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PubMed1996

The HLA system: an update and relevance to patient-donor matching strategies in clinical transplantation.

In recent years the development of recombinant DNA and sequencing techniques has led to a greatly increased understanding of the genetic complexity, structure and function of the human major histocompatibility complex. This system may be subdivided into the "classical' HLA (human leukocyte antigen) class I and II transplantation antigens and novel HLA and non-HLA genes, involved in antigen processing and presentation to T cells. Parallel technological developments in HLA DNA typing in the clinical laboratory have resulted in a more precise awareness of the role of HLA matching for the classical HLA antigens in bone marrow and solid organ transplantation, while alternative strategies and techniques for donor selection are currently under evaluation. This review offers a current perspective on the genetics, structure and function of the HLA system, its relevance to clinical transplantation and future prospects for improvements in donor selection.

Bone Marrow Transplantation↗
PubMed2006

Application of invariant grey scale features for analysis of porous minerals.

Three-dimensional (3D) texture analysis can be used to differentiate similar materials which have a complex structural nature that is not easily reduced to geometric primitives. A method which extends the concept of invariant grey scale features to non-structured 3D textures is introduced and applied to the study of five processed mineral carbon materials which are characteristically similar but derive from different industrial sources. X-ray microtomography (XRMT) was used to obtain 3D tomographic data with isotropic voxel spacing of 9.8 microm. These data were used to construct invariant features for 3D texture measurement via Monte Carlo based sampling routines and integrals of grey scale relational kernel functions. The procedure produced multi-component texture vectors, which were successfully tested against texture samples as a classification-recognition tool. Identification accuracies ranging from 69% to approximately 84% were achieved for the five material sources examined. This result provides a sound basis for quantitative analysis of these materials which to date have proved very difficult to examine using traditional image analysis tools because of their complex natural structure.

Journal Article↗
PubMed1995

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Antibodies, Catalytic↗
PubMed1974

The mechanism of viral replication. Structure of replication complexes of encephalomyocarditis virus.

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a "bush" of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA.

Centrifugation, Density Gradient↗
PubMed1992

New insights into T-cell antigen receptor structure and signal transduction.

Recent studies have provided insights into how the complex structure of the T-cell antigen receptor relates to its signal transduction function. Both the CD3 and zeta subunits contain functioning signaling modules that regulate the activation of tyrosine kinases and phosphorylation of cellular substrates.

Amino Acid Sequence↗
PubMed2005

Fully dimensional ab initio description of the structure and energetics of azabenzene-argon complexes.

The structure and energetics of van der Waals complexes of argon with azabenzenes: pyridine, pyrazine, pyrimidine, pyridazine, s-triazine, and s-tetrazine are studied using the second-order Moller-Plesset perturbation theory combined with well-balanced basis sets. The full optimization of the cluster structures and computation of the inter- and intramolecular vibrational frequencies is performed by eliminating the basis set superposition error. The argon equilibrium coordinates are calculated with the accuracy comparable to that reached by standard methods of the structure determination from the spectral data. A simple rule to predict the position of argon with respect to the geometric center of the azabenzene ring is found. The calculated harmonic frequencies of the intermolecular vibrational modes are scaled by the factor of 0.85 to eliminate systematic errors coming from the neglect of anharmonic effects. The scaled frequencies agree with the experimental ones to about 1 cm(-1), except for pyrimidine-argon and tetrazine-argon for which empirical fundamental frequency estimates are problematic. A simple relation connecting the intermolecular bending frequencies and the monomer quadrupole tensor is found. The perturbation of the monomer properties caused by complexation is analyzed. The modification of the monomer structure by the interaction with argon and its influence on the binding energy appears to be negligible in all complexes studied. However, this interaction affects appreciably the intramolecular modes and causes their frequency shifts. As a consequence, the dissociation energy of the complexes increases by about 5 cm(-1).

Journal Article↗
PubMed1989

Lysosomal H+-translocating ATPase has a similar subunit structure to chromaffin granule H+-ATPase complex.

Subunit structure of the lysosomal H+-ATPase was investigated using cold inactivation, immunological cross-reactivity with antibodies against individual subunits of the H+-ATPase from chromaffin granules and chemical modification with N,N'-dicyclohexyl[14C]carbodiimide. The lysosomal H+-ATPase was irreversibly inhibited when incubated at 0 degrees C in the presence of chloride or nitrate and MgATP. Inactivation in the cold resulted in the release of several polypeptides (72, 57, 41, 34 and 33 kDa) from the membrane, which had the same electrophoretic mobility as the corresponding subunits of chromaffin granule H+-ATPase. Cross-reactivity of antibodies revealed that the 72, 57 and 34 kDa polypeptides were immunologically identical to the corresponding subunits of chromaffin granule H+-ATPase. Dicyclohexylcarbodiimide, which inhibits proton translocation in the vacuolar ATPase, predominantly labeled two polypeptides of 18 and 15 kDa, which compose the membrane sector of the enzyme. These results suggest that the lysosomal H+-ATPase is a multimeric enzyme, whose subunit structure is similar to the chromaffin granule H+-ATPase. The subunit structure of other vacuolar H+-ATPases, revealed by cold inactivation and immunological cross-reactivity, is also presented.

Adrenal Glands↗
PubMed2001

Insights into autoimmunity gained from structural analysis of MHC-peptide complexes.

The structural and functional properties of HLA-DQ and -DR molecules that confer susceptibility to several common autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis and multiple sclerosis, have been defined. The relevant polymorphisms directly affect interaction with peptides, which provides strong support for the hypothesis that these diseases are peptide-antigen driven. Several studies indicate that structural modifications of peptides can affect MHC class II binding and/or TCR recognition and should be considered in the analysis of T cell responses in autoimmune diseases.

Amino Acid Sequence↗
PubMed2006

186Re-HEDP in the treatment of patients with inoperable osteosarcoma.

UNLABELLED: The aim of this study was to examine the safety and efficacy of (186)Re-hydroxyethylidene diphosphonate (HEDP) as an adjuvant to external-beam radiotherapy (EBRT) in the treatment of patients with osteosarcoma. METHODS: Thirteen patients (9 male, 4 female; age range, 12-42 y) were treated with combination chemotherapy (standard U.K. protocol) and (186)Re-HEDP therapy (18.5 MBq/kg, intravenously), followed by EBRT. A full blood count; liver function test; and measurements of urea and electrolytes, glomerular filtration rate, and left ventricular function were performed on all patients before and after therapy. Tumor volume and composition were obtained from CT or MRI data. Dosimetric calculations were performed using the MIRD formalism. RESULTS: Of the 13 patients, 1 is still under follow-up. The median survival time was 36 mo (range, 12-216 mo) from diagnosis and 5 mo (range, 1-60 mo) from the last (186)Re-HEDP treatment. The mean tumor dose delivered with (186)Re-HEDP was calculated to be 5.8 Gy (range, 0.5-16 Gy). CT and MRI revealed the tumors to have a complex structure, comprising "ossified," "partially calcified," and "soft-tissue" components. Posttherapy scans showed a heterogeneous distribution of (186)Re-HEDP in the tumor mass: Although the "soft-tissue" component showed minimal uptake of the therapeutic dose, the "ossified component" showed intense uptake. The 3 long-term survivors in whom tumor sterilization was achieved received calculated mean tumor doses in the range of 2.0-3.1 Gy, which was believed to be an underestimate of the actual tumor doses delivered. CONCLUSION: This study indicates that a simple approach to tumor dosimetry based on mean tumor dose is inappropriate because it may underestimate the dose delivered to these heterogeneous tumors. The data also indicate that EBRT combined with a standard dose of 18.5 MBq/kg of (186)Re-HEDP does not provide a sufficient dose to achieve tumor sterilization. A dose estimation technique is required that is based on the determination of tumor dose at the individual voxel level and that is able to represent the heterogeneous uptake observed in these complex tumor structures with highly nonuniform composition. This, coupled with individualized dose escalation, may then achieve the goal of tumor sterilization.

Adolescent↗
PubMed2000

Studies on the structure of the complex of the boron neutron capture therapy drug, L-p-boronophenylalanine, with fructose and related carbohydrates: chemical and 13C NMR evidence for the beta-D-fructofuranose 2,3,6-(p-phenylalanylorthoboronate) structure.

The complex of L-L-boronophenylalanine (L-p-BPA) with fructose has been used for the past 5 years in clinical trials of boron neutron capture therapy to treat both melanoma and glioblastoma multiforme. However, the structure of this complex in water buffered at physiologic pH has not been established. In the (1)H NMR spectra (D(2)O buffered at pD 7.4) of the complex of L-p-BPA with various carbohydrates, the upfield chemical shifts of the aromatic protons of L-p-BPA confirm that the boron atom is negatively charged and tetrahedral. In the (13)C NMR spectrum of the complex of L-p-BPA with U-(13)C labeled fructose, the chemical shifts and (1)J(CC) coupling constants are consistent with fructose adopting the beta-D-fructofuranose form. In addition, the (1)J(CC) coupling constants along with the binding constants measured for L-p-BPA with a series of monosaccharides and disaccharides seem to suggest that the beta-D-fructofuranose 2,3,6-(p-phenylalanylorthoboronate) structure strongly predominates, with free L-p-BPA and fructose the only other species detected.

Boron Compounds↗
PubMed2006

History, anatomical nomenclature, comparative anatomy and functions of the hippocampal formation.

The complex structures in the cerebral hemispheres is included under one term, the limbic system. Our conception of this system and its special functions rises from the comparative neuroanatomical and neurophysiological studies. The components of the limbic system are the hippocampus, gyrus parahippocampalis, gyrus dentatus, gyrus cinguli, corpus amygdaloideum, nuclei anteriores thalami, hypothalamus and gyrus paraterminalis Because of its unique macroscopic and microscopic structure, the hippocampus is a conspicuous part of the limbic system. During phylogenetic development, the hippocampus developed from a simple cortical plate in amphibians into complex three-dimensional convoluted structure in mammals. In the last few decades, structures of the limbic system were extensively studied. Attention was directed to the physiological functions and pathological changes of the hippocampus. Experimental studies proved that the hippocampus has a very important role in the process of learning and memory. Another important functions of the hippocampus as a part of the limbic system is its role in regulation of sexual and emotional behaviour. The term "hippocampal formation" is defined as the complex of six structures: gyrus dentatus, hippocampus proprius, subiculum proprium, presubiculum, parasubiculum and area entorhinalis In this work we attempt to present a brief review of knowledge about the hippocampus from the point of view of history, anatomical nomenclature, comparative anatomy and functions (Tab. 1, Fig. 2, Ref. 33).

Anatomy, Comparative↗
PubMed1999

Protein dynamics: imidazole binding to class I C-type cytochromes.

The oxidized cytochrome c(2) from the purple phototrophic bacteria, Rhodobacter sphaeroides and Rhodobacter capsulatus, bind the neutral species of imidazole (K(a) = 1440 +/- 40 M(-1)) 50 times more strongly than does horse mitochondrial cytochrome c (K(a) = 30 +/- 1 M(-1)). The kinetics of imidazole binding are consistent with a change in rate-limiting step at high ligand concentrations for all three proteins. This is attributed to a conformational change leading to breakage of the iron-methionine bond which precedes imidazole binding. The three-dimensional structure of the Rb. sphaeroides cytochrome c(2) imidazole complex (Axelrod et al., Acta Crystalogr. D50, 596-602) supports the view that the conformational changes are essentially localized to approximately seven residues on either side of the ligated methionine and there is a hydrogen bond between the Phe 102 carbonyl, an internal water, and the bound imidazole. Insertions and deletions in this region of cytochrome c(2), the presence of a proline near the methionine, and the smaller size of the dynamic region of horse cytochrome c suggest that the stabilizing hydrogen bond is not present in horse cytochrome c, hence, the dramatic difference in affinity for imidazole. The kinetics of ligand binding do not correlate with either the strength of the iron-methionine bond as measured by the pK of the 695-nm absorption band or the overall stability of the cytochromes studied. However, the very similar imidazole binding properties of the two cytochromes c(2) indicate that the Rb. sphaeroides cytochrome c(2)-imidazole complex structure is an excellent model for the corresponding Rb. capsulatus cytochrome c(2) complex. It is notable that the movement of the peptide chain in the vicinity of the ligated methionine has been preserved throughout evolution and suggests a role in the function of c-type cytochromes.

Azides↗
PubMed1990

The Cytoskeleton of trypanosomes.

From the concept of cells as mere bags full of enzymes, cell biology has come a long way towards understanding the highly complex structural organization of eukaryotic cells. The cytoskeleton, ie. the complex of fibrous elements that are crucial for cell shape, motility and the structural organization of cytoplasm and cell membranes, is now recognized as vital for supporting many critical functions in eukaryotic cells. Surprisingly, this subject, which has provided scores of cell biologists with excitement and fascination, has been largely overlooked with respect to parasitic protozoa. A notable change of perception has taken place over the past few years as the cytoskeleton of parasitic protozoa has been increasingly recognized as a potential target for antiparasitic intervention. The following article by Thomas Seebeck, Andrew Hemphill and Durward Lawson highlights some recent developments in the analysis of what is presently the best-studied parasite cytoskeleton, that of the trypanosome.

Journal Article↗
PubMed1990

Binding of foreign DNA to mouse sperm mediated by its MHC class II structure.

By means of radioimmunoassay, the expression of the major histocompatibility complex (MHC) class II molecules on murine sperm cells was clearly demonstrated as well as by our previous enzyme immunoassay (Mori T, et al. The expression of class II major histocompatibility antigen on mouse sperm and its role in fertilization. Am J Reprod Immunol. 1990; 24:9-14). The present study revealed that the site of sperm for binding foreign DNA was mediated by the complex structure of the MHC class II molecules localized at the posterior region of sperm head. This binding activity of sperm was time-, temperature-, and viability-dependent and completely inhibited by the treatment of sperm cells with mouse anti Iak serum, but not with mouse normal serum. Scatchard analysis of this binding activity also showed a single receptor type on sperm cells. These results were directly confirmed morphologically by taking autoradiography of sperm cells binding foreign DNA.

Animals↗
PubMedDate not supplied

Structure of intercellular junctions in the endothelium.

Endothelial cell junctions are complex structures formed by transmembrane adhesive molecules linked to a network of cytoplasmic/cytoskeletal proteins. At least three different types of endothelial junctions have been described: tight junctions, gap junctions and adherens junctions. These structures have some features and components in common with epithelium but also some which are specific for endothelium. We still know very little about the pathologic consequences of alterations in the functional behaviour or synthesis of endothelial cell junction proteins. It is possible that pathologies linked to altered endothelial permeability and vascular organization (e.g. hemangiomas, scleroderma, and other types of vasculitis) are associated with structural alterations in endothelial junction organization. In addition, changes in endothelial permeability properties are associated with the early stages of atherosclerosis and many inflammatory diseases.

Capillary Permeability↗
PubMed1995

Determination of the NMR solution structure of a specific DNA complex of the Myb DNA-binding domain.

The solution structure of a specific DNA complex of the minimum DNA-binding domain of the mouse c-Myb protein was determined by distance geometry calculations using a set of 1732 nuclear Overhauser enhancement (NOE) distance restraints. In order to determine the complex structure independent of the initial guess, we have developed two different procedures for the docking calculation using simulated annealing in four-dimensional space (4D-SA). One is a multiple-step procedure, where the protein and the DNA were first constructed independently by 4D-SA using only the individual intramolecular NOE distance restraints. Here, the initial structure of the protein was a random coil and that of the DNA was a typical B-form duplex. Then, as the starting structure for the next docking procedure, the converged protein and DNA structures were placed in random molecular orientations, separated by 50 A. The two molecules were docked by 4D-SA utilizing all the restraints, including the additional 66 intermolecular distance restraints. The second procedure comprised a single step, in which a random-cell protein and a typical B-form DNA duplex were first placed 70 A from each other. Then, using all the intramolecular and intermolecular NOE distance restraints, the complex structure was constructed by 4D-SA. Both procedures yielded the converged complex structures with similar quality and structural divergence, but the multiple-step procedure has much better convergence power than the single-step procedure. A model study of the two procedures was performed to confirm the structural quality, depending upon the number of intermolecular distance restraints, using the X-ray structure of the engrailed homeodomain-DNA complex.

Animals↗
PubMed1998

Tetragonal Crystal Structure of Mung Bean Inhibitor-porcine Trypsin Complex.

Crystal structure of the mung bean inhibitor-porcine trypsin (1:2) ternary complex in the tetragonal crystal with space group I422 was determined at 0.25nm resolution. 56 residues of the mung bean inhibitor were resolved among which one more residue Pro11 was determined than the previously reported structure in the trigonal crystal of the same complex. The structure of the inhibitor in the tetragonal crystal is similar to that in the trigonal crystal and the complexes in tetragonal crystal is also in packing disorder as in trigonal crystal, i.e., the complexes pack in two orientations Ta : MaMb : Tb and Tb : MbMa : Ta(Ta, Tb=trypsin, Ma, Mb=loop I and loop II of mung bean inhibitor respectively). But there are some differences in the two crystal forms. First, the inhibitor in the tetragonal crystal has no pseudo- beta-sheet structure which the trigonal crystal has. Second, its conformation is somewhat different from that in the trigonal crystal.Analysis showed that the linkage peptides between the two regid domains of the inhibitor were flexible, which also accounted for the formation of different crystal forms of this complex. Moreover, comparing mung bean inhibitor to other Bowman-Birk inhibitors showed that the two double-stranded antiparallel beta-sheets and the reactive binding loops were highly conservative.

Journal Article↗
PubMed1998

Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach.

A hybrid differential-discrete mathematical model has been used to simulate biofilm structures (surface shape, roughness, porosity) as a result of microbial growth in different environmental conditions. In this study, quantitative two- and three-dimensional models were evaluated by introducing statistical measures to characterize the complete biofilm structure, both the surface structure and volume structure. The surface enlargement, coefficient of roughness, fractal dimension of surface, biofilm compactness, and solids hold-up were found to be good measures of biofilm structure complexity. Among many possible factors affecting the biofilm structure, the influence of biomass growth in relation to the diffusive substrate transport was investigated. Porous biofilms, with many channels and voids between the "finger-like" or "mushroom" outgrowth, were obtained in a substrate-transport-limited regime. Conversely, compact and dense biofilms occurred in systems limited by the biomass growth rate and not by the substrate transfer rate. The surface complexity measures (enlargement, roughness, fractal dimension) all increased with increased transport limitation, whereas the volume measures (compactness, solid hold-up) decreased, showing the change from a compact and dense to a highly porous and open biofilm.

Automation↗