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PubMed1984

Characterization of thrombin binding to alpha 2-macroglobulin.

The formation and structural characteristics of the human alpha 2-macroglobulin (alpha 2M)-thrombin complex were studied by intrinsic protein fluorescence, sulfhydryl group titration, electrophoresis in denaturing and nondenaturing polyacrylamide gel systems, and in macromolecular inhibitor assays. The interaction between alpha 2M and thrombin was also assessed by comparison of sodium dodecyl sulfate-gel electrophoretic patterns of peptides produced by Staphylococcus aureus V-8 proteinase digests of denatured alpha 2M-125I-thrombin and alpha 2M-125I-trypsin complexes. In experiments measuring fluorescence changes and sulfhydryl group exposure caused by methylamine, we found that thrombin produced its maximum effects at a mole ratio of approximately 1.3:1 (thrombin:alpha 2M). Measurements of the ability of alpha 2M to bind trypsin after prior reaction with thrombin indicated that thrombin binds rapidly at one site on alpha 2M, but occupies the second site with some difficulty. Intrinsic fluorescence studies of trypsin binding to alpha 2M at pH 5.0, 6.5, and 8.0 not only revealed striking differences in trypsin's behavior over this pH range, but also some similarities between the behavior of thrombin and trypsin not heretofore recognized. Structural studies, using sodium dodecyl sulfate-polyacrylamide gel electrophoresis to measure alpha 2M-125I-thrombin covalent complex formation, indicated that covalency reached a maximum at a mole ratio of approximately 1.5:1. At this ratio, only 1 mol of thrombin is bound covalently per mol of alpha 2M. These gel studies and those of proteolytic digests of denatured alpha 2M-125I-trypsin and alpha 2M-125I-thrombin complexes suggest that proteinases form covalent bonds with uncleaved alpha 2M subunits. The sum of our results is consistent with a mechanism of proteinase binding to alpha 2M in which the affinity of the proteinase for alpha 2M during an initial reversible interaction determines its binding ratio to the inhibitor.

Electrophoresis, Polyacrylamide Gel↗
PubMed1997

Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR.

Two protein expression vectors have been designed for the preparation of NMR samples. The vectors encode the immunoglobulin-binding domain of streptococcal protein G (GB1 domain) linked to the N-terminus of the desired proteins. This fusion strategy takes advantage of the small size, stable fold, and high bacterial expression capability of the GB1 domain to allow direct NMR spectroscopic analysis of the fusion protein by 1H-15N correlation spectroscopy. Using this system accelerates the initial assessment of protein NMR projects such that, in a matter of days, the solubility and stability of a protein can be determined. In addition, 15N-labeling of peptides and their testing for DNA binding are facilitated. Several examples are presented that demonstrate the usefulness of this technique for screening protein/DNA complexes, as well as for probing ligand-receptor interactions, using 15N-labeled GB1-peptide fusions and unlabeled target.

Bacterial Proteins↗
PubMed2002

MIAX: a new paradigm for modeling biomacromolecular interactions and complex formation in condensed phases.

A new paradigm is proposed for modeling biomacromolecular interactions and complex formation in solution (protein-protein interactions so far in this report) that constitutes the scaffold of the automatic system MIAX (acronym for Macromolecular Interaction Assessment X). It combines in a rational way a series of computational methodologies, the goal being the prediction of the most native-like protein complex that may be formed when two isolated (unbound) protein monomers interact in a liquid environment. The overall strategy consists of first inferring putative precomplex structures by identification of binding sites or epitopes on the proteins surfaces and a simultaneous rigid-body docking process using geometric instances alone. Precomplex configurations are defined here as all those decoys the interfaces of which comply substantially with the inferred binding sites and whose free energy values are lower. Retaining all those precomplex configurations with low energies leads to a reasonable number of decoys for which a flexible treatment is amenable. A novel algorithm is introduced here for automatically inferring binding sites in proteins given their 3-D structure. The procedure combines an unsupervised learning algorithm based on the self-organizing map or Kohonen network with a 2-D Fourier spectral analysis. To model interaction, the potential function proposed here plays a central role in the system and is constituted by empirical terms expressing well-characterized factors influencing biomacromolecular interaction processes, essentially electrostatic, van der Waals, and hydrophobic. Each of these procedures is validated by comparing results with observed instances. Finally, the more demanding process of flexible docking is performed in MIAX embedding the potential function in a simulated annealing optimization procedure. Whereas search of the entire configuration hyperspace is a major factor precluding hitherto systems from efficiently modeling macromolecular interaction modes and complex structures, the paradigm presented here may constitute a step forward in the field because it is shown that a rational treatment of the information available from the 3-D structure of the interacting monomers combined with conveniently selected computational techniques can assist to elude search of regions of low probability in configuration space and indeed lead to a highly efficient system oriented to solve this intriguing and fundamental biologic problem.

Algorithms↗
PubMed2003

NMR analysis of methyl groups at 100-500 kDa: model systems and Arp2/3 complex.

Large macromolecular machines are among the most important and challenging targets for structural and mechanistic analyses. Consequently, there is great interest in development of NMR methods for the study of multicomponent systems in the 50-500 kDa range. Biochemical methods also must be developed in concert to produce such systems in selectively labeled form. Here, we present (1)H/(13)C-HSQC spectra of protonated methyl groups in a model system that mimics molecular weights up to approximately 560 kDa. Signals from side chain methyl groups of Ile, Leu, and Val residues are clearly detectable at correlation times up to approximately 330 ns. We have also developed a biochemical procedure to produce the 240 kDa, heteroheptameric Arp2/3 actin nucleation complex selectively labeled at one subunit and obtained (1)H/(13)C-HSQC spectra of this assembly. Sensitivity in spectra of both the Arp2/3 complex and the model system indicate that methyl groups will be useful sources of information in nonsymmetric systems with molecular weights greater than 600 kDa at concentrations less than 100 microM. Methyl analyses will complement TROSY and CRINEPT analyses of amides in NMR studies of structure and molecular interactions of extremely large macromolecules and assemblies.

Actin-Related Protein 2↗
PubMed1977

Evidence for macromolecular synthesis in stimulation of the estrogen synthesizing system of the immature rat ovary by PMS.

Exposure of immature rat ovaries to pregnant mare's serum gonadotropin (PMS) results in a prompt increase in testosterone and progesterone output but synthesis of estradiol (E2) increases only after a lag period of several hours. Actinomycin D (Act-D) given with PMS did not inhibit testosterone or progesterone production but the estrogenic response was prevented. Delay in administration of the Act-D until 12 hr after PMS resulted in a transient increase in E2 secretion lasting less than 12 hrs. When Act-D was given 12, 16 or 20 hrs after PMS, and ovarian steroid production measured by a one hr incubation, no inhibition of progesterone, testosterone or E2 was found; the synthesis of the latter two steroids was increased by the drug. Cycloheximide, on the other hand, was most effective at inhibiting testosterone and E2 production when it was given at 12 hrs; the drug was progressively less effective in lowering production of these steroids when it was given at 16 or 20 hrs. Cycloheximide did not alter progesterone production unless it was given at the same time as PMS. The results are consistent with the view that the induction of the estrogen synthesizing system of the immature rat ovary by gonadotropin involves, during the first 12 hrs, production of a material sensitive to Act-D inhibition (mRNA?) and then production of a material sensitive to cycloheximide inhibition (protein-enzymes?). The continued production of both of these materials appears to require the continual presence of gonadotropin.

Animals↗
PubMed2005

Analysis of macromolecular changes and drug release from hydrophilic matrix systems.

The influence of water-soluble and insoluble excipients on dynamics of hydration, front movement, erosion, and drug release from hydrophilic matrix tablets containing water-soluble drug was studied. Tablets were manufactured by direct compression, and their un-constrained swelling behavior and gel strength were assessed with a texture analyzer. Dissolution was performed using USP 26 apparatus II modified by insertion of a mesh to prevent sticking of tablets to the bottom of the vessel and to allow free three-dimensional matrix swelling. Significant release differences between tablet batches were observed and this was consistent with changes in swelling rate, gel thickness, and swelling front movement within the tablets. Matrices containing approximately 30% drug load and water-soluble lactose, demonstrated more pronounced swelling front movement and hence drug release relative to the matrix tablets containing dicalcium phosphate dihydrate. The observed differences in release were verified by calculating the similarity and difference factors. The interdependence of front movement and mass erosion in relation to excipient types on progression of swelling front movement and alteration of water penetration, erosion, and drug release are explained. It is concluded that unlike in conventional dosage forms inclusion of excipients in hydrophilic controlled-release tablets containing water-soluble drugs should be carefully analyzed as their various physico-chemical properties may have significant implications on swelling dynamics, front movement, drug release kinetics, and consequently in vivo performance.

Biological Availability↗
PubMed1975

Macromolecular turnover in mice (C57BL times C3H) liver, thymus and kidney after partial hepatectomy.

Studies have been presented concerning the definition of bioassay systems, in terms of macromolecular kinetics as it pertains in advance to ENU carciogenic sensitivity. Male mice (C57BL female times C3H male) 6 weeks of age were partially hepatectomized and labelled with thymidine 3-H, uridine 3-H and leucine 3-H as precursors for DNA, RNA and protein synthesis respectively. Specific activity of all these three parameters of liver, thymus and kidney were followed for 5 days at regular intervals, and for 6 weeks at randomly chosen intervals. The goal of this study which we obtained, is a three-phased curve in liver for each macromolecule studied; RNA synthesis reached its first peak 18 hours, protein synthesis 24 hours, and DNA synthesis 30 hours after partial hepatectomy. Synthetic macromolecular turnover in other organs (thymus, lung, kidney, brain) were not affected in a similar way, inspite expecting some factors of a humoral nature. An accurate knowledge of the timing in macromolecular synthesis after partial hepatectomy in mice is an essential preliminary study for the development and definition of a model protocol for ENU--single dose having approximately 10-15 minutes half-life carcinogenic response.

Animals↗
PubMed1987

[Modern electron microscopy at cellular and macromolecular levels. Strategies for preparation, imaging and image interpretation].

Conventional electron microscopy has significantly contributed to the understanding of structure-function relationships in living systems on cellular and macromolecular levels. New approaches and strategies will provide further insight into the organization of life. These new developments include cryopreparation and imaging techniques, X-ray microanalysis on frozen samples, electron energy loss spectroscopy, electron spectroscopic imaging, electron microscopic immunocytochemistry, preparation and imaging of ordered two-dimensional arrays of macromolecules, and computer image analysis and reconstruction. The techniques are described. Selected examples illustrate potential and limitations of these approaches and strategies.

Aspergillus nidulans↗
PubMed1988

Modulation of phosphofructokinase action by macromolecular interactions. Quantitative analysis of the phosphofructokinase-aldolase-calmodulin system.

The simultaneous effect of calmodulin and aldolase (D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase, EC 4.1.2.13) on the concentration-dependent behaviour of muscle phosphofructokinase (ATP: D-fructose-6-phosphate 1-phosphotransferase, EC 2.7.1.11) has been analysed by means of a covalently attached fluorescent probe, gel penetration experiments, and using a kinetic approach. We found that calmodulin-induced inactivation of phosphofructokinase is suspended by addition of an equimolar amount of aldolase. This effect was attributed to an apparent competition of calmodulin and aldolase for the dimeric forms of kinase. Moreover, the direct binding of aldolase to calmodulin has also been demonstrated, which resulted in a significant decrease in the kcat value of the enzyme. The quantitative analysis of these interactions in the system phosphofructokinase-calmodulin-aldolase is presented. A possible molecular model for the modulation of phosphofructokinase action by macromolecular interactions is envisaged.

Animals↗
PubMed2000

Improvement of macromolecular clearance via lymph flow in hamster gingiva by topical warming and massage.

The lymphatic system is very important for macromolecular clearance in various tissues, especially in the gingiva. However, the kinetics of macromolecular clearance via the lymph flow in the gingiva are poorly understood. The aim of this study was to investigate whether thermal or mechanical stimulation affects macromolecular clearance via the lymph flow in the gingiva. Carbon black suspension was injected into the mandibular gingiva of anesthetized hamsters and its drainage into cervical lymph nodes was examined. Clearance of 14C-methylated bovine albumin and tritiated water from the gingiva and their drainage into submandibular lymph nodes and blood was quantified. The effect of topical warming or massage on clearance of 14C-methylated albumin from the gingiva during a 15 min period was examined. In addition, the influence of neurochemical antagonists on the stimulatory effect of topical warming on albumin clearance was investigated. Submandibular lymph nodes were clearly delineated by carbon black 10 min after the injection. More radiolabeled albumin appeared in submandibular lymph nodes than in serum, while more tritiated water appeared in serum. Topical warming (45 degrees C, 2 min) and warming plus massage (with a silicon rubber brush, 20 s) decreased the radiolabeled albumin in the gingiva 15 min after the injection. There was less radiolabeled albumin in the gingiva after gingival warming plus massage than after warming. Previous injection of HOE140 or propranolol into the gingiva diminished the stimulatory effect of topical warming on albumin clearance. It was concluded that topical warming plus massage improves macromolecular clearance via the lymph flow in hamster gingiva.

Albumins↗
PubMedDate not supplied

EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information.

This paper describes the design and implementation of a Web-based deposition system, EMDep, for macro-molecular volumes determined by electron microscopy and deposited at the European Bioinformatics Institute (EBI) for inclusion in the Electron Microscopy Data Base (EMDB). EMDep is a flexible and portable system (http://www.ebi.ac.uk/msd-srv/emdep/) that allows for the acceptance and validation of data, by an interactive depositor-driven operation. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators, for the complete and accurate description of the structural experiment and its results.

Algorithms↗
PubMed2006

Simulation of molecular crowding effects on an Alzheimer's beta-amyloid peptide.

Fibril formation by the Alzheimer's beta-amyloid (Abeta) peptide in brain tissue is integral to the Alzheimer's disease pathology. Understanding the conformational properties and the mechanisms triggering aggregation of the Abeta peptides, at an atomic level of detail, is of crucial importance for the design of effective therapeutic agents against this disease. In this work, the conformational transitions and dynamic properties of an amyloidogenic peptide fragment (Abeta10-35) were studied by molecular dynamics simulations in systems modeling infinite dilution and the presence of macromolecular crowding agents (CA). The model system consists of the peptide described with an atomistic force field, the CA represented by inert, quasi-hard spheres and a continuum solvent model. This combined model allowed the simulations to be extended to 100 ns each. Simulations were carried out starting from a completely extended structure, a beta-strand structure, and four nuclear magnetic resonance structures in dilute aqueous solution. For all structures, two additional simulations were performed that included the inert CA in the solution and occupied approx 30 and 40% of the volume, respectively. For two of the nuclear magnetic resonance structures, additional simulations were carried out with 35% volume fraction of CA to further examine the diffusive behavior of the peptide. The peptide adopted a collapsed coil conformation in all simulations. The results of the simulations in dilute solution showed reasonable qualitative agreement with experimental and other simulation results, whereas the presence of volume excluding agents resulted in some distinct changes in properties (e.g., an increase in the appearance of transient beta-structure or decreases in diffusivity with increasing CA concentration). At the same time, internal motion such as order parameters or atomic root mean square fluctuations showed less systematic responses to volume exclusion.

Amyloid beta-Peptides↗
PubMedDate not supplied

Effects of rat hepatocytes on macromolecular permeability of bovine aortic endothelial cell monolayer.

The aim of this study was to examine whether the hyperpermeable structure of the liver endothelium in vivo is related to the interactions of hepatocytes in a culture system. The permeation of macromolecular FITC-labeled dextran (molecular weight 70,000) through a monolayer of bovine aortic endothelial cells (BAEC), cocultured with rat parenchymal hepatocytes (P-hep), was increased. When the BAEC were cocultured with nonparenchymal hepatocytes (N-hep), the permeability of the BAEC monolayer was not increased. However, when the BAEC were cocultured with a mixture of P-hep and N-hep (PN-hep), the BAEC monolayer was more permeable than when BAEC were cocultured with P-hep alone. The conditioned medium of P-hep did not alter the BAEC monolayer permeability, nor did the extracellular matrix of P-hep alter BAEC permeability. When the BAEC were cocultured with PN-hep, the F-actin content was not altered. These findings suggest that the interaction between hepatocytes and endothelial cells exerts an important effect on the hyperpermeable structure of the liver vessels in vivo.

Actins↗
PubMed1997

Pulmonary drug delivery: physiologic and mechanistic aspects.

Peptide and protein drugs are being used increasingly in major research and development programs in the pharmaceutical industry and are also an important class of therapeutic agents due to advances in genetic engineering and biotechnology. Systemic delivery of these macromolecular drugs, however, has been limited to the parenteral route largely because of their extensive presystemic elimination when taken orally. Faced with this dilemma concerning the systemic delivery of these macromolecules with their unique conformational complexity for therapeutic activity, pharmaceutical scientists have evaluated the potential of various non-oral routes of administration as alternatives. Despite the tremendous efforts that have been devoted to this problem, only limited success has been achieved--mostly with small peptides. Growing attention has been given to the potential of a pulmonary route as an alternative non-invasive means for systemic delivery of peptide/protein-based therapeutic agents due to the fact that the lung provides a huge but extremely thin absorptive mucosal membrane. Although current studies show great promise, pulmonary delivery of therapeutic peptides and proteins is complicated by the complexity of the anatomic structure of the human respiratory system and the influence on drug deposition exerted by respiration. This review discusses the fundamental structure and physiology of the human respiratory system, current methodology used to study pulmonary drug absorption, approaches of drug delivery to the distal lung, and recent progress in pulmonary drug delivery by case studies. The mechanisms of pulmonary drug absorption are also discussed.

Absorption↗
PubMed2003

Cytoplasmic delivery and nuclear targeting of synthetic macromolecules.

Delivery of macromolecular drugs (e.g. antisense oligonucleotides, polymer-drug conjugates, etc.) designed to work in specific sites inside cells is complicated as macromolecules typically have access to fewer biological compartments than small molecules. To better understand the fate of macromolecules in cells and begin to alter that fate, we investigated the internalization and subcellular fate of N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers and HPMA copolymer-drug conjugates in Hep G2 and A2780 cells. The subcellular fate of fluorescently labeled polymers was monitored by confocal microscopy and subcellular fractionation. Initially, the HPMA copolymers and HPMA copolymer-drug conjugates were internalized by endocytosis and remained in endosomes/lysosomes. At longer incubation times (>8 h), small amounts of the HPMA copolymers were observed to enter the cytoplasm and accumulate in the nucleus of the cells. Nuclear accumulation was confirmed after cytoplasmic microinjection. Oligonucleotides conjugated via lysosomally degradable spacers entered into the cytoplasm and nucleus of the cells faster than the polymers. The effect of the subcellular location was correlated to the toxicity of the photosensitizer, mesochlorin e(6) (Mce(6))-HPMA copolymer conjugates. The plasma membrane and late endosomes were more sensitive to damage by Mce(6). Targeting the polymer conjugates to the nucleus with the nuclear localization sequence (NLS) as well as conjugating the Mce(6) via a degradable spacer increased cell adhesion and uptake, promoted their entry into the cytoplasm and nucleus of the cells, and increased their toxicity. To further promote entry of the polymers into the cytoplasm and nucleus of the cells, the protein transduction domain, Tat peptide, was conjugated to the HPMA copolymers. This resulted in high binding to the cell membrane, but also facilitated rapid (<5 min) entry of the macromolecules into the cytoplasm and nucleus of cells. These results will prove valuable in the future design of macromolecular therapeutics.

Animals↗
PubMed1986

Development of a chemically defined serum- and protein-free medium for growth of human peripheral lymphocytes.

A chemically defined, protein-free medium (designated CFBI 1000, where CFBI = Clayton Foundation Biochemical Institute) that supports human peripheral lymphocyte proliferation has been developed. This medium allows exploration of individual metabolic differences by varying the medium composition as well as providing a base to explore further the mechanisms of lymphocyte activation in a system initially free of added macromolecular species other than mitogen. The peripheral blood lymphocyte is an ideal system for metabolic studies because it is easily obtained, is a primary resting cell that can be activated to proliferate, and presumably reflects both the genetic makeup and biochemical environmental history of the individual at the time the cells were formed. Examination of the role of various factors in lymphocyte activation and subsequent events may be simplified by the utilization of a medium that is protein-free and chemically defined. The CFBI 1000 medium supports the growth response of human peripheral lymphocytes to mitogen as measured by [3H]thymidine incorporation to an extent comparable to other media used widely in assessment of lymphocyte proliferation.

Aphidicolin↗
PubMed2002

Drug absorption by the respiratory mucosa: cell culture models and particulate drug carriers.

The inhalation route is of increasing interest for both local and systemic drug delivery, including macromolecular biopharmaceuticals, such as peptides, proteins, and gene therapeutics. In addition to appropriate aerosolization for deposition in relevant areas of the respiratory tract, therapeutic molecules may require an advanced carrier system for safe and efficient delivery to their target. Two approaches to obtain novel carrier systems for pulmonary drug delivery are large porous microparticles with a low aerodynamic diameter and lectin-functionalized liposomes. Epithelial cells of alveolar or bronchial origin, obtained either from patient material or from established cell lines, can be grown on permeable filter supports, resulting in polarized monolayers with functional intercellular junctions. With such in vitro models, transport of drugs into pulmonary epithelial cells and/or across the air-blood barrier, as well as the effect and efficacy of novel drug carrier systems can be systematically studied.

Absorption↗