions can be computed. The final step is to search for maxima in these probability functions and then to construct from these extremes an optimal motion field. A number of simulation examples will be presented.

Algorithms↗
PubMed2002

The RNA binding protein nuclear factor 90 functions as both a positive and negative regulator of gene expression in mammalian cells.

Nuclear factor 90 (NF90) was originally isolated in a complex that binds to the antigen recognition response element (ARRE-2) present in the interleukin-2 promoter. To characterize the transcriptional properties of NF90 in mammalian cells, we examined its ability to modulate promoter function in cellular transfection assays. NF90-Gal4 fusion proteins inhibited transcription from the adenovirus major late promoter in a fashion that was dependent on Gal4 targeting. Conversely, NF90 activated the cytomegalovirus immediate-early promoter, to which it was not targeted. These effects required distinct but overlapping domains in the C terminus of NF90, which contains a functional nuclear localization signal and two double-stranded-RNA binding motifs. NF90 is present in cellular complexes together with the NF45 protein. Transfection assays showed that NF45 binds NF90 strongly and stimulates its ability to activate but not to inhibit gene expression. This report characterizes NF90 as both a positive and negative regulator of gene expression, depending on the promoter context, and suggests a role for NF45 as a regulator of NF90.

Adenoviridae↗
PubMed1995

Specificity in recognition of amyloid-beta peptide by the serpin-enzyme complex receptor in hepatoma cells and neuronal cells.

The serpin-enzyme complex (SEC) receptor was originally identified using a synthetic peptide (peptide 105Y) based on the sequence of a candidate receptor-binding domain of alpha 1-antitrypsin (1-AT) and was subsequently shown to be a receptor on the surface of hepatocytes, monocytes, and neutrophils for recognition of alpha 1-AT-elastase and several other serpin-enzyme complexes (Perlmutter, D. H., Glover, G. I., Rivetna, M., Schasteen, C. S., and Fallon, R.J. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3753-3757). Studies of the minimal requirements for binding to SEC receptor (SEC-R) showed that a pentapeptide FVFLM within the carboxyl-terminal tail of alpha 1-AT was sufficient for binding to SEC-R and interacted with SEC-R in a sequence-specific manner (Joslin, G., Krause, J. E., Hershey, A. D., Adams, S. P., Fallon, R. J., and Perlmutter, D. H. (1991) J. Biol. Chem. 266, 21897-21902). Sequence motifs bearing homology with this pentapeptide domain were found in the amyloid-beta peptide, and amyloid-beta peptide 1-42 was shown to compete for binding to SEC-R on hepatoma cells (Joslin, G., Fallon, R. J., Bullock, J., Adams, S. P., and Perlmutter, D. H. (1991) J. Biol. Chem, 266, 11281-11288). In this study we examined the sequence specificity by which amyloid-beta peptide competes for binding to SEC-R and examined the possibility that SEC-R is expressed in cells of neuronal origin. The results show that amyloid-beta-(25-35) and amyloid-beta-(31-35) compete for binding to SEC-R as effectively as amyloid-beta-(1-39), amyloid-beta-(1-40), and amyloid-beta-(1-42). Amyloid-beta-(1-16) does not compete for binding to SEC-R. There is cross-competition for binding to the same site by 125I-peptide 105Y and amyloid-beta-(25-35) as well as by 125I-Y amyloid-beta-(25-35) and peptide 105Y. By deletions and substitutions within amyloid-beta-(25-35) and generation of chimeric amyloid-beta-alpha 1-AT peptides, amyloid-beta-(31-35) is shown to be critical for binding to the SEC receptor. However, the upstream region, amyloid-beta-(25-30), also contributes to recognition by SEC-R. The SEC-R is present on the surface of a neuronal cell line PC12 as well as that of murine cortical neurons in primary culture, and the specificity of neuronal SEC-R for amyloid-beta peptide is identical to that on hepatoma cells. Finally SEC-R mediates internalization and degradation of amyloid beta-peptide in PC12 cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2000

The hinge of the human papillomavirus type 11 E2 protein contains major determinants for nuclear localization and nuclear matrix association.

The E2 protein of papillomaviruses is a site-specific DNA binding nuclear protein. It functions as the primary replication origin recognition protein and assists in the assembly of the preinitiation complex. It also helps regulate transcription from the native viral promoter. The E2 protein consists of an amino-terminal (N) trans-acting domain, a central hinge (H) domain, and a carboxyl-terminal (C) protein dimerization and DNA binding domain. The hinge is highly divergent among papillomaviruses, and little is known about its functions. We fused the enhanced green fluorescent protein (GFP) with the full-length human papillomavirus type 11 (HPV-11) E2 protein and showed that the resultant fusion, called gfpE2, maintained transcription and replication functions of the wild-type protein and formed similar subnuclear foci. Using a series of GFP fusion proteins, we showed that the hinge conferred strong nuclear localization, whereas the N or C domain was present in both cytoplasm and nucleus. Biochemical fractionation demonstrated that the N domain and hinge, but not the C domain, independently associated with the nuclear matrix. Mutational analyses showed that a cluster of basic amino acid residues, which is conserved among many mucosotropic papillomaviruses, was required for efficient nuclear localization and nuclear matrix association. This mutation no longer repressed the HPV-11 upstream regulatory region-controlled reporter expression. However, a very small fraction of this mutant colocalized with E1 in the nucleus, perhaps by a piggyback mechanism, and was able to support transient replication. We propose that the hinge is critical for the diverse regulatory functions of the HPV-11 E2 protein during mRNA transcription and viral DNA replication.

Animals↗
PubMed1983

Mixed lymphocyte reactivity nonresponsiveness in couples with multiple spontaneous abortions.

We have endeavored to ascertain the possible existence of deviant recognition of antigens controlled by the major histocompatibility complex by lymphocytes originating in couples with a history of multiple spontaneous abortions of unknown cause. Human leukocyte antigen (HLA) typing, as well as one-way mixed lymphocyte culture (MLC) tests, were performed on 33 couples with multiple spontaneous abortions and subsequently compared to 30 fertile couples with no abortion history. No significant differences in the frequency of HLA were detected between the fertile and infertile groups. The frequencies of shared HLA-A and -B antigens among members of the couples were similar in both groups. In 70% of the cases studied, the husbands revealed a depressed cellular response to their respective wives; whereas reactivity to cells from other women proved normal. However, the response of allogeneic controls to these infertile women was normal. This implies that women with multiple abortions are not poor stimulators. The specific one-way decrease in the MLC reactivity appeared to be mediated by female-derived suppressor mechanisms and may be considered as one of the causes of the interrupted development of pregnancy in vivo.

Abortion, Habitual↗
PubMed1991

Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.

Replication factors A and C (RF-A and RF-C) and the proliferating cell nuclear antigen (PCNA) differentially augment the activities of DNA polymerases alpha and delta. The mechanism of stimulation by these replication factors was investigated using a limiting concentration of primed, single-stranded template DNA. RF-A stimulated polymerase alpha activity in a concentration-dependent manner, but also suppressed nonspecific initiation of DNA synthesis by both polymerases alpha and delta. The primer recognition complex, RF-C.PCNA.ATP, stimulated pol delta activity in cooperation with RF-A, but also functioned to prevent abnormal initiation of DNA synthesis by polymerase alpha. Reconstitution of DNA replication with purified factors and a plasmid containing the SV40 origin sequences directly demonstrated DNA polymerase alpha dependent synthesis of lagging strands and DNA polymerase delta/PCNA/RF-C dependent synthesis of leading strands. RF-A and the primer recognition complex both affected the relative levels of leading and lagging strands. These results, in addition to results in an accompanying paper (Tsurimoto, T., and Stillman, B. (1991) J. Biol. Chem. 266, 1950-1960), suggest that an exchange of DNA polymerase complexes occurs during initiation of bidirectional DNA replication at the SV40 origin.

Adenosine Triphosphate↗
PubMed1993

Phage P4 alpha protein is multifunctional with origin recognition, helicase and primase activities.

alpha Protein of satellite phage P4 of Escherichia coli is multifunctional in P4 replication with three activities. First, the protein (subunit M(r) = 84,900) complexes specifically the P4 origin and the cis replication region required for replication. alpha Protein interacts with all six type I repeats (TGTTCACC) present in the origin. Second, associated with the alpha protein is a DNA helicase activity that is fueled by hydrolysis of a nucleoside 5' triphosphate. All common NTPs except UTP and dTTP can serve as cofactors. Strand separation of partial duplexes containing tailed ends that resemble a replication fork is preferred, although a preformed fork is not absolutely required for the enzyme to invade and unwind duplex DNA. alpha Protein catalyzes unwinding in the 3'-5' direction with respect to the strand it has bound. Finally, the primase activity already demonstrated for alpha protein is due to synthesis of RNA primers. In vitro, alpha protein generates di- to pentaribonucleotides on single-stranded phage fd DNA. The predominant product is the dimer pppApG, on which most of the longer oligoribonucleotides are based. Using DNA oligonucleotides of defined sequence as templates, synthesis of pppApG was also detectable. To date, among prokaryotic and eukaryotic replication systems, gp alpha is the only protein known that combines three activities on one single polypeptide chain.

Adenosine Triphosphate↗
PubMed2003

Oxidative stress and Graves' ophthalmopathy: in vitro studies and therapeutic implications.

Graves' ophthalmopathy (GO) is a disorder of autoimmune origin caused by a complex interplay of endogenous and environmental factors. After recognition of one or more antigens shared by thyroid and orbit, activated T lymphocytes infiltrating the orbit trigger a cascade of events leading to production of cytokines, growth factors and oxygen reactive species. Proliferation of adipocytes and fibroblasts then follows, with an increased synthesis of glycosaminoglycans (GAG), which attract water and cause edema of orbital structures and venous congestion. Proliferation of orbital fibroblasts and adipocytes, both in the retroocular tissue and in the perimysium of extraocular muscles, are among the most important events leading to the increased volume of orbital structures (fibroadipose tissue and extraocular muscles). The contribution of oxygen reactive species to the changes occurring in the orbit is underscored by in vitro studies. Superoxide radical stimulates orbital fibroblasts to proliferate and to produce GAG. Furthermore, hydrogen peroxide induces expression of HLA-DR and heat shock protein-72, involved in antigen recognition and T-lymphocyte recruitment. Cigarette smoking, which is probably the most important environmental factor associated with GO occurrence and maintenance, might also act, among other mechanisms, by enhancing generation of oxygen reactive species and reducing antioxidant production. Substances such as nicotinamide, allopurinol and pentoxifylline reduce superoxide- or hydrogen peroxide-induced proliferation of fibroblasts, GAG production and HLA-DR or HSP-72 expression by GO orbital fibroblasts, possibly through scavenging oxygen free radicals. Two small, non-randomized and/or uncontrolled studies investigated the effects of nicotinamide, allopurinol or pentoxifylline on GO. Favorable results were reported, but data are not fully convincing and the true effectiveness of these agents needs to be verified in randomized, controlled trials enrolling a larger number of patients. It currently seems unlikely that they may find a relevant place in the limited armamentarium available for the management of severe GO.

Dose-Response Relationship, Drug↗
PubMed1988

[Trophoblastic proteins].

Many studies conducted on human or animal placenta (chorion) suggest that the trophoblast is not only a passive filter between maternal and foetal blood flow, but is also endowed with complex functions. Factors of trophoblast origin involved in the mechanism of pregnancy recognition or maintenance of the progesterone environment required for the embryo survival, are reviewed. The main proteins involved in pregnancy are reported in table 1. Emphasis is laid on early signals of pregnancy which are of practical interest in human clinical medicine and animal husbandry. Among them, human chorionic gonadotropin (hCG), protein SP1 ("Schwangerschaftsprotein" 1) and some pregnancy-associated plasma proteins such as the PAPP A are very useful in the diagnosis of pregnancy, abortion, foetal abnormality or tumor in the human species. The presence of trophoblastin (presently studied in our laboratory) of a pregnancy-specific protein B and of early pregnancy factor (EPF) attest the establishment of pregnancy in domestic animals and in other mammals. The biological properties of some hormones such as placental lactogens (PL) or chorionic somatomammotropins (CS), human placental growth hormone (hPGH) contribute to a better understanding of the gestation function. Many other factors participate in the foetal development, for example, proliferin. Some proteins can display immunosuppressive properties or be responsible for the immune tolerance between the mother and the foetus. Although many placental proteins have already been defined, their biological functions have not yet been elucidated.

Animals↗