[Level of organization and complex formation in living systems].
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Biochemical Phenomena↗
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Chemical systems and chemical evolution: the philosophy of molecular biology.
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Macromolecular Substances↗
Heat injury to cells in perfused systems.
Tissue injury in response to excessive heat results in a clinical burn. Burns cause a range of physiologic derangements, including denaturation of macromolecular structures, leakage of cell membranes, activation of cytokines, and cessation of blood flow, all leading to tissue death. The purpose of this paper is to examine the mechanisms and consequences of burn injury and to discuss potential therapies based on these mechanisms. Knowledge of the thermal properties of tissues can predict the time-temperature relationship necessary to cause a specified thermal insult. Changes in cell membrane biochemistry and the stabilization of proteins through the heat-shock response can enable biomacromolecules to withstand supraphysiological temperatures. Mechanisms of cellular repair allow recovery of cellular function after thermal insult. An understanding of the response of proteins, cellular organelles, and cells to heat provides the foundation for understanding the pathophysiology and treatment of burn injury. The physics, biochemistry, and cellular biology behind the host response to thermal injury in perfused systems are reviewed.
Burns↗
Protein A-tagging for purification of native macromolecular complexes from Candida albicans.
Protein A-tagging has become an important tool in characterization of protein-protein interactions in many systems, allowing purification of multicomponent complexes under native conditions. Here we provide a set of vectors that allow protein A-tagging in Candida albicans, through addition of the tag to open reading frames. These vectors were successfully used to generate stably tagged proteins that were functional, shown to be localized appropriately or assembled into complexes. These new vectors comprise a useful addition to the C. albicans molecular toolbox.
Base Sequence↗
Luminescent metal-ligand complexes as probes of macromolecular interactions and biopolymer dynamics.
The knowledge of microsecond dynamics is important for an understanding of the mechanism and function of biological systems. Fluorescent techniques are well established in biophysical studies, but their applicability to probe microsecond timescale processes is limited. Luminescent metal-ligand complexes (MLCs) have created interest mainly due to their unique luminescent properties, such as the exceptionally long decay times and large fundamental anisotropy values, allowing examination of microsecond dynamics by fluorescence methods. MLC properties also greatly simplify instrumentation requirements and enable the use of light emitting diode excitation for time-resolved measurements. Recent literature illustrates how MLC labels take full advantage of well developed fluorescence techniques and how those methods can be extended to timescales not easily accessible with nanosecond probes. MLCs are now commercially available as reactive labels which give researchers access to methods that previously required more complex approaches. The present paper gives an overview of the applications of MLC probes to studies of molecular dynamics and interactions of proteins, membranes and nucleic acids.
Biopolymers↗
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information.
We present an evaluation of our results for the first Critical Assessment of PRedicted Interaction (CAPRI). The methods used include the molecular docking program DOT, shape analysis tool FADE, cluster analysis and filtering based on biological data. Good results were obtained for most of the seven CAPRI targets, and for two systems, submissions having the highest number of correctly predicted contacts were produced.
Algorithms↗
Escherichia coli phosphoenolpyruvate-dependent phosphotransferase system. Evidence that the dimer is the active form of enzyme I.
In vitro kinetic measurements have been performed by using purified HPr, EI, and a membrane fraction of EII from the Escherichia coli phosphoenolypyruvate-dependent sugar transport system. These measurements reveal very large lag times in the formation of methyl alpha-glucoside phosphate which are a function of the EI and the EII concentrations. The lag times decrease with increasing concentrations of EI but they increase with increasing concentrations of EII. When EI, together with Mg2+ and phosphoenolpyruvate, is preincubated at 37 degrees C before starting the kinetic measurements, the lag time can be decreased or eliminated. We have shown that the process responsible for the lag time is the activation of EI by dimerization which is influenced by Mg2+ and phosphoenolpyruvate.
Biological Transport↗
Collagenolytic enzyme systems in human intervertebral disc: their control, mechanism, and their possible role in the initiation of biomechanical failure.
Changes in the macromolecular matrix of the intervertebral disc may predispose to biomechanical failure of the disc. Such changes would involve extracellular enzymes capable of altering the collagen and proteoglycan of the disc matrix. In this study, extracts from homogenates of both annuli fibrosi and nuclei pulposi of human lumbar discs were found to contain neutral collagenolytic, gelatinolytic, and elastinolytic enzymes in all samples assayed. The specific activity of the collagenase was higher in extracts from nuclear than from annular tissue, a difference not seen with gelatinase or elastase. The collagenase was present as both a latent and active enzyme, the other enzymes being fully active. Human intervertebral discs therefore contain enzymes capable of degrading their extracellular macromolecular matrix.
Age Factors↗
The specificity of uptake of model immune complexes and other protein aggregates by the murine reticuloendothelial system.
We have studied the selectivity of the murine reticuloendothelial system in recognizing and removing from the blood model immune complexes and several aggregated proteins. Although both IgG anti-DNP model immune complexes and micro-aggregated albumin exhibited rapid hepatic uptake, which is saturable, they did not cross-inhibit each other. Aggregates of ovalbumin, a glycoprotein rich in mannose (a sugar recognized by Kupffer cells), had no effect on the uptake by the liver of either IgG immune complexes or micro-aggregated albumin. The finding that transferrin aggregates were not taken up by the liver at all suggests that aggregation alone is not sufficient to overcome the lack of a specific hepatic receptor for that protein. Thus, several mechanisms exist whereby aggregated proteins can be cleared from the blood by the reticuloendothelial system, an observation consistent with the selective failure of reticuloendothelial function found in several human diseases.
Animals↗
Turbo cloning: a fast, efficient method for cloning PCR products and other blunt-ended DNA fragments into plasmids.
The method uses a novel plasmid vector, p9lox5, containing a site-specific recombination sequence lox from the lox/Cre recombinase system of bacteriophage P1. There are two distinct stages. Firstly, vector and fragment DNAs are ligated intermolecularly under conditions of macromolecular crowding (15% polyethylene glycol 6000) which accelerate blunt-end joining a thousandfold. Secondly, circular recombinant molecules are efficiently excised from the ligation products by Cre recombinase acting on pairs of lox sites within directly repeated vector molecules flanking insert DNA. Recombinants are introduced into cells conventionally by transformation or electroporation. In both a model system and the cloning of PCR products, yields approaching those obtainable in cohesive-end cloning were achieved. Applications of the technique to cDNA library generation and recovery of DNA from archive material are discussed.
Base Sequence↗
Recent progress in drug delivery systems for anticancer agents.
Recent progress in understanding the molecular basis of cancer brought out new materials such as oligonucleotides, genes, peptides and proteins as a source of new anticancer agents. Due to their macromolecular properties, however, new strategies of delivery for them are required to achieve their full therapeutic efficacy in clinical setting. Development of improved dosage forms of currently marketed anticancer drugs can also enhance their therapeutic values. Currently developed delivery systems for anticancer agents include colloidal systems (liposomes, emulsions, nanoparticles and micelles), polymer implants and polymer conjugates. These delivery systems have been able to provide enhanced therapeutic activity and reduced toxicity of anticancer agents mainly by altering their pharmacokinetics and biodistribution. Furthermore, the identification of cell-specific receptor/antigens on cancer cells have brought the development of ligand- or antibody-bearing delivery systems which can be targeted to cancer cells by specific binding to receptors or antigens. They have exhibited specific and selective delivery of anticancer agents to cancer. As a consequence of extensive research, clinical development of anticancer agents utilizing various delivery systems is undergoing worldwide. New technologies and multidisciplinary expertise to develop advanced drug delivery systems, applicable to a wide range of anticancer agents, may eventually lead to an effective cancer therapy in the future.
Antineoplastic Agents↗
In vitro properties of an in situ forming gel for the parenteral delivery of macromolecular drugs.
The purpose of this research was to (i) formulate a solution of a water-insoluble interpolymeric complex (IPC) containing poly(methacrylic acid) (PMA), 15 kDa, and poly(ethylene glycol) (PEG), 20 kDa, in a biocompatible cosolvent system; (ii) demonstrate that the IPC solution can transform into a gel, in situ, at physiological pH; and (iii) determine the ability of the gel to entrap, protect, and control the release of macromolecular drugs such as proteins and oligonucleotides. Ternary phase diagrams were prepared to identify cosolvent composition containing N-methylpyrrolidone (NMP), ethanol, and water that dissolve the IPC. IPC solutions (40, 50, or 60% w/v) each containing 1 mg of either model proteins, fluorescein isothiocyanate (FITC)-insulin and FITC-albumin, or 24-mer phosphorothioate oligonucleotides, were placed in containers that were immersed in buffer, pH 7.4. Aliquots of the buffer were sampled periodically and analyzed for the macromolecular content. In addition, in vitro bioactivity of another model protein, alpha-amylase, contained in the IPC solution was also determined. The studies demonstrated that a cosolvent containing 1:1:2 ratio of NMP/ethanol/water was most suitable for dissolving the IPC. Concentrations > 30% w/v IPC were required to form the gel, however, those mixtures containing > 60% w/v IPC could not be easily injected via 18-22 gauge needle. The gel can entrap and control the release of the model macromolecules for up to 6 days, in vitro. In addition, the gel can maintain the bioactivity of the protein, alpha-amylase, for 6 days. Therefore, an IPC gel can entrap, protect, and control the release of macromolecular drugs over a period of 6 days, in vitro, and therefore can be considered for in vivo investigation.
Albumins↗
1,3,5-2,4,6-functionalized, facially segregated benzenes-exploitation of sterically predisposed systems in supramolecular chemistry.
In the present article, we introduce the unique steric features of 1,3,5-substituted triethylbenzenes as a design principle for host molecules and supramolecular systems. Due to steric gearing, all three functional substituents are disposed on the same side of the phenyl plane. The use of this benzene scaffold has lead to the synthesis of various receptor molecules for a wide range of different guest species. Furthermore, the facially segregated systems can be used as building blocks with a controlled conformation in the synthesis of macrocycles or self-assembled supramolecular systems.
Anions↗
A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions.
We derive a series of novel mean-field potentials from statistical analyses of protein-protein contact regions in crystal structures. These potentials are parameterized in terms of the number of contacts made by an atom in an interface region. Such an explicit number dependence avoids the pairwise assumption and is intrinsically softer than distance-based approaches. It appears well suited to protein-protein docking applications, for which detailed interface geometry is generally lacking. In tests including protein complex reconstitution and docking of independently determined protein structures, we show that a hydrophobic potential of this type performs remarkably well, identifying native-like complexes by their favourable potential energies and in several cases demonstrating a recognition energy gap of 4-8 kcal/mol according to the system.
Binding Sites↗
Solution structure of the motile major sperm protein (MSP) of Ascaris suum - evidence for two manganese binding sites and the possible role of divalent cations in filament formation.
The major sperm protein (MSP) of Ascaris suum mediates amoeboid motility by forming an extensive intermeshed system of cytoskeletal filaments analogous to that formed by actin in many other amoeboid cells. MSP is a dimeric molecule that polymerizes to form non-polar filaments constructed from two helical subfilaments that wind round one another. Moreover, MSP filaments can interact with one another to form higher-order assemblies without requiring the range of accessory proteins usually employed in actin-based systems. A knowledge of how MSP polymerizes and forms the hierarchical series of helical MSP macromolecular assemblies is fundamental to understanding locomotion in these cells. Here we describe the solution structure of MSP dimers determined by NMR spectroscopy under conditions where MSP does not polymerize to form filaments. The solution structure is indistinguishable from that observed in putative MSP subfilament helices by X-ray crystallography, indicating that MSP polymerization is not accompanied by a major conformational change. We also show that the rate of MSP polymerization associated with movement of vesicles in an in vitro motility assay is enhanced by the presence of magnesium and manganese ions and use NMR to show that the primary residues that bind these ions are 24-25 and 83-86. These residues are distant from the interface formed between MSP dimers in subfilament helices, and so are probably not involved in this level of polymerization. Instead the manganese and magnesium ion binding appears to be associated with the assembly of subfilaments into filaments and their subsequent aggregation into bundles.
Animals↗
The role of specific side groups and pH in magnetization transfer in polymers.
The nature of water-macromolecule interactions in aqueous model polymers has been investigated using quantitative measurements of magnetization transfer. Cross-linked polymer gels composed of 94% water, 3% N,N'-methylene-bis-acrylamide, and 3% functional monomer (acrylamide, methacrylamide, acrylic acid, methacrylic acid, 2-hydroxyethyl-acrylate, or 2-hydroxyethyl-methacrylate) were studied. Water-macromolecule interactions were modified by varying the pH and specific functional group on the monomer. The magnitudes of the interactions were quantified by measuring the rate of proton nuclear spin magnetization exchange between the polymer matrix and the water. This rate was highly sensitive to the presence of carboxyl side groups on the macromolecule. However, the dependence of the rate on pH was not consistent with simple acid/base-catalyzed chemical exchange, and instead, the data suggest that multiequilibria proton exchange, a wide distribution in surface group pK values, and/or a macromolecular structural dependence on pH may play a significant role in magnetization transfer in polymer systems. These model polymer gels afford useful insights into the relevance of chemical composition and chemical dynamics on relaxation in tissues.
Acrylamides↗
The role of structure-based ligand design and molecular modelling in drug discovery.
Structure-based ligand design is a technique that is used in the initial stages of a drug development programme. The role of various computational methods in the characterization of the chemical properties and behaviour of molecular systems is discussed. The determination of the three-dimensional properties of small molecules and macromolecular receptor structures is a core activity in the efforts towards a better understanding of structure-activity relationships.
Computer-Aided Design↗