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Results for “Origin Recognition Complex”

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At least 631 records · Page 35Linked to original sources

PubMed2001

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".

Bisbenzimidazole↗

PubMed1989

Alloreactive T cell recognition of the HLA-DR beta N-terminal polymorphic region.

T cell alloreactivity, originally discovered as a tissue transplantation effect, is believed to be a manifestation of the normal major histocompatibility complex (MHC) restriction of antigen presentation by accessory cells to T cells. The molecular features of the human class II-MHC proteins (HLA) which are recognized by alloreactive T cells are not at present understood, although they are clearly related to the polymorphic nature of the MHC proteins. Human CD4+ T cell clones were selected by response to the HLA-DR2 peptides beta 1-15 or beta 51-65, in an MHC-restricted manner. In addition, these clones respond to cell lines expressing the DR2 haplotype, without the requirement for accessory antigen presenting cells. DR2 beta peptide 1-15 blocks the T cell alloresponse and polymorphic residues are shown to stimulate the peptide-specific response of these clones. Thus, the polymorphic residues contained within the DR beta sequence 1-15 are demonstrated to be directly recognized by alloreactive T cells.

Amino Acid Sequence↗

PubMed1995

Expression of two H-2K genes, syngeneic and allogeneic, as a strategy for potentiating immune recognition of tumor cells.

Metastatic clones of some tumors manifest an impaired expression of class I major histocompatibility complex (MHC) antigens. High metastatic, low immunogenic Lewis lung carcinoma clones (C57BL-H-2b origin) express low levels of the H-2Kb MHC antigen. These cells metastasize spontaneously in C57BL/6J mice. Transfection of syngeneic or allogeneic H-2K genes converted such cells to the nonmetastatic state, but did not prevent the growth of the local tumors. Transfection of two H-2K genes, syngeneic and allogeneic, into the highly metastatic clone D122, resulted in reduction of the growth rates of the transfectants and protected the mice from D122 metastases. In contrast, cells transfected with a single class I gene (syngeneic or allogeneic) gave partial protection, or did not protect the mice at all from D122 metastases. The combination of syngeneic and allogeneic genes in the same tumor cell elevated the immunogenic properties of the expressing cells and potentiated the immune response as was demonstrated by in vitro cytotoxicity analysis and by limiting dilution cytotoxicity analysis. Increased immunogenicity by double transfection may constitute an effective therapeutic modality.

Animals↗

PubMed2003

Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.

Relaxases are DNA strand transferases that catalyze the initial and final stages of DNA processing during conjugative cell-to-cell DNA transfer. Upon binding to the origin of transfer (oriT) DNA, relaxase TrwC melts the double helix. The three-dimensional structure of the relaxase domain of TrwC in complex with its cognate DNA at oriT shows a fold built on a two-layer alpha/beta sandwich, with a deep narrow cleft that houses the active site. The DNA includes one arm of an extruded cruciform, an essential feature for specific recognition. This arm is firmly embraced by the protein through a beta-ribbon positioned in the DNA major groove and a loop occupying the minor groove. It is followed by a single-stranded DNA segment that enters the active site, after a sharp U-turn forming a hydrophobic cage that traps the N-terminal methionine. Structural analysis combined with site-directed mutagenesis defines the architecture of the active site.

Amino Acid Sequence↗

PubMed2002

The pab1 gene of Coprinus cinereus encodes a bifunctional protein for para-aminobenzoic acid (PABA) synthesis: implications for the evolution of fused PABA synthases.

The pab1 gene of the basidiomycete Coprinus cinereus encodes PABA synthase, necessary for para-aminobenzoic acid production. The C. cinereus protein is bifunctional with an N-terminal glutamine amidotransferase domain and a C-terminal chorismate amination domain. In most bacteria, these two functions are encoded in separate genes (e.g., pabA and pabB of E. coli). Fused PABA synthases have so far been detected in actinomycetes, Plasmodium falciparum, fungi and Arabidopsis thaliana. Phylogenetic analysis shows that the fused PAB sequences form a tight group that also includes uncharacterized PabB homologues from several bacteria. Unfused bacterial PabA proteins group with the glutamine amidotransferase subunits of bacterial anthranilate synthases, independent of organismal systematics, indicating a complex and perhaps independent evolutionary origin. In contrast, unfused PabB group and fused PabA/B proteins form a monophyletic group on a branch separate from the chorismate amination subunits of anthranilate synthases, probably reflecting a need for recognition of different positions in the common substrate chorismate.

4-Aminobenzoic Acid↗

PubMed2006

Value of host range, morphological, and genetic characteristics within the Entomophthora muscae species complex.

Entomopthora muscae sensu lato is a complex of morphologically similar fungal species pathogenic to evolutionarily advanced flies (Cyclorrhapha). To reach an operational species definition and recognition of species within this complex, the values of host range, morphological and genetic characteristics are reconsidered. Within the E. muscae species complex morphological and nuclear characteristics of the primary conidia are taxonomically important. In this study we compared the dimensions and nuclear numbers of the primary conidia of isolates from their original (natural) hosts and after being transferred to alternative hosts (cross-transmission) in order to check the stability of these characteristics. The conidial characteristics change substantially when produced in alternative host species, but their overall range in variability still fit within the traditional morphological species circumscriptions. The phylogenetic analyses of the ITS II and LSU rRNA gene sequences, revealed three distinct lineages within the complex: E. schizophorae, E. muscae and E. syrphi. Within each of these lineages sequence divergence was seen between isolates originating from different host species. Our studies on the physiological host range showed that several isolates were able to infect alternative dipteran species. Musca domestica was a particularly good receptor. The ecological host range of any individual isolate seems, however, to be limited to one host species evidenced by the occurrence of distinct genotypes within each natural infected host species shown by RAPD. The high host specificity of these fungi emphasizes the importance of identifying the host taxon at species level in the recognition of Entomophthora species. We recommend that morphological characteristics of fungal structures and host taxon, together with molecular data, serve as criteria for species determination in future studies on members of the E. muscae complex.

Animals↗

PubMed1994

Peptide-induced T cell clones: specificity, MHC restriction, proliferation and cytokine pattern as a function of different stimulations.

CD4+ T cell clones were generated to tetanus toxin or to two tetanus toxin-derived peptides p2 (AA 830-834) and p30 (AA 947-976). 11 of the 24 p30-specific clones reacted to shorter p30 subunits (p301 or p302), and only 14 of the p2 or p30-specific clones reacted with TT presented by EBV-transformed B cell lines (B-LCL). The p30-specific clones were HLA-DP4 restricted. In contrast to autologous B cell lines, the majority of allogeneic, but HLA-DP4-positive cell lines failed to present p30 to the specific clones. We concluded that T cell clones are highly specific and that both, small alterations of the peptide length as well as discrete differences of the HLA-molecule may abrogate recognition of the peptide HLA complex by T cells. Moreover, use of peptides as stimulators of T cells may recruit and activate T cells which fail the "original" peptide, derived from normal antigen processing. Clones could usually be maintained in culture for 4-6 months, but with the help of freezing and thawing some clones are now available for over 2 years and still specific. Comparison of different autologous antigen-presenting cells, namely B-LCL and activated MHC class II-positive T cells revealed that not all clones were able to mount a proliferative response to peptide presentation by T cells, while all clones proliferated to B cells as APC. If stimulated with peptide and B-LCL, the clone proliferating to T cells as APC (so-called T responder clones) secreted a broad spectrum of cytokines (Th0-like) and were easier to maintain in culture. In contrast, clones which were unable to proliferate to peptide presentation, so-called T-nonresponder clones, showed a more restricted cytokine pattern and elevated or very low IL4/IFN gamma ratio upon antigen specific stimulation. However, all clones secreted at least small amounts of IL2, IL4, IFN gamma and TNF alpha, if stimulated by PMA and ionomycin. Thus, both chemical and antigen-specific stimulations should be considered if T cell clones are classified as Th1 or Th2, whereby those clones, which secrete a limited cytokine pattern after antigen stimulation only, might be named Th1 or Th2 like clones, while clones which even after PMA/ionomycin do not secrete all cytokines, might represent "real" Th1 or Th2 clones.

Clone Cells↗

PubMed2001

DNA recognition by F factor TraI36: highly sequence-specific binding of single-stranded DNA.

The TraI protein has two essential roles in transfer of conjugative plasmid F Factor. As part of a complex of DNA-binding proteins, TraI introduces a site- and strand-specific nick at the plasmid origin of transfer (oriT), cutting the DNA strand that is transferred to the recipient cell. TraI also acts as a helicase, presumably unwinding the plasmid strands prior to transfer. As an essential feature of its nicking activity, TraI is capable of binding and cleaving single-stranded DNA oligonucleotides containing an oriT sequence. The specificity of TraI DNA recognition was examined by measuring the binding of oriT oligonucleotide variants to TraI36, a 36-kD amino-terminal domain of TraI that retains the sequence-specific nucleolytic activity. TraI36 recognition is highly sequence-specific for an 11-base region of oriT, with single base changes reducing affinity by as much as 8000-fold. The binding data correlate with plasmid mobilization efficiencies: plasmids containing sequences bound with lower affinities by TraI36 are transferred between cells at reduced frequencies. In addition to the requirement for high affinity binding to oriT, efficient in vitro nicking and in vivo plasmid mobilization requires a pyrimidine immediately 5' of the nick site. The high sequence specificity of TraI single-stranded DNA recognition suggests that despite its recognition of single-stranded DNA, TraI is capable of playing a major regulatory role in initiation and/or termination of plasmid transfer.

Base Sequence↗

PubMed2003

Epididymis as a target for contraception.

Advantage of using a vaccine based on sperm antigens is that it can be used both in males and females as individuals who have antisperm antibodies are usually infertile but otherwise healthy. Several sperm specific antigens identified as prospective candidates for immunocontraception are of testicular origin. For the purpose of immunocontraception it may be desirable not to disrupt spermatogenesis and testicular function. Concept of post testicular maturation of spermatozoa has been very well established. During post testicular voyage spermatozoa undergo a series of complex and sequential events which transforms the immature immotile spermatozoa into mature sperm. Acquisition of functional maturity is necessary for progressive motility, zona pellucida recognition culminating in sperm egg binding. Importance of epididymal maturation is highlighted by the fact that high percentage of male infertility in human originates from the malfunction of the epididymis. The epididymis has also shown to be involved in sperm storage and provides an adequate environment for final maturation of the sperm. It provides a conducive microenvironment by virtue of which the spermatozoa are protected during the storage. In view of this it is imperative that more attention needs to be focused on epididymal antigens. The information obtained will enable us to identify epididymal antigens relevant to fertility and also help in infertility diagnosis.

Animals↗

PubMed1986

Cooperation between major histocompatibility complex mismatched mononuclear cells from a human chimera in the production of antigen-specific antibody.

Fetal liver and thymus transplantation can be successfully employed for the treatment of severe combined immunodeficiency disease. In virtually all cases, donor and recipient cells are HLA mismatched. In a patient suffering from a severe combined immunodeficiency disease, full immunological reconstitution was obtained after fetal liver and thymus transplantation. HLA typing revealed that the patient's T cells were of donor origin, while the B cells and monocytes were of host origin. Despite this complete HLA mismatch, the patient was found to mount a subnormal to normal antibody response in vivo. This finding is in contrast with the concept that antigen recognition by T cells is major histocompatibility complex (MHC) restricted. To define the mechanism responsible for this in vivo antibody response, antibody production by peripheral blood mononuclear cells from the patient was tested in vitro after in vivo booster. The in vitro anti-tetanus toxoid antibody production was similar to that of the control group. In addition, specific proliferative responses to tetanus toxoid were obtained. Immunoglobulin allotype determination showed that antibodies were synthetized by host B cells. The results of the present study indicate that transplanted T lymphocytes and recipient cells cooperate despite complete HLA mismatch.

Antibody Formation↗

PubMed1996

A Decomposition Principle for Complexity Reduction of Artificial Neural Networks.

A decomposition principle is developed for systematic determination of the dimensionality and the connections of Hopfield-type associative memory networks. Given a set of high dimensional prototype vectors of given memory objects, we develop decomposition algorithms to extract a set of lower dimensional key features of the pattern vectors. Every key feature can be used to build an associative memory with the lowest complexity, and more than one key feature can be simultaneously used to build networks with higher recognition accuracy. In the latter case, we further propose a "decomposed neural network" based on a new encoding scheme to reduce the network complexity. In contrast to the original Hopfield network, the decomposed networks not only increase the network's storage capacity, but also reduce the network's connection complexity from quadratic to linear growth with the network dimension. Both theoretical analysis and simulation results demonstrate that the proposed principle is powerful. Copyright 1996 Elsevier Science Ltd

Journal Article↗

PubMed2004

Molecular recognition in purinergic receptors. 2. Diastereoselectivity of the h-P2Y1-receptor.

In the companion paper, part 1, we described the construction of an improved molecular model for the h-P2Y1 receptor (h-P2Y1-R) and proposed a rational for the stereoelectronic selectivity of the receptor. Here, we extend our studies on the molecular recognition of the h-P2Y1-R to the exploration of the diastereoselectivity of this receptor. For this purpose, we implemented an integrative approach combining synthesis, spectral analysis, biochemical assays, and computational analysis. Specifically, we selected and synthesized novel ATP analogues bearing a chiral center on the phosphate chain. We analyzed the conformation of the chiral ATP analogues in solution by 1H/13C NMR and assigned the absolute configuration of the diastereoisomers. The coordination mode of these analogues with a Mg2+ ion was evaluated by 31P NMR. These chiral analogues were biochemically evaluated and found to be potent h-P2Y1-R ligands. An EC50 difference of ca. 20-fold was observed between the diastereoisomers. Their spectral absolute configuration assignment was confirmed by comparison of the biochemical results to those of ATP-alpha-S diastereoisomers whose chirality is known. Finally, a computational analysis was performed for the elucidation of molecular recognition employing molecular mechanics (docking) studies on the receptor:ligands complexes. On the basis of the current results, we hypothesize that h-P2Y1-R's chiral discrimination originates from the requirement that the nucleotide analogue interacts with a Mg2+ ion within the receptor binding site. This Mg2+ ion is possibly coordinated with both Asp204 and the ATP's alpha, beta, gamma-phosphates in a Lambda configuration.

Adenosine Triphosphate↗

PubMed2000

Reactive spindle cell nodules of the breast after core biopsy or fine-needle aspiration.

Reactive spindle cell nodules (RSCNs) arising postoperatively or after fine-needle aspiration (FNA) have been reported previously in the genitourinary tract and thyroid. We describe 18 cases of similar lesions in breast, associated with a history of core needle biopsy or FNA. The majority of the RSCNs (15 cases) were associated with papillary lesions or complex sclerosing lesions. The RSCNs were nonencapsulated and relatively nodular, measuring 1.5 to 9 mm. They were composed of spindle cells with mild to moderate nuclear pleomorphism and a low mitotic count. A network of small blood vessels, macrophages, and lymphocytes was present in all cases. Immunohistochemically, the spindle cells expressed smooth and specific muscle actins, supporting a myofibroblastic origin. The association of RSCNs with needle trauma to fibrosclerotic lesions, such as complex sclerosing lesions and papillary lesions that regularly have myofibroblasts, suggests an exuberant reparative cause. Recognition of this reactive process will avoid overdiagnosis of mammary spindle cell malignant neoplasm.

Actins↗

PubMed2000

Transport of proteins into and across the thylakoid membrane.

The biogenesis of thylakoid proteins is a complex issue that requires the operation of at least four pathways within the chloroplast. Two of the pathways are used for soluble lumenal proteins, where the proteins bear cleavable targeting signals that are recognized by one of two distinct translocases. These pathways differ in fundamental respects. A subset of lumenal proteins are transported in an unfolded state by a typical Sec system, whereas others are transported by a novel class of translocase that appears to function primarily in the transport of fully-folded proteins. Related protein translocases have now been shown to operate in a wide variety of bacterial species, suggesting a widespread requirement for the translocation of folded proteins across biological membranes. Numerous integral membrane proteins are also targeted into the thylakoid membrane, and these too follow at least two distinct routes. Some proteins use a signal recognition particle-dependent pathway that requires GTP and unidentified apparatus in the thylakoid membrane. Others, however, require none of the known targeting factors and may insert spontaneously into the membrane. In this article, the rationale behind this pathway complexity is discussed in relation to the properties of the substrate proteins and the evolutionary origins of the chloroplast.

Amino Acid Sequence↗

PubMed1999

Chloroplast precursor protein translocon.

Chloroplasts are believed to have originated from a photosynthetic, prokaryotic ancestor. As the result of endosymbiotic evolution, most of the genes of the endocytobiont were displaced to the host nucleus. Today's chloroplasts must import most of their proteins from the cytosol as precursors. Oligomeric protein complexes in the chloroplast outer and inner envelope membranes are responsible for the specific recognition and membrane translocation of precursor proteins. The translocon at the outer membrane of chloroplasts and the inner membrane of chloroplasts act jointly during the import process. Several translocon subunits have been partially characterized in their molecular structure and function. Initial evidence indicates the prokaryotic origin of some chloroplast translocon components.

Biological Transport↗

PubMed1994

Identification of a mannose-acetate-specific 87-kDa receptor responsible for human NK and LAK activity.

Target cell recognition and cytotoxicity of human CD56+ NK and LAK cells is readily inhibited by acetylated mannose. Two respective NK cell receptor candidates were isolated from human leukocyte lysates by mannose acetate affinity chromatography. The 87-kDa receptor showed sequence homologies with lactoferrin and the 59-kDa receptor represented a complex of two Ca-binding proteins MRP-8 and MRP-14 reportedly expressed only by cells of myeloid origin. The 87-kDa receptor exhibited heterogeneity in isoelectric focusing and behaved entirely differently from lactoferrin. Preincubation of tumor target cells with the 87-kDa receptor inhibited competitively target cell recognition and cytotoxicity of human CD56+ NK and LAK cells.

Acetylation↗

PubMed2006

Generation of time delays: simplified models of intracellular signalling in cerebellar Purkinje cells.

In many neuronal systems, information is encoded in temporal spike patterns. The recognition and storage of temporal patterns requires the generation and modulation of time delays between inputs and outputs. In cerebellar Purkinje cells, stimulation of metabotropic glutamate receptors (mGluRs) results in a delayed calcium and voltage response that has been implicated in classical conditioning and temporal pattern recognition. Here, we analyse and simplify a complex model of the intracellular signalling network that has been proposed as a substrate for this delayed response. We systematically simplify the original model, present a minimal model of time delay generation, and show that a delayed response can be produced by the combination of negative feedback and autocatalysis, without any intervening signalling steps that would contribute additive delays. The minimal model is analysed using phase plane methods, and classified as an excitable system. We discuss the implication of excitability for computations performed by intracellular signalling networks in general.

Animals↗

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↗