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 649 records · Page 36Linked to original sources
PubMed1992

The retinoblastoma protein region required for interaction with the E2F transcription factor includes the T/E1A binding and carboxy-terminal sequences.

Recent experiments in understanding the mechanism of the retinoblastoma protein (RB) function have revealed the existence of several cellular proteins that are complexed with RB. One of these cellular proteins is the E2F transcription factor, which was originally identified due to its inducibility by E1A during an adenovirus infection. The E2F recognition sequence is found in the promoters of several cellular genes involved in growth control, including several oncogenes. In this report, we provide evidence that the interaction of E2F and RB is mediated through a region on RB where viral oncogenes such as SV40 T antigen and adenovirus E1A bind and where tumorigenic mutations also cluster. Additional carboxy-terminal sequences are also required for the interaction with E2F. These observations provide evidence for a direct connection between tumor suppressor function and the gene expression program leading to cellular growth regulation.

Adenovirus E1A Proteins↗
PubMed2005

Non-additivity in protein-DNA binding.

MOTIVATION: Localizing protein binding sites within genomic DNA is of considerable importance, but remains difficult for protein families, such as transcription factors, which have loosely defined target sequences. It is generally assumed that protein affinity for DNA involves additive contributions from successive nucleotide pairs within the target sequence. This is not necessarily true, and non-additive effects have already been experimentally demonstrated in a small number of cases. The principal origin of non-additivity involves the so-called indirect component of protein-DNA recognition which is related to the sequence dependence of DNA deformation induced during complex formation. Non-additive effects are difficult to study because they require the identification of many more binding sequences than are normally necessary for describing additive specificity (typically via the construction of weight matrices). RESULTS: In the present work we will use theoretically estimated binding energies as a basis for overcoming this problem. Our approach enables us to study the full combinatorial set of sequences for a variety of DNA-binding proteins, make a detailed analysis of non-additive effects and exploit this information to improve binding site predictions using either weight matrices or support vector machines. The results underline the fact that, even in the presence of significant deformation, non-additive effects may involve only a limited number of dinucleotide steps. This information helps to reduce the number of binding sites which need to be identified for successful predictions and to avoid problems of over-fitting. AVAILABILITY: The SVM software is available upon request from the authors.

Algorithms↗
PubMed1991

Inhibition of homologous complement by CD59 is mediated by a species-selective recognition conferred through binding to C8 within C5b-8 or C9 within C5b-9.

The capacity of the human complement regulatory protein CD59 to interact with terminal complement proteins in a species-selective manner was examined. When incorporated into chicken E, CD59 (purified from human E membranes) inhibited the cytolytic activity of the C5b-9 complex in a manner dependent on the species of origin of C8 and C9. Inhibition of C5b-9-mediated hemolysis was maximal when C8 and C9 were derived from human (hu) or baboon serum. By contrast, CD59 showed reduced activity when C8 and C9 were derived from dog or sheep serum, and no activity when C8 and C9 were derived from either rabbit or guinea pig (gp) serum. Similar specificity on the basis of the species of origin of C8 and C9 was also observed for CD59 endogenous to the human E membrane, using functionally blocking antibody against this cell surface protein to selectively abrogate its C5b-9-inhibitory activity. When E bearing human CD59 were exposed to C5b-8hu, CD59 was found to inhibit C5b-9-mediated lysis, regardless of the species of origin of C9, suggesting that the inhibitory function of CD59 can be mediated through recognition of species-specific domains expressed by human C8. Consistent with this interpretation, CD59 was found to bind to C5b-8hu but not to C5b67hu or C5b67huC8gp. Although CD59 failed to inhibit hemolysis mediated by C5b67huC8gpC9gp, its inhibitory function was observed for C5b67huC8gpC9hu, suggesting that, in addition to its interaction with C5b-8hu, CD59 also interacts in a species-selective manner with C9hu incorporated into C5b-9. Consistent with this interpretation, CD59 was found to bind both C5b67huC8gpC9hu and C5b-8huC9gp, but not C5b67huC8gpC9gp. Taken together, these data suggest that the capacity of CD59 to restrict the hemolytic activity of human serum complement involves a species-selective interaction of CD59, which involves binding to both the C8 and C9 components of the membrane attack complex. Although CD59 expresses selectivity for C8 and C9 of human origin, this "homologous restriction" is not absolute, and this human complement regulatory protein retains functional activity toward C8 and C9 of some nonprimate species.

Antigens, Differentiation↗
PubMed1992

Mapping the orientation of an antigenic peptide bound in the antigen binding groove of H-2Kb using a monoclonal antibody.

The major histocompatibility complex class I molecules are receptors for intracellular peptides, both of self and non-self origin. When non-self peptides (eg., pathogen derived) are bound to the class I molecules, they form ligands for T cell receptors resulting in antigen specific lysis of the infected cells by cytotoxic T lymphocytes. Therefore, an understanding of the process of antigen recognition requires the precise definition of the structural features of the bimolecular complex formed by a single well defined antigenic peptide bound to the class I molecule. A strategy using antibodies was developed to probe the structural features of the H-2Kb containing a defined peptide in the antigen cleft. We report that the binding surface area of a Kb specific monoclonal antibody (28-13-3s) includes residues in the alpha 1 (Gly56 and Glu58) and alpha 2 (Trp167) helices of Kb thus, binding across the antigen binding groove. When cells treated with the antigenic peptide of vesicular stomatitis virus, N52-59, and its alanine substituted analogs were tested for 28-13-3s binding, it was found that position 1 of the peptide also forms a part of the antibody binding site. This finding strongly supports the positioning of the N-terminus of N52-59 proximal to pocket A, thus, assuming an orientation parallel to the alpha 1 helix.

Abelson murine leukemia virus↗
PubMed1994

The skin immune system: lupus erythematosus as a paradigm.

Lupus erythematosus (LE) was first described as a clinical dermatological entity in 1851. The possibility of serious systemic manifestations became recognized by 1872 as the result of the work of M. Kaposi. Since then, it took a long time before LE was recognized to be an immunological disease. Recognition of antinuclear antibodies and their deposition at the basal membrane region in skin resulted in two concepts of LE pathogenesis. In one, antibody complexing and complement activation with generation of the membrane attack complex (C5-C9) is thought to be the origin of the chronic inflammatory reaction. In the other, antibody deposition enables antibody dependent cellular cytotoxicity, leading to hydropic degeneration of the basal epidermal layer and subsequent chronic inflammation. Norris postulated in 1993, that the epidermis acts as a pro-inflammatory organ, in which an UVB-induced increase in cytokine production is followed by increased expression of adhesion molecules on keratinocytes as well as dermal endothelial cells. Translocation of certain antigens (i.e. Ro & La) to which circulating auto-antibodies exist in LE, enables recognition by adhesion molecule directed skin-invading T cells with subsequent cytotoxic effector activity. A persistent chronic inflammatory reaction then ensues. A similar development in knowledge may be seen in the history of immunodermatology. Originally, lupus erythematosus could not be recognized as an immune disease, since concepts of immunology were virtually non-existent when LE was first described. Immunology, In the first half of this century, was mainly antibody-oriented and thus came the concept of (S)LE as an antibody-mediated disease.(ABSTRACT TRUNCATED AT 250 WORDS)

Allergy and Immunology↗
PubMed1994

Adenosine in wide complex tachycardia: potential pitfalls in diagnostic value.

Adenosine is an efficacious diagnostic and therapeutic agent in the acute management of wide complex tachycardias. Its potent negative dromotropic effect terminates supraventricular tachycardias involving the atrioventricular node, allowing differentiation from tachycardias of atrial and ventricular origin. Its extranodal actions, however, may lead to potential pitfalls in arrhythmia diagnosis. We report three unusual cases of patients with adenosine-sensitive tachycardias. One patient had idiopathic ventricular tachycardia originating from the right ventricular outflow tract, one had ectopic atrial tachycardia, and one had atrial fibrillation with rate-related intraventricular aberration. Recognition of the extranodal actions of adenosine and careful ECG evaluation before and after adenosine administration should maximize the diagnostic accuracy of adenosine in wide complex tachycardias.

Adenosine Triphosphate↗
PubMed2006

Parathyroid development and the role of tubulin chaperone E.

The development of the parathyroid glands involves complex embryonic processes of cell-specific differentiation and migration of the glands from their sites of origin in the pharynx and pharyngeal pouches to their final positions along the ventral midline of the pharyngeal and upper thoracic region. The recognition of several distinct genetic forms of isolated and syndromic hypoparathyroidism led us to review the recent findings on the molecular mechanisms of the development of the parathyroid glands. Although far from being understood, a special emphasis was given to the possible role of tubulin chaperone E (TBCE), which was implicated in the pathogenesis of the hypopathyroidism, retardation and dysmorphism (HRD) syndrome. The novel finding that TBCE plays a critical role in the formation of the parathyroid opens a novel domain of research, not anticipated previously, into the complex process of parathyroid development.

Gene Expression Regulation↗
PubMed1992

The ES-242s, novel N-methyl-D-aspartate antagonists of microbial origin, interact with both the neurotransmitter recognition site and the ion channel domain.

ES-242-1 approximately 5 are novel microbial bioxanthracenes which do not contain nitrogen. The ES-242s inhibited the binding of [3H]TCP and [3H]CGS19755 to the N-methyl-D-aspartate (NMDA) receptor complex. They had no effect on the binding of the specific ligands for the non-NMDA receptor. The biochemical and pharmacological properties of ES-242-1 were fully examined since it is the most potent of the five compounds. ES-242-1 is highly specific for the NMDA receptor; it has no effect on other receptors. Kinetic analyses indicated that ES-242-1 inhibited the binding of [3H]TCP and [3H]CGS19755 in a competitive manner, respectively, suggesting that ES-242-1 interacts with both the transmitter recognition site and the channel domain. ES-242-1 selectively inhibited NMDA-induced Ca2+ influx in primary cultures of mouse hippocampal neurons. ES-242-1 also specifically blocked the increase in cyclic GMP accumulation induced by NMDA or L-glutamate in rat cerebellar slices. In a concentration range of 0.1-1.0 microM, ES-242-1 was as potent as MK-801 in preventing glutamate-induced neurotoxicity in primary cultures of mouse hippocampal neurons. These results show that ES-242-1 is a potent and specific antagonist for the NMDA receptor. The antagonistic properties of the ES-242s appear to be due to a novel mechanism of action at the NMDA receptor.

Animals↗
PubMed1989

QRS feature extraction using linear prediction.

This communication proposes a method called linear prediction (a high performant technique in digital speech processing) for analyzing digital ECG signals. There are several significant properties indicating that ECG signals have an important feature in the residual error signal obtained after processing by Durbin's linear prediction algorithm. This communication also indicates that the prediction order need not be more than two for fast arrhythmia detection. The ECG signal classification puts an emphasis on the residual error signal. For each ECG's QRS complex, the feature for recognition is obtained from a nonlinear transformation which transforms every residual error signal to a set of three states pulse-code train relative to the original ECG signal. The pulse-code train has the advantage of easy implementation in digital hardware circuits to achieve automated ECG diagnosis. The algorithm performs very well in feature extraction in arrhythmia detection. Using this method, our studies indicate that the PVC (premature ventricular contraction) detection has at least a 92 percent sensitivity for MIT/BIH arrhythmia database.

Algorithms↗
PubMedDate not supplied

Antigen presentation by cells that are not of bone marrow origin.

T cells do not see antigen directly, but rather recognize antigen only when displayed by an antigen-presenting cell (APC). APC take up, internalize, and degrade antigen and present the relevant antigenic fragment in association with class II major histocompatibility complex (MHC) molecules to antigen-specific T cells. In addition to presenting the antigenic fragment-MHC complex to T cells, APC must also provide a variety of antigen-nonspecific influences to T cells for antigen recognition to result in T-cell activation. These influences include the effects of various cytokines and signals transmitted by a number of nonspecific receptor-ligand interactions. Traditionally, cells of bone marrow origin that express class II MHC molecules, such as mononuclear phagocytes and B lymphocytes, have been regarded as the only APC. Recently, however, it has been suggested that under various physiologic and pathologic conditions, other tissue cells may develop the capacity to express class II MHC molecules and function as APC. The capacity of these cells to function as APC, however, varies widely, depending on the cell type examined. One determinant of the capacity of a cell to function as an APC appears to be its ability to provide antigen-nonspecific signals. Cells with limited abilities to provide these signals have limited APC function. Indeed, it has been suggested that such cells may induce antigen-specific tolerance. In contrast, cells with the capacity to deliver these signals function as fully competent APC. The functional phenotype of the responding T cell may also vary, depending on the nonspecific signals provided by the APC. Some APC may preferentially stimulate antigen-specific T cells that promote the immune response, whereas others promote the activation of suppressor T cells, thereby limiting the response. Thus, it is likely that cells that are not of bone marrow origin play a role in normal immune responses. Moreover, they may also be important in the development of certain forms of autoimmunity.

Animals↗
PubMed2001

Epstein-Barr nuclear antigen 1 binds and destabilizes nucleosomes at the viral origin of latent DNA replication.

The EBNA1 protein of Epstein-Barr virus (EBV) activates latent-phase DNA replication by an unknown mechanism that involves binding to four recognition sites in the dyad symmetry (DS) element of the viral latent origin of DNA replication. Since EBV episomes are assembled into nucleosomes, we have examined the ability of Epstein-Barr virus nuclear antigen 1 (EBNA1) to interact with the DS element when it is assembled into a nucleosome core particle. EBNA1 bound to its recognition sites within this nucleosome, forming a ternary complex, and displaced the histone octamer upon competitor DNA challenge. The DNA binding and dimerization region of EBNA1 was sufficient for nucleosome binding and destabilization. Although EBNA1 was able to bind to nucleosomes containing two recognition sites from the DS element positioned at the edge of the nucleosome, nucleosome destabilization was only observed when all four sites of the DS element were present. Our results indicate that the presence of a nucleosome at the viral origin will not prevent EBNA1 binding to its recognition sites. In addition, since four EBNA1 recognition sites are required for both nucleosome destabilization and efficient origin activation, our findings also suggest that nucleosome destabilization by EBNA1 is important for origin activation.

Animals↗
PubMed1996

Solvent exposed side chains of peptides bound to HLA A*1101 have similar effects on the reactivity of alloantibodies and specific TCR.

Peptides can affect the recognition of MHC class I molecules by allospecific antibodies. Two explanations have been proposed for this phenomenon. The 'conformational change' hypothesis suggests that peptide binding affects the availability of serologic determinants in the class I alpha1 and alpha2 domains while the 'peptide-side-chain effect' predicts that solvent exposed residues in the peptide are part of the serologic epitope. We have tested these possibilities by examining the recognition of peptide loaded HLA A*1101 molecules expressed in transporters associated with antigen processing (TAP)-deficient cell lines by three A11-specific mAb, and by comparing the effect of peptide analogues on the recognition of A11 complexes containing peptide epitopes from the Epstein-Barr virus nuclear antigen EBNA4 by antibodies and cytotoxic T lymphocytes (CT). The AUF5.13 and HB164 antibodies showed selective recognition of A11 molecules bound to partially overlapping sets of peptides from viral or cellular origin. The peptide dependence of AUF5.13 was confirmed in reconstitution experiments where A11 molecules were refolded at the surface of TAP-deficient T2/A11 cells that had been cultured at 26 degrees C and treated at pH3. Molecular modelling and Ala scanning mutagenesis of the IVTDFSVIK (IVT) and AVFDRKSDAK (AVF) peptides demonstrated that solvent-exposed peptide side chains affect CTL recognition as well as antibody binding. Substitution of Phe-P5 or Ser-P6 of the IVT peptide with Arg or Lys inhibited AUF5.13 recognition while binding was induced by substitution of the Arg-P5 and Lys-P6 of the AVF peptide with Ala. The results suggest that some allospecific antibodies recognized the surface of MHC class I-peptide complexes in a fashion similar to the TCR. This may involve direct interaction with the peptide side chains as well as recognition of peptide-induced perturbations in the class I complex.

ATP-Binding Cassette Transporters↗
PubMed1992

Triple-helix formation is compatible with an adjacent DNA-protein complex.

The effect of oligonucleotide-directed triple-helix formation on the binding of a protein to an immediately adjacent sequence has been examined. A double-stranded oligonucleotide was designed with a target site for the binding of a pyrimidine oligonucleotide located immediately adjacent to the recognition sequence for the herpes simplex virus type 1 (HSV-1) origin of replication binding protein, which is encoded by the UL9 gene of HSV-1. Since the optimal conditions for the binding of the UL9 protein and the pyrimidine oligonucleotide to the duplex DNA are markedly different, a pyrimidine oligonucleotide was designed to optimize binding affinity and specificity for the target duplex oligonucleotide. Consideration was given to length and sequence composition in an effort to maximize triple-strand formation under conditions amenable to the formation of the UL9-DNA complex. Using gel mobility shift assays, a trimolecular complex composed of duplex DNA bound to both a third oligonucleotide strand and the UL9 protein was detected, indicating that the UL9-DNA complex is compatible with the presence of a triple helix in the immediately adjacent sequences.

Animals↗
PubMed1999

Mechanisms of lipid antigen presentation by CD1.

CD1 is a family of cell surface glycoproteins that are related in structure and evolutionary origin to the major histocompatibility complex (MHC)-encoded antigen-presenting molecules. In contrast to MHC-encoded antigen-presenting molecules, CD1 binds and presents lipid and glycolipid antigens for specific recognition by T cell antigen receptors. Recent work shows that several CD1 family members colocalize with MHC class II proteins within the endocytic system of antigen-presenting cells. Detailed studies of the intracellular trafficking of CD1 proteins reveal new mechanisms controlling delivery of antigen-presenting molecules to particular compartments within cells. The combination of overlapping yet distinct trafficking routes for the various CD1 family members, combined with emerging information on the heterogeneity of CD1-presented lipid antigens, suggest a model whereby different members of the CD1 family could present antigens that occur in various cellular compartments. Furthermore, the CD1 family as a group may present antigens from pathogens that are not normally accessible to or efficiently surveyed by the MHC Class I or II systems. The discovery of this third pathway for antigen presentation, together with the appreciation of a previously unrecognized universe of nonpeptide lipid antigens for T cell responses, are likely to have broad implications for our understanding of the cell-mediated immune response and its role in health and disease.

Animals↗
PubMed1989

Sequence recognition protein for the 17-base-pair A + T-rich tract in the replication origin of simian virus 40 DNA.

A DNA-binding protein has been identified that recognizes runs of deoxyadenines and/or deoxythymines (dA/dT sequences) and purified from a chromatographic fraction containing the multiprotein DNA polymerase alpha-primase complex of HeLa cells by successive steps of chromatography on oligo(dT)-cellulose and Q-Sepharose. Polyacrylamide gel electrophoresis of the purified dA/dT sequence-binding protein in the presence of NaDodSO4 showed a single protein band of 62 kDa. Nitrocellulose filter binding assays using homopolydeoxynucleotides indicated that the purified protein preferentially binds to dA/dT sequences in single-stranded or duplex DNAs. Gel mobility shift assays with a variety of DNAs showed that the purified protein specifically binds to a fragment of simian virus 40 DNA containing the minimal (core) origin for replication. The binding occurred in a protein-dependent manner and in the presence of a vast excess of competing DNAs lacking the simian virus replication origin. The origin binding was reduced, however, when DNA fragments from simian virus 40 deletion mutants containing deletions within the 17-base-pair A + T-rich tract in the core DNA replication origin were used in the assays. These results indicate that the dA/dT sequence-binding protein preferentially binds to the 17-base-pair A + T-rich tract and suggest a possible role for the protein in the initiation of DNA replication.

Adenine↗
PubMed2001

Ten ERK-related proteins in three distinct classes associate with AP-1 proteins and/or AP-1 DNA.

We have identified seven ERK-related proteins ("ERPs"), including ERK2, that are stably associated in vivo with AP-1 dimers composed of diverse Jun and Fos family proteins. These complexes have kinase activity. We designate them as "class I ERPs." We originally hypothesized that these ERPs associate with DNA along with AP-1 proteins. We devised a DNA affinity chromatography-based analytical assay for DNA binding, the "nucleotide affinity preincubation specificity test recognition" (NAPSTER) assay. In this assay, class I ERPs do not associate with AP-1 DNA. However, several new "class II" ERPs do associate with DNA. p41 and p44 are ERK1/2-related ERPs that lack kinase activity and associate along with AP-1 proteins with AP-1 DNA. Class I ERPs and their associated kinase activity thus appear to bind AP-1 dimers when they are not bound to DNA and then disengage and are replaced by class II ERPs to form higher order complexes when AP-1 dimers bind DNA. p97 is a class III ERP, related to ERK3, that associates with AP-1 DNA without AP-1 proteins. With the exception of ERK2, none of the 10 ERPs appear to be known mitogen-activated protein kinase superfamily members.

Binding Sites↗
PubMed2000

Major groove recognition by three-stranded beta-sheets: affinity determinants and conserved structural features.

We present the results of a rational mutagenesis and binding-affinity study of the three-stranded beta-sheet-DNA interface in the complex formed by the amino-terminal DNA-binding domain of the Tn916 integrase protein and its cognate binding site. The relative importance of interfacial contacts present in its NMR-derived solution structure have been tested through mutagenesis, fluorescence anisotropy, and intrinsic quenching DNA-binding assays. We find that seven protein-DNA hydrogen bonds (two base-specific and five to phosphate groups) significantly contribute to the level of affinity. These interactions span the entire DNA-binding surface on the protein, but primarily originate from residues in only two strands of the sheet and loop L2. Interestingly, we show that highly populated, precisely defined intermolecular hydrogen bonds in the ensemble of conformers are invariably important for DNA-binding, implying that NMR-derived solution structures provide direct insight into the energetics of recognition. Unusual three-stranded beta-sheet-DNA interfaces have recently been discovered in three unrelated protein-DNA complexes. A comparative analysis of these structures reveals similar sheet positioning, the presence of two invariant interfacial contacts to the phosphodiester backbone, and two semi-conserved base-specific hydrogen bonds. Two of these conserved contacts significantly contribute to the affinity of the integrase-DNA complex, suggesting that the three-stranded beta-sheet DNA-binding motif exhibits conserved principles of recognition.

Amino Acid Motifs↗
PubMed1987

Postictal Capgras syndrome.

The Capgras syndrome of delusions that familiar persons are being impersonated by identical doubles has occasionally been associated with cerebral disease, often of the nondominant hemisphere. A patient with chronic right cerebral hemisphere dysfunction and complex partial seizures of right temporal origin manifested the Capgras syndrome in the postictal state, and the delusions ceased with optimal seizure control. The delusions could result from postictal disinhibition of dominant hemisphere recognition functions, or from dysfunction of nondominant hemisphere centers involved in perceptual integration.

Adult↗