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PubMed1964

THE MACROMOLECULAR NATURE OF THE FIRST COMPONENT OF HUMAN COMPLEMENT.

Kinetic and ultracentrifugal experiments demonstrated that the previously described subcomponents of human C'1, designated C'1q, C'1r, and C'1s, interacted with each other in liquid phase to form a macromolecule which was then capable of converting sensitized erythrocytes (EA) to the state EAC'1. The apparent sedimentation constants of C'1q, C'1r, and C'1s and of the macromolecular product of their interaction were approximately 11S, 7S, 4S, and 18S respectively. Association of C'1 subcomponents was prevented and dissociation of macromolecular C'1 was effected by Na(3)HEDTA and Na(2)MgEDTA but not by Na(2)CaEDTA. The rate of formation of macromolecular C'1 was a function of concentration of subcomponents and temperature of interaction, with an apparent energy of activation of 21,000 calories per mol. Ultracentrifugal studies further indicated the macromolecular nature of C'1 in normal human serum. In the absence of EDTA, C'1 sedimented with the serum macroglobulins and C'1 subcomponents were not detected. Conversely, in the presence of EDTA, macromolecular C'1 was not demonstrable and individual C'1 subcomponents could be measured in lighter fractions. The significance of these observations in relation to previous studies on C'1 subcomponents, the role of Ca(++) in C'1 function, and the subunit structure of Enzymes has been discussed.

Biochemical Phenomena↗
PubMed2006

Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems.

An ability to accurately simulate the dynamic behavior of concentrated macromolecular solutions would be of considerable utility in studies of a wide range of biological systems. With this goal in mind, a Brownian dynamics (BD) simulation method is reported here that allows systems to be modeled that comprise in excess of 1000 protein molecules, all of which are treated in atomic detail. Intermolecular forces are described in the method using an energy function that incorporates electrostatic and hydrophobic interactions and that is calibrated to reproduce experimental thermodynamic information with a single adjustable parameter. Using the method, BD simulations have been performed over a wide range of pH and ionic strengths for three proteins: hen egg white lysozyme (HEWL), chymotrypsinogen, and T4 lysozyme. The simulations reproduce experimental trends in second virial coefficients (B(22)) and translational diffusion coefficients, correctly capture changes in B(22) values due to single amino acid substitutions, and reveal a new explanation for the difficulties reported previously in the literature in reproducing B(22) values for protein solutions of very low ionic strength. In addition, a strong correlation is found between a residue's probability of being involved in a protein-protein contact in the simulations and its probability of being involved in an experimental crystal contact. Finally, exploratory simulations of HEWL indicate that the simulation model also gives a promising description of behavior at very high protein concentrations (approximately 250 g/L), suggesting that it may provide a suitable computational framework for modeling the complex behavior exhibited by macromolecules in cellular conditions.

Bacteriophage T4↗
PubMed2001

Deposition of the NG2 proteoglycan at nodes of Ranvier in the peripheral nervous system.

The node of Ranvier is a complex macromolecular assembly of ion channels and other proteins that is specialized for the rapid propagation of the action potential. A full understanding of the processes responsible for the assembly and maintenance of the node requires first the identification and characterization of the proteins found there. Here we show that NG2, a structurally unique chondroitin sulfate proteoglycan, is a molecular component of the node of Ranvier in the peripheral nervous system. In adult sciatic nerve, NG2 is (1) associated with thin, elongated fibroblast-like cells, (2) on some but not all basal laminae, and (3) at nodes of Ranvier. At the nodes, NG2 is restricted to the nodal gap and is absent from the paranodal or juxtaparanodal region. In dissociated cell cultures of adult sciatic nerve, perineurial fibroblasts but not Schwann cells express NG2 on their surfaces. Approximately 45% of the total NG2 in peripheral nerves is in a soluble, rather than particulate, subcellular compartment. NG2 is also present in membrane fractions that also contain high levels of voltage-dependent sodium channels, caspr, and neuron-glia related cell adhesion molecule. These medium-density membranes likely correspond to the nodal and paranodal region of the axon-Schwann cell unit. These results suggest a model in which perineurial fibroblasts secrete or shed NG2, which subsequently associates with nodes of Ranvier. The growth-inhibitory and anti-adhesive properties of NG2 may limit the lateral extension of myelinating Schwann cells as nodes mature. NG2 may also participate in the barrier functions of the perineurial linings of the nerve.

Animals↗
PubMedDate not supplied

Activated clearance of a biotinylated macromolecular MRI contrast agent from the blood pool using an avidin chase.

The enhancement characteristics of a contrast agent are dependent on its pharmacokinetics within the body. In the case of macromolecular contrast agents, prolonged enhancement of the blood pool is seen after the first dose, limiting opportunities for repeated injection in the same session. If the enhancement within the blood pool could be intentionally switched off, the macromolecular contrast agents could be used both to define blood volume and vessel permeability, properties that could be useful in studying angiogenesis. In the current study, the avidin-biotin system was coupled to a dendrimer-based macromolecular MRI contrast agent to switch enhancement from the blood pool to the liver. Because avidin causes rapid trapping of the contrast agent in the liver, the blood pool cleared within 2 min of the injection of avidin. This system can be applied to all dendrimer-based macromolecular MRI contrast agents to investigate blood volume and vascular permeability. Moreover, it permits the repeated injection of the contrast agent and the "avidin switch" during a single MR experiment.

Animals↗
PubMed1998

Macromolecular assembly and secretion across the bacterial cell envelope: type II protein secretion systems.

A decade ago, Pugsley and colleagues reported the existence of a large region of Klebsiella DNA, distinct from the Klebsiella gene encoding pullulanase, which was necessary for secretion of this enzyme to the cell surface in Escherichia coli (d'Enfert et al., 1987a,b). The pul genes it contained proved to be the tip of an iceberg. The sequences reported before 1992 (d'Enfert et al., 1987a,b; d'Enfert & Pugsley, 1989; Pugsley & Reyss, 1990; Reyss & Pugsley, 1990) included only one gene (pulD) that matched any sequence in the data base; a 220 amino acid residue segment of PulD was 32% identical with a portion of the filamentous phage-encoded protein, pIV. But by the time the sequence of the 18.8 kb DNA fragment that contained the pul genes had been completed (Possot et al., 1992), reports of sets of homologous genes in several species of Gram-negative plant and animal pathogens had appeared. For the most part, these gene clusters were cloned by their ability to complement mutants that produced, but failed to secrete, proteins normally found in the extracellular milieu; when tested, the mutants showed reduced pathogenicity or were totally avirulent. The secreted proteins included hydrolytic enzymes such as cellulase and pectinase from plant pathogens, and proteases and toxins from animal pathogens. The multi-gene family necessary for secretion of these enzymes is now known as the type II system or the main terminal branch (MTB) of the general secretion pathway (GSP). As summarized by Pugsley et al. (1997), the current tally includes type II systems from Klebsiella oxytoca (pul), Erwinia chrysanthemi and carotovora (out), Xanthomonas campestris (xps), Pseudomonas aeruginosa (xcp), Aeromonas hydrophila (exe), and Vibrio cholerae (eps). A second type II system (sps) necessary for deposition of the S-layer on the cell surface in A. hydrophila is more similar to the X. campestris than A. hydrophila genes (Thomas & Trust, 1995). The biggest surprise has been the discovery of a complete set of type II secretion genes in E. coli K12. The E. coli genes are not expressed under normal growth conditions, and a search is underway to find inducing conditions and secretion substrates (Francetic & Pugsley, 1996). Impressive progress has already been made in defining components of the pathway. What remains to be understood in mechanistic detail is how this protein secretion system functions.

Bacterial Proteins↗
PubMedDate not supplied

Morphogenesis of the small intestine during fetal development.

During the last five days ('last trimester') of the 22-day gestation period of the rat the mucosa of the small intestine changes from undifferentiated stratified epithelium without villi to a mucosa with villi covered with simple columnar epithelium. During this process many secondary lumina form in the primitive stratified epithelium; these lumina enlarge and eventually fuse with the main intestinal lumen as degenerating superficial epithelial cells are exfoliated and as upward growth of mesenchyme towards the main lumen takes place. Proliferation of intestinal epithelial cells occurs along the entire length of the newly formed villi until one or two days before birth, when proliferating epithelial cells become confined to incompletely formed crypts at the base of the villi. In contrast, differentiation of the small intestinal mucosa in human fetuses begins much earlier in gestation. Villi form at 9 to 10 weeks and crypts are well developed by 12 weeks (first trimester). By 17 weeks, all epithelial cells types seen in intestinal crypts of adults are present. Absorptive cells on villi have a prominent apical tubular system, large meconium-filled lysosomes and abundant glycogen between 10 and 22 weeks' gestation. Whereas there is uptake of the macromolecular marker, ferritin, into the apical tubular system after eight or more minutes of in vitro exposure, there is no evidence of transport of ferritin across the absorptive cells after up to 40 minutes of exposure between 11 and 12 weeks' gestation.

Animals↗
PubMed2006

In vivo, in vitro and ex vivo models to assess pulmonary absorption and disposition of inhaled therapeutics for systemic delivery.

Despite the interest in systemic delivery of therapeutic molecules including macromolecular proteins and peptides via the lung, the accurate assessment of their pulmonary biopharmaceutics is a challenging experimental task. This article reviews in vivo, in vitro and ex vivo models currently available for studying lung absorption and disposition for inhaled therapeutic molecules. The general methodologies are discussed with recent advances, current challenges and perspectives, especially in the context of their use in systemic pulmonary delivery research. In vivo approaches in small rodents continue to be the mainstay of assessment by virtue of the acquisition of direct pharmacokinetic data, more meaningful when attention is given to reproducible dosing and control of lung-regional distribution through use of more sophisticated lung-dosing methods, such as forced instillation, microspray, nebulization and aerosol puff. A variety of in vitro lung epithelial cell lines models and primary cultured alveolar epithelial (AE) cells when grown to monolayer status offer new opportunity to clarify the more detailed kinetics and mechanisms of transepithelial drug transport. While continuous cell lines, Calu-3 and 16HBE14o-, show potential, primary cultured AE cell models from rat and human origins may be of greater use, by virtue of their universally tight intercellular junctions that discriminate the transport kinetics of different therapeutic entities. Nevertheless, the relevance of using these reconstructed barriers to represent complex disposition of intact lung may still be debatable. Meanwhile, the intermediate ex vivo model of the isolated perfused lung (IPL) appears to resolve deficiencies of these in vivo and in vitro models. While controlling lung-regional distributions, the preparation alongside a novel kinetic modeling analysis enables separate determinations of kinetic descriptors for lung absorption and non-absorptive clearances, i.e., mucociliary clearance, phagocytosis and/or metabolism. This ex vivo model has been shown to be kinetically predictive of in vivo, with respect to macromolecular disposition, despite limitations concerning short viable periods of 2-3 h and likely absence of tracheobronchial circulation. Given the advantages and disadvantages of each model, scientists must make appropriate selection and timely exploitation of the best model at each stage of the research and development program, affording efficient progress toward clinical trials for future inhaled therapeutic entities for systemic delivery.

Absorption↗
PubMed2007

Temperature and pH sensitive hydrogels: an approach towards smart semen-triggered vaginal microbicidal vehicles.

Microbicides are drug delivery systems (DDSs) for the prevention of sexual transmission of HIV and other STDs. A topically applied vaginal microbicidal gel should provide uniform coating of vaginal tissue, retention of this gel layer prior to intercourse, and controlled release kinetics of antivirals to inactivate the viral load potentially introduced during sexual activity. Here, we describe the microbicide-oriented characterization of a DDS made with a dual pH sensitive and thermosensitive smart polymer gel composed of a random terpolymer of N-isopropyl acrylamide, butyl methacrylate, and acrylic acid. The system was engineered to coat vaginal tissue with a stable gel layer and to release entrapped model agents in a burst release profile in response to the presence of the infecting agent: semen. The gel rheology, layer erosion properties, model drug release kinetics, and cytocompatibility of the terpolymer system were studied. Negligible erosion of the gel in the presence of vaginal fluid simulant suggests prolonged retention. Burst release of molecular and macromolecular model compounds was observed when the system's pH changed from the vaginal pH to the pH of semen, and cytotoxicity studies showed that the terpolymer is equally cytocompatible as a commonly used polymeric vaginal carrier.

Administration, Intravaginal↗
PubMed2000

Partitioning and concentrating biomaterials in aqueous phase systems.

Aqueous phase separation is a general phenomenon which occurs when structurally distinct water-soluble macromolecules are dissolved, above certain concentrations, in water. The number of aqueous phases obtained depends on the number of such distinct macromolecular species used. Aqueous two-phase systems, primarily those containing poly(ethylene glycol) and dextran, have been widely used for the separation of biomaterials (macromolecules, membranes, organelles, cells) by partitioning. The polymer and salt compositions and concentrations chosen greatly affect the physical properties of the phases. These, in turn, interact with the physical properties of biomaterials included in the phases and affect their partitioning. Specific extractions of biomaterials can be effected by including affinity ligands in the systems. The phase systems can also be used to obtain information on the surface properties of materials partitioned in them; to study interactions between biomaterials; and to concentrate such materials.

Animals↗
PubMed1995

Integrating molecular and digital computing: an information systems design perspective.

Biological systems use a non-programmable, but evolvable and efficient mode of information processing that can be traced to its underlying macromolecular basis (Conrad, 1985, Commun. ACM 28, 464-480). Digital computers, on the other hand, are structurally programmable, but not evolvable, nor efficient. In this paper we explore ways to provide effective support of function in organizations by combining the molecular and digital modes of information processing in a synergistic manner. In particular, we look at the potential of molecular computing technology for extending the problem-solving and decision-making capabilities of humans in complex organizational systems. Synergies resulting from the integration of molecular computing (including both human and molecular computing devices) and digital computing, are analyzed from an information systems design perspective.

Biotechnology↗
PubMed1991

Ordered water in hydrated solid-state polysaccharide systems.

Water molecules within a monolayer or so of macromolecular surfaces are often located in well-defined positions and have restricted mobility. These ordered water molecules play a role in stabilizing polysaccharide ordered structures and intermolecular interactions that are the basis of the rheological properties utilized in food systems. X-ray fiber diffraction can be used to determine the three-dimensional structures of polysaccharides in solid, but well-hydrated, polycrystalline fibers. In favorable cases, difference Fourier synthesis can be used to locate ordered water molecules in these systems, allowing one to visualize their functionally important interactions. These studies provide relevant evidence regarding water interactions in more hydrated systems and in solution. The functionality of ordered water in some polysaccharides used in food systems, as well as in some connective tissue glycosaminoglycans where the ordered water has been defined in considerable detail, as determined by fiber diffraction, is described in this chapter. These structures allow one to derive some general features of the role of ordered water in such systems.

Carbohydrate Sequence↗
PubMed2005

Structural characterization of the molecular platform for type III secretion system assembly.

Type III secretion systems (TTSSs) are multi-protein macromolecular 'machines' that have a central function in the virulence of many Gram-negative pathogens by directly mediating the secretion and translocation of bacterial proteins (termed effectors) into the cytoplasm of eukaryotic cells. Most of the 20 unique structural components constituting this secretion apparatus are highly conserved among animal and plant pathogens and are also evolutionarily related to proteins in the flagellar-specific export system. Recent electron microscopy experiments have revealed the gross 'needle-shaped' morphology of the TTSS, yet a detailed understanding of the structural characteristics and organization of these protein components within the bacterial membranes is lacking. Here we report the 1.8-A crystal structure of EscJ from enteropathogenic Escherichia coli (EPEC), a member of the YscJ/PrgK family whose oligomerization represents one of the earliest events in TTSS assembly. Crystal packing analysis and molecular modelling indicate that EscJ could form a large 24-subunit 'ring' superstructure with extensive grooves, ridges and electrostatic features. Electron microscopy, labelling and mass spectrometry studies on the orthologous Salmonella typhimurium PrgK within the context of the assembled TTSS support the stoichiometry, membrane association and surface accessibility of the modelled ring. We propose that the YscJ/PrgK protein family functions as an essential molecular platform for TTSS assembly.

Amino Acid Sequence↗
PubMed1995

Glutamine transport by mouse inner cell masses.

Mouse blastocysts take up glutamine by specific transport systems. Glutamine is an important precursor for macromolecular synthesis and a potential alternative fuel to glucose. This study compared glutamine uptake in blastocysts and isolated inner cell masses and characterized the major participating systems in the latter. Inner cell masses take up glutamine by facilitated transport systems. The identity of these was investigated using substrate competition and kinetic studies. Na(+)-dependent uptake of 13 mumol glutamine l-1 was inhibited by 60% by 1 mmol tryptophan l-1, 25% by 1 mmol 2-amino-2-norbornanecarboxylic acid l-1 and 50% by 1 mmol lysine l-1. Furthermore, 1 mmol 2-methyl(amino)isobutyric acid (MeAIB) l-1 inhibited uptake by 29%. Kinetic analysis of MeAIB-resistant uptake revealed a predominant Na(+)-dependent facilitated uptake system with Km and Vmax values of 434 +/- 72 mumol l-1 and 237 +/- 38 fmol per inner cell mass per 10 min, respectively. The inhibition of Na(+)-dependent uptake by tryptophan, lysine and the analogue 2-amino-2-norbornanecarboxylic acid suggests that most uptake of glutamine by inner cell masses occurs via the same system that predominates in whole blastocysts, Bo,+. The period of assay was so brief that significant participation of the inner cell mass in whole blastocyst uptake was precluded showing that system Bo,+ is expressed by both the trophectoderm and inner cell mass components of the blastocyst. However, MeAIB inhibited uptake by inner cell masses but not by blastocysts. This MeAIB-sensitive uptake had a Km value of 4.3 +/- 1.7 mmol l-1 and a Vmax value of 451 +/- 119 fmol per inner cell mass per 10 min. These characteristics suggest the first embryonic appearance of system A, which is a common Na(+)-dependent transporter in many somatic cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed1992

Programmed cell death: concept, mechanism and control.

Programmed cell death or apoptosis occurs under physiological conditions as a result of physiological effectors. It is a relatively slower process and requires active participation of the cell in the suicidal mechanism. Apoptosis is controlled by precise intrinsic genetic programme and may be induced by almost all those stimuli causing necrosis. The role played by the intensity in determining the death process and the underlying mechanism is imperfectly understood. Morphologically apoptotic cells appear as small condensed body. The chromatin is dense and fragmented, packed into compact membrane-bound bodies together with randomly distributed cell organelles. The plasma membrane loses its characteristic architecture and shows extensive blebbing. It buds off projections so that the whole cell may split into several membrane-bound apoptotic bodies. Significant chemical changes take place in the plasma membrane. This helps in recognition of the apoptotic bodies by phagocytes. At this moment it is unclear if all cells can undergo apoptosis or it is a characteristic of only some tissues which are predisposed to apoptotic death being directly under the control of hormones or growth factors. Experimental studies aimed at comparison of induction of apoptosis in cells of different origin are warranted to elucidate this point. Biochemically a pre-commitment step for induction of death programmation through macromolecular synthesis is essential for most systems. The double-stranded linker DNA between nucleosomes is cleaved at regular inter-nucleosomal sites through the action of a Ca2+, Mg(2+)-sensitive neutral endonuclease. Zinc is a potent inhibitor of the enzyme. Calcium probably plays a key controlling role in activation of the enzyme since prevention of Ca2+ increase prevents endonuclease activation. It is becoming evident that signal transduction through appropriate receptors control the Ca2+ flux in the cells. Most apoptotic cells require synthesis of RNA and proteins. Delay or abrogation of apoptosis by inhibition of macromolecular synthesis is well known. The dying cells show high mRNA levels for several enzymes. Several degradative enzymes become active. Regulatory proteins maintain control over the apoptotic cascade. At the molecular level, search has been initiated for the mammalian equivalents of the cell death (ced) gene. Activation of several specific genes is indicated. Specific expression of cell death-associated gene products (e.g. TRPM-2/SGP-2) has been reported in several unrelated apoptotic cell systems. Sequential induction of c-fos, c-myc and 70 kDa heat shock protein is reported. Studies demonstrate that certain genes must remain in a transcriptionally active demethylated state during programmed cell death. Recent evidences clearly indicate that apoptosis may be positively or negatively modulated by certain genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2001

The poly(phenolic) domain of potato suberin: a non-lignin cell wall bio-polymer.

Suberized plant cell walls have three distinguishing features: (1) tissue specificity, (2) a poly(aliphatic) domain and (3) a unique, "lignin-like" poly(phenolic) domain. With respect to the latter, comparisons have often been made to lignin, but the unique phenolic composition of suberized cells yields a unique polymer better designated as a poly(phenolic) domain. Potato tubers that have been induced to suberize through wounding make an excellent model system with which the chemistry, biochemistry and macromolecular assembly of the suberin poly(phenolic) domain can be monitored. For example, wound healing potato tubers have been used to determine the unique hydroxycinnamic acid nature of its poly(phenolic) domain using specific carbon-13 labeling studies and specific chemical degradation techniques (e.g. thioacidolysis). Furthermore, a suberization-associated anionic peroxidase has been purified from suberizing potato tubers and subsequently shown to oxidize hydroxycinnamic acids (and their derivatives) in preference to monolignols, as well as yield an unique polymer in vitro. We have since extended these studies to begin analyzing the macromolecular assembly process leading to the deposition of this suberized tissue specific domain. To this end we have begun to describe an H(2)O(2)-generating system with NAD(P)H-dependent oxidase-like properties that is temporally associated with the formation of potato suberin poly(phenolics) during suberization. Herein we describe our progress to date.

Biopolymers↗
PubMed2005

Resmap: automated representation of macromolecular interfaces as two-dimensional networks.

UNLABELLED: To aid detailed comparison of a large number of macromolecular structures, Resmap imports Protein Data Bank files and represents subunit/domain interfaces as two-dimensional networks. AVAILABILITY: http://www.kumc.edu/biochemistry/resmap/. SUPPLEMENTARY INFORMATION: Default definitions and directions for graphically managing networks are available at the same website.

Artificial Intelligence↗