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PubMed1989

Antigen-specific recognition of autologous leukemia cells and allogeneic class-I MHC antigens by IL-2-activated cytotoxic T cells from a patient with acute T-cell leukemia.

Culturing of leukemic blood lymphocytes from a patient with acute T-cell lymphoblastic leukemia (T-ALL) with interleukin-2 (IL-2) yielded T-cell line AK-1 with a remarkable cytotoxic specificity. This line mediated strong lysis of tumor target lines expressing major histocompatibility complex (MHC) class I antigens, such as Raji, CEM, and Molt-4 cells, but no killing of K562 and Daudi cells, which are deficient in MHC class I. In contrast, lymphokine-activated killer (LAK) cells from normal donors destroyed all these tumor targets, without MHC restriction. Line AK-1, originating from residual normal T cells present in the leukemic blood, lysed autologous leukemic blasts and peripheral blood lymphocytes (PBL) from many but not all allogeneic individuals but failed to kill autologous remission lymphocytes. Destruction of the autologous leukemic targets by AK-1 could be inhibited by unlabeled competitor target cells that were lysed by AK-1, but not by target cells that were not lysed. This suggests that AK-1 specifically recognized an alien determinant on the autologous ALL cells, crossreactive with allogeneic MHC class I antigens. This reactivity with some degree of tumor specificity may be a leukemic equivalent to responses reported for populations of tumor infiltrating lymphocytes (TIL) seen in some solid tumors.

Adult↗
PubMed1989

Model of the interactions of calichemicin gamma 1 with a DNA fragment from pBR322.

An analysis of the binding interactions of several DNA-drug complexes that utilize carbohydrates for DNA recognition has been undertaken. It is proposed that the carbohydrate residues function as general minor groove binding elements, and the stereochemistry of aglycone attachment sites is generally disposed to promote a right-handed helical geometry that is complementary to right-handed DNA. The constitution and stereochemistry of the DNA double-strand cleaving agent calichemicin gamma 1 is consistent with this analysis. Docking experiments with computer-generated models of this drug and a dodecamer duplex that was found to serve as a calichemicin cleavage site were performed to gain insight into the origin of the drug's sequence-selective binding and cutting properties. A model is presented that provides a molecular level understanding of the double-strand cleavage patterns that result from the action of calichemicin gamma 1 on DNA.

Aminoglycosides↗
PubMed1998

Conserved cis- and trans-acting determinants for replication initiation and regulation of replication fork movement in tetrahymenid species.

The rDNA minichromosomes of Tetrahymena thermophila and Tetrahymena pyriformis share a high degree of sequence similarity and structural organization. The T.thermophila 5' non-transcribed spacer (5' NTS) is sufficient for replication and contains three repeated sequence elements that are conserved in T.pyriformis , including type I elements, the only known determinant for replication control. To assess the role of conserved sequences in replication control, structural and functional studies were performed on T.pyriformis rDNA. Similar to T.thermophila , replication initiates exclusively in the 5' NTS, localizing to a 900 bp segment. Elongating replication forks arrest transiently at one site which bears strong similarity to a tripartite sequence element present at fork arrest sites in T.thermophila rDNA. An in vitro type I element binding activity indistinguishable from the T.thermophila protein, ssA-TIBF, was detected in T.pyriformis extracts. The respective TIBF proteins bind with comparable affinity to type I elements from both species, suggesting that in vivo recognition could cross species boundaries. Despite these similarities, the T.pyriformis 5' NTS failed to support replication in transformed T.thermophila cells, suggesting a more complex genetic organization than previously realized.

Animals↗
PubMed1985

Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites.

A system has been developed for facile generation and characterization of mutant lac operator sites, free of competing pseudo operator sequences. The interaction of lac repressor with these sites has been investigated by the nitrocellulose filter binding assay. The equilibrium binding affinity for each of three single-site changes was reduced by more than three orders of magnitude relative to the wild-type operator under standard assay conditions. The free-energy changes associated with single base-pair substitutions are not additive. We propose that adaptations in the recognition surface of the repressor involving significant trade-offs between electrostatic versus non-electrostatic interactions and between enthalpic versus entropic contributions to the binding free energy occur, in order to achieve the most stable complex with a given DNA sequence.

Alleles↗
PubMed1996

Analysis of the disulfide linkage pattern in circulin A and B, HIV-inhibitory macrocyclic peptides.

Circulin A and B are members of a family of macrocyclic peptides, originally isolated from the tropical tree Chassalia parvifolia, that have been shown to display anti-HIV activity. Complete structural elucidation of these highly constrained peptides was difficult due to their cyclic amide backbone and the presence of six disulfide-linked cysteines. In the present study, the disulfide pairing motif of circulin A and circulin B was determined. Since the circulins were resistant to enzymatic proteolysis, cysteine residue pairings were identified by analysis of the complex mixture of cleavage products that resulted from partial acid hydrolysis of the native peptides. Combined utilization of HPLC, fast atom bombardment mass spectrometry and peptide recognition software ("F-MASS" and "F-LINK" programs) were employed to identify the cleavage products. Thus, we were able to unambiguously identify the disulfide linkage pattern in circulin A and circulin B as Cys1-Cys4, Cys2-Cys5 and Cys3-Cys6, where the numbers on the cystine residues refer to their respective order in the peptides.

Amino Acid Sequence↗
PubMed1989

Epitopes within the HLA-B5,B35 cross-reacting group.

The HLA-B5,B35 cross-reacting group is a large and serologically complex antigen family which includes the World Health Organization-recognized specificities HLA-B5,B51,Bw52,B35,Bw53,B18,Bw70,Bw71, and Bw72. In addition, several variants of antigens in this cross-reacting group have been described in the past but have not yet gained official recognition. A genetic basis for the complexity and the protein and molecular bases of this highly cross-reactive and polymorphic cross-reacting group have yet to be established. The potential contributions of shared amino acid sequences, the occurrence of multiple epitopes on a single HLA-B molecule, and the presence of new HLA-C antigens have been difficult to resolve. To address this issue, we have carefully examined the serologic reactions of more than 900 allo- and monoclonal antibodies (Tenth International Workshop, Third Asia-Oceanic Workshop, and local reagents) versus lymphocytes from 92 individuals of diverse ethnic origin (North American Caucasians, North American blacks, Amerindians, Middle Eastern Caucasians), 84 of whom were informative for the HLA-B5,B35 cross-reacting group and related antigens. Our results demonstrate that the HLA-B5,B35 gene products share different combinations of distinct epitopes. We have constructed a model for the evolution of this cross-reacting group by assigning polarity to distinct diversification steps utilizing principles of maximum parsimony.

Antibodies, Monoclonal↗
PubMed2004

The ISG15 isopeptidase UBP43 is regulated by proteolysis via the SCFSkp2 ubiquitin ligase.

The Skp2 oncoprotein belongs to the family of F-box proteins that function as substrate recognition factors for SCF (Skp1, cullin, F-box protein) E3 ubiquitin-ligase complexes. Binding of the substrate to the SCFSkp2 complex catalyzes the conjugation of ubiquitin molecules to the bound substrate, resulting in multi-ubiquitination and rapid degradation by the 26 S proteasome. Using Skp2 as bait in a yeast two-hybrid screen, we have identified UBP43 as a novel substrate for Skp2. UBP43 belongs to the family of ubiquitin isopeptidases and specifically cleaves ISG15, a ubiquitin-like molecule that is induced by cellular stresses, such as type 1 interferons (IFN), nephrotoxic damage, and bacterial infection. UBP43 was originally identified as an up-regulated gene in knock-in mice expressing an acute myelogenous leukemia fusion protein, AML1-ETO, as well as in melanoma cell lines treated with IFN-beta. The phenotype of UBP43 knockout mice includes shortened life span, hypersensitivity to IFN, and neuronal damage, suggesting that tight regulation of ISG15 conjugation is critical for normal cellular function. In this study, we demonstrate that UBP43 is ubiquitinated in vivo and accumulates in cells treated with proteasome inhibitors. We also show that Skp2 promotes UBP43 ubiquitination and degradation, resulting in higher levels of ISG15 conjugates. In Skp2-/- mouse cells, levels of UBP43 are consistently up-regulated, whereas levels of ISG15 conjugates are reduced. Our results demonstrate that the SCFSkp2 is involved in controlling UBP43 protein levels and may therefore play an important role in modulating type 1 IFN signaling.

Animals↗
PubMed1987

The origin of the immune system. The possibility that immunoglobulin superfamily molecules and cell adhesion molecules of chicken and slime mould are all related.

It has been suggested that the neural cell adhesion molecules (N-CAM) are members of the Ig superfamily. We have examined structural homology between the N-CAM and other superfamily molecules in detail. The Ig-like domains of N-CAM have overall sizes similar to those of Ig constant domains or major histocompatibility complex (MHC) domains. Significant sequence homology was found between the N-CAM Ig-like domains and several other Ig superfamily members, such as T4, T8, IgA transport receptor, Ig VH, Ig C mu 4, and others. A comparison of the second domain of T4 (255 amino acids) with the central domain of N-CAM (302 amino acids) has demonstrated a significant sequence homology. Furthermore, a cell adhesion protein, cs-A, of slime mould, Dictyostelium, also seems to be related to N-CAM. It appears that the Ig superfamily of the immune system originated from more ubiquitous cell recognition molecules which are common in all metazoan species.

Amino Acid Sequence↗
PubMed1992

Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF.

Opening of the three tandem repeats of a 13-mer in the replication origin (oriC) of Escherichia coli is a prime event in the replication in vitro of minichromosomes (Bramhill, D., and Kornberg, A. (1988) Cell 54, 915-918). DnaA, the initiator protein, requires protein HU or IHF, along with a millimolar level of ATP and negative superhelical density in the plasmid to open this region. The extent of opening, as judged by cleavage by a single-strand-specific endonuclease (i.e. P1 nuclease), correlated closely with replication of the oriC plasmid. In an initial complex, preceding opening of the 13-mers, the footprint of DnaA protein bound by ATP covered its four 9-mer recognition sequences. The footprint of the nucleotide-free form of the protein, by contrast, was more extensive and thus, less specific.

Bacterial Proteins↗
PubMed2006

Object color affects identification and repetition priming.

We investigated the influence of color on the identification of both non-studied and studied objects. Participants studied black and white and color photos of common objects and memory was assessed with an identification test. Consistent with our meta-analysis of prior research, we found that objects were easier to identify from color than from black and white photos. We also found substantial priming in all conditions, and study-to-test changes in an object's color reduced the magnitude of priming. Color-specific priming effects were large for color-complex objects, but minimal for color-simple objects. The pattern and magnitude of priming effects was not influenced either by the extent to which an object always appears in the same color (i.e., whether a color is symptomatic of an object) or by the object's origin (natural versus fabricated). We discuss the implications of our findings for theoretical accounts of object perception and repetition priming.

Color Perception↗
PubMed2006

Stereoselective recognition of vicinal diamines with a Zn(II) complex.

Zn(II) complex of L (N,N'-bis(2-pyridylmethyl)-N,N'-dimethyl-trans-1,2-diaminocyclohexane) binds chiral vicinal diamines (1,2-diphenylethylenediamine (dpen) and 1,2-diaminocyclohexane (dach)) stereoselectively. Crystallographic studies reveal that the ternary complex has the C2 symmetric cis-alpha topology. 1H NMR shows that the R,R form of the tetradentate zinc complex binds rapidly and reversibly to the R,R form of the diamine over the S,S form with a stereoselectivity of about 5:1. Although the diamine exchange rate is rapid it is slower than the NMR time scale, and distinct signals for the diastereomeric complexes are observed when racemic mixtures of the host and guest molecules are mixed. Origin of stereoselectivity is discussed in terms of steric effects.

Journal Article↗
PubMed1981

Expression of serologically detectable H-2 antigens on mid-gestation mouse embryonic tissues.

Mixed haemadsorption assays using antibody-coated indicator sheep erythrocytes and mouse alloantisera revealed that major histocompatibility complex (H-2) antigens were expressed on cells of 24-72 h cultures of mid-gestation mouse embryonic skin, gut, lung, limb-bud and heart but not of embryonic gonad or kidney. The precise time of detection of H-2 antigen expression and the proportions of cells expressing these determinants depended on inbred strain, specific haplotype, tissue of origin and antiserum batch employed. In all tissues the proportion of cells expressing H-2 increased progressively from day 11-12 post-coitum onwards. The findings are discussed with respect to hypotheses concerning the possible role of major histocompatibility antigens in cellular recognition and interactions during embryogenesis.

Animals↗
PubMed2003

Adapting Active Shape Models for 3D segmentation of tubular structures in medical images.

Active Shape Models (ASM) have proven to be an effective approach for image segmentation. In some applications, however, the linear model of gray level appearance around a contour that is used in ASM is not sufficient for accurate boundary localization. Furthermore, the statistical shape model may be too restricted if the training set is limited. This paper describes modifications to both the shape and the appearance model of the original ASM formulation. Shape model flexibility is increased, for tubular objects, by modeling the axis deformation independent of the cross-sectional deformation, and by adding supplementary cylindrical deformation modes. Furthermore, a novel appearance modeling scheme that effectively deals with a highly varying background is developed. In contrast with the conventional ASM approach, the new appearance model is trained on both boundary and non-boundary points, and the probability that a given point belongs to the boundary is estimated non-parametrically. The methods are evaluated on the complex task of segmenting thrombus in abdominal aortic aneurysms (AAA). Shape approximation errors were successfully reduced using the two shape model extensions. Segmentation using the new appearance model significantly outperformed the original ASM scheme; average volume errors are 5.1% and 45% respectively.

Algorithms↗
PubMed1992

Analysis of striate activity underlying the pattern onset EP of children.

The checkerboard onset Evoked Potential (EP) does not obtain its adult form before puberty. To determine the site of origin of these processes we studied the origin of the checkerboard onset EP in a group of 10 children between the ages of 6 and 16 years. Since the development of the waveform of the pattern onset EP varies with check size we also studied the dependence of these EPs on check size. The child checkerboard onset EPs described in this paper are dominated by a single source. Following an equivalent dipole source localization approach, the position, orientation and variation in strength of the equivalent dipole is estimated. The position and orientation of this dipole indicates an origin in the primary visual cortex (area 17). The variation in strength of the dipole changes from a single positive deflection, specific for children of 8 years and younger, into a negative-positive complex for the children studied between the age of 9 and 16 years. These changes in waveform must be due to changes in the activity pattern of the striate cortex.

Adolescent↗
PubMed1989

[A novel experimental approach to immunotherapy against malignant brain tumor with the mouse IFN-gamma gene transfer].

To investigate the effect of interferon-gamma (IFN-gamma) on the immunotherapy, we used the autocrinically stimulated system in which a mouse IFN-gamma cDNA was transferred by infection with a chimeric retrovirus containing the IFN-gamma gene. First, we established a tumor specific CTL clone (E-4) against 203-glioma cells (a 20-methylcholanthrene induced mouse ependymoblastoma line of C57BL/6 mouse origin), and then transferred murine IFN-gamma cDNA into E-4 by using retroviral vector (pSVX(Mu gamma delta A]. Out of five gene-transferred subclones, E gamma-4, E gamma-5, E gamma-6, E gamma-7 and E gamma-9, two subclones (E gamma-6 and E gamma-9) constitutively produced 8- to 10-fold amounts of IFN-gamma as compared with the parental E-4. Moreover, these two subclones exhibited two to three times higher killing activity against 203-glioma than the parental cells. The enhancement of the killing activities was abrogated by an adequate addition of anti-IFN-gamma antibody. No alteration was seen after the gene transfer in cell surface phenotypes, Thy-1+, Lyt-1-, Lyt-2+3+ and asialo-GM1-. Fluorescence-activated cell sorter (FACS) analysis showed that the surface expression of major histocompatibility complex (MHC) Class I antigen, H-2Kb, of parental E-4 was augmented remarkably, and it was not altered by the IFN-gamma gene transfer, but the Class II antigen, I-Ab, was slightly enhanced on the two IFN-gamma-producing sublines. Since it is considered that in the vicinity of the constitutively IFN-gamma-producing CTL cells, tumor cells are exposed to a high concentration of IFN-gamma and may be stimulated to induce or enhance the expression of surface antigens including MHC antigens as well as tumor associated antigens in relation to immune recognition. The 203-glioma cells pretreated with IFN-gamma were more efficiently killed by both the parental E-4 and the gene-transferred sublines. It was thus suggested that the specific tumor killing activity of the gene-transferred CTLs was augmented by the constitutive production of IFN-gamma derived from the exogenous gene. As the next step, a mouse IFN-gamma cDNA was transferred into a neuroblastoma line C1300 of A/JAx mouse origin. Two infected subclones C gamma 3 and C gamma 22, were obtained as a low and a high producers, respectively. Both IFN-gamma gene transferred cells remained unchanged as regards in vitro cell growth, morphological appearance and differentiation antigen expression such as neurofilaments after the IFN-gamma gene transfer. On the other hand, expression of MHC Class I antigens of both subcloned lines was extremely augmented at the surface expression level as well as at the transcription level, re

Animals↗
PubMed2007

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions.

A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.

Benzamidines↗
PubMed1989

Signals at the bacteriophage phi 29 DNA replication origins required for protein p6 binding and activity.

Protein p6 of Bacillus subtilis phage phi 29 binds specifically to the ends of the viral DNA that contain the replication origins, giving rise to a nucleoprotein structure. DNA regions recognized by protein p6 have been mapped by deletion analysis and DNase I footprinting. Main protein p6-recognition signals have been located between nucleotides 62 and 125 at the right phi 29 DNA end and between nucleotides 46 and 68 at the left end. In addition, recognition signals are also present at other sites within 200-300 bp at each phi 29 DNA end. Protein p6 does not seem to recognize a specific sequence in the DNA, but rather a structural feature, which could be bendability. The formation of the protein p6-DNA nucleoprotein complex is likely to be the structural basis for the protein p6 activity in the initiation of replication.

Bacteriophages↗
PubMed2006

A RecA mutant, RecA(730), suppresses the recombination deficiency of the RecBC(1004)D-chi* interaction in vitro and in vivo.

In Escherichia coli, homologous recombination initiated at double-stranded DNA breaks requires the RecBCD enzyme, a multifunctional heterotrimeric complex that possesses processive helicase and exonuclease activities. Upon encountering the DNA regulatory sequence, chi, the enzymatic properties of RecBCD enzyme are altered. Its helicase activity is reduced, the 3'-->5'nuclease activity is attenuated, the 5'-->3' nuclease activity is up-regulated, and it manifests an ability to load RecA protein onto single-stranded DNA. The net result of these changes is the production of a highly recombinogenic structure known as the presynaptic filament. Previously, we found that the recC1004 mutation alters chi-recognition so that this mutant enzyme recognizes an altered chi sequence, chi*, which comprises seven of the original nucleotides in chi, plus four novel nucleotides. Although some consequences of this mutant enzyme-mutant chi interaction could be detected in vivo and in vitro, stimulation of recombination in vivo could not. To resolve this seemingly contradictory observation, we examined the behavior of a RecA mutant, RecA(730), that displays enhanced biochemical activity in vitro and possesses suppressor function in vivo. We show that the recombination deficiency of the RecBC(1004)D-chi* interaction can be overcome by the enhanced ability of RecA(730) to assemble on single-stranded DNA in vitro and in vivo. These data are consistent with findings showing that the loading of RecA protein by RecBCD is necessary in vivo, and they show that RecA proteins with enhanced single-stranded DNA-binding capacity can partially bypass the need for RecBCD-mediated loading.

DNA, Bacterial↗