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At least 199 records · Page 11Linked to original sources
PubMed2001

Type IV secretion: intercellular transfer of macromolecules by systems ancestrally related to conjugation machines.

Bacterial conjugation systems are highly promiscuous macromolecular transfer systems that impact human health significantly. In clinical settings, conjugation is exceptionally problematic, leading to the rapid dissemination of antibiotic resistance genes and other virulence traits among bacterial populations. Recent work has shown that several pathogens of plants and mammals - Agrobacterium tumefaciens, Bordetella pertussis, Helicobacter pylori and Legionella pneumophila - have evolved secretion pathways ancestrally related to conjugation systems for the purpose of delivering effector molecules to eukaryotic target cells. Each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now referred to as the type IV secretion family. The list of putative type IV family members is increasing rapidly, suggesting that macromolecular transfer by these systems is a widespread phenomenon in nature.

Bacterial Proteins↗
PubMed2006

Enhancing the site-specific targeting of macromolecular anticancer drug delivery systems.

The application of macromolecules as vehicles for anticancer drug delivery is a burgeoning field of interest. One of the hallmarks of using such systems, however, is that they must be capable of site-specific drug delivery. As such, augmenting the targeting of drug delivery systems to specified sites is paramount. To date, a number of synthetic strategies have been utilized to introduce targeting moieties to macromolecular drug delivery systems to enhance specific targeting. This scheme frequently involves the introduction of some type of biologically recognizable marker to the delivery system. Biological evaluations have substantiated the rationale that introducing targeting groups can significantly increase specificity. This concise review will attempt to encompass what strategies have been done to increase the specificity of macromolecular anticancer drug delivery systems along with their biological activities.

Animals↗
PubMed2004

Machine-learning techniques for macromolecular crystallization data.

Systematizing belief systems regarding macromolecular crystallization has two major advantages: automation and clarification. In this paper, methodologies are presented for systematizing and representing knowledge about the chemical and physical properties of additives used in crystallization experiments. A novel autonomous discovery program is introduced as a method to prune rule-based models produced from crystallization data augmented with such knowledge. Computational experiments indicate that such a system can retain and present informative rules pertaining to protein crystallization that warrant further confirmation via experimental techniques.

Algorithms↗
PubMed1998

Hysteresis in force probe measurements: a dynamical systems perspective.

Macromolecular binding forces between single protein-ligand pairs have been directly measured with the Atomic Force Microscope (AFM) in several recent experiments. In a typical measurement, the AFM probe, or cantilever, is attached to the ligand and exerts a disruptive force on the bond between the macromolecular pair while the receptor is held fixed; the probe is then moved away from the substrate until the bond is broken. When the bond actually breaks, the tip is observed to slip; in fact, the ligand is jumping to a new equilibrium point determined purely by the cantilever, as if the receptor had been instantaneously moved to infinity. This "jumping-off" or "minimum rupture force" is determined by measuring cantilever deflection. In a similar manner, the two molecules can be brought together and the "jumping-on" force can be determined. These two measurements will result in different estimates of the binding force due to hysteresis. This hysteresis is caused by a cusp catastrophe in the space defined by probe position and cantilever stiffness. The phenomena of "jumping-off" in macromolecular rupture experiments and "jumping-on" when molecules are brought together occur when the system passes through a saddle-node bifurcation as the probe position is varied. Probe approach and withdrawal result in different post-bifurcation equilibria, different energy dissipation, and different force measurements.

Animals↗
PubMedDate not supplied

Macromolecular crowding in biological systems: hydrodynamics and NMR methods.

Most biologically relevant environments involve highly concentrated macromolecular solutions and most biological processes involve macromolecules that diffuse and interact with other macromolecules. Macromolecular crowding is a general phenomenon that strongly affects the transport properties of macromolecules (rotational and translational diffusion) as well as the position of their equilibria. NMR methods can provide information on molecular interactions, as well as on translational and rotational diffusion. In fact, rotational diffusion, through its determinant role in NMR relaxation, places a practical limit on the systems that can be studied by NMR. While in dilute solutions of non-aggregating macromolecules this limit is set by macromolecular size, in crowded solutions excluded volume effects can have a strong effect on the observed diffusion rates. Hydrodynamic theory offers some insight into the magnitude of crowding effects on NMR observable parameters.

DNA↗
PubMed1999

Structural parameters from 19F homonuclear dipolar couplings, obtained by multipulse solid-state NMR on static and oriented systems.

Local macromolecular structure can be determined by solid-state NMR measurements of weak dipolar couplings between selectively labeled groups. The nonperturbing use of 2H, 13C, or 15N in biological systems, however, faces drawbacks in terms of a low sensitivity and a comparatively short distance range relative to 1H. To extend these limitations, we illustrate the use of 19F as an alternative NMR probe. The Carr-Purcell-Meiboom-Gill (CPMG) multipulse sequence was adapted here to measure homonuclear dipolar couplings between two fluorine labels in static samples at 470 MHz. Two lipids (4, 4-DMPC-F2, and a difluorinated sterol), which are arranged in liquid crystalline bilayers, serve as models to assess the scope of the technique. In these 19F-background-free biological samples, weak couplings down to 100 Hz could be resolved directly from the splitting of the pure dipolar powder lineshape, and 1H-decoupling was not required. Order parameters were determined for the anisotropic motion of the lipids, consistent with their expected behavior in the membrane. Besides measuring the distance-dependent term of the dipolar coupling in powder samples, we have also used oriented membranes to extract additional angular information from the dipolar anisotropy. The strategy presented here thus has the potential to obtain not only the internuclear distance between two labels, but also their angular orientation in the sample, provided the molecules are aligned as a membrane or a fiber.

Feasibility Studies↗
PubMed1996

Tricorn protease--the core of a modular proteolytic system.

Large macromolecular assemblies have evolved as a means of compartmentalizing reactions in organisms lacking membrane-bounded compartments. A tricorn-shaped protease was isolated from the archaeon Thermoplasma and was shown to form a multisubunit proteolytic complex. The 120-kilodalton monomer assembled to form a hexameric toroid that could assemble further into a capsid structure. Tricorn protease appeared to act as the core of a proteolytic system; when it interacted with several smaller proteins, it displayed multicatalytic activities.

Amino Acid Sequence↗
PubMed1998

Intracellular disposition and cytotoxicity of transferrin-mitomycin C conjugate in HL60 cells as a receptor-mediated drug targeting system.

A macromolecular conjugate of mitomycin C (MMC) with transferrin (TF) which possessed binding ability for TF receptor was synthesized. The conjugate (TF-MMC) was internalized into the human leukemia cell line HL60 cells and distributed into intracellular fractions, then exocytosed into an incubation medium. Although these phenomena were similar to those of TF, part of the internalized TF-MMC was degraded to a trichloroacetic acid (TCA)-soluble fraction. Therefore, the intracellular disposition of the conjugate was analyzed kinetically. The mean time of internalization of TF-MMC (7.14 min) was longer than that of TF (5.46 min). The mean exocytosis time of TF-MMC (22.1 min) was also longer than that of TF (13.0 min). Although elongation of both the internalization and exocytosis steps was responsible for the increase in recycling time of the conjugate, the binding process to the TF receptor in the internalization stage was found to be markedly retarded. The recycling times of TF-MMC and TF were 29.2 and 18.5 min, respectively. The mean decomposition time of TF-MMC was 76.3 min. Proliferation of HL60 cells was inhibited by TF-MMC in vitro. These results indicate that the TF-MMC was internalized via a TF receptor and a part of the internalized TF-MMC was degraded, so the released MMC might represent antitumor activity. TF-MMC was demonstrated to be a useful hybrid as a receptor-mediated targeting system.

Antineoplastic Agents↗
PubMed1980

The frequency of cyclic processes in biological multistate systems.

Cyclic processes in stochastic models of macromolecular biological systems are considered. The diagram solution of the model equations (master equation) gives rise to special functions of the rate constants, called the circuit (or one-way cycle) fluxes. As Hill has shown, these functions are the fundamental theoretical components of the operational fluxes, i.e., of the rates of reaction, of transport, of energy conversion, etc. Evidence recently has been found by Monte Carlo simulations that the circuit fluxes can be interpreted as the frequencies of circuit completions. Making use of the theory of graphs, we prove that this physical interpretation of the circuit fluxes is generally valid.

Kinetics↗
PubMed1999

MIAX: A Novel System for Assessment of Macromolecular Interaction in Condensed Phases. 1) Description of the Interaction Model and Simulation Algorithm.

We describe a novel computer system directed to evaluate protein complex formation in a liquid environment. The relevant feature of the system is a potential function expressing the main thermodynamic and kinetic factors leading to protein interaction in solution. The protein interaction model expresses the interaction energy as basically composed of three forces: electrostatic (hydrogen bond), van der Waals, and hydrophobic. The latter is defined in function of the forces that the solvent molecules exert on the surface of the complex, and the van der Waals forces between the monomers and the solvent. The interaction model implemented in the system has proven a high discrimination ability between different protein dockings, scoring high those close to the observed crystal structures. These results have led to the establishment of the basic principles underlying protein interaction, which constitutes the main way of expression of the biological function of these macromolecules.

Journal Article↗
PubMed1999

Study of the effects of aging on macromolecular synthesis in various organ systems using microscopic radioautography.

In order to elucidate the effects of aging on macromolecular synthesis such as DNA, RNA, proteins, glucides and lipids in various organ systems of experimental animals and humans, systematic studies using light and electron microscopic radioautography in various organ systems including skeletal, muscular, digestive, respiratory, urinary, reproductive, endocrine, circulatory, nervous and sensory systems were studied after incorporation with macromolecular precursors. The experimental animals used were mainly ddY strain mice from embryo to postnatal days 1 and 3, weeks 1 and 2 or months 1, 2 and 6 months up to 1 and 2 years senescent stages. Animals were injected with [3H]-thymidine for DNA, [3H]-uridine for RNA, [3H]-amino acids for proteins, [3H]-glucose, [3H]-glucosamine and [35S]O4 for glucides, [3H]-glycerol for lipids and some low molecular target tracers such as hormones, inorganic substances and drugs. Results demonstrate that these precursors when incorporated into various cell types in various organs showed specific patterns of macromolecular synthesis as observed in perinatal to juvenile, mature and senescent stages. These effects of aging could answer some of the questions as to how but not why we get old.

Aging↗
PubMed2000

MIAX: a system for assessment of macromolecular interaction. 3) A parallel hybrid GA for flexible protein docking.

We propose a parallel hybrid genetic algorithm for flexible protein-protein docking in order to improve the conventional rigid-body models to manipulate protein-protein interactions. The proposed hybrid algorithm is a combination of an evolutionary algorithm with a simulated annealing one, yielding a powerful protein-complex conformation-searching engine. Parallelization of the procedure makes possible to reach high algorithm performance, in both, execution times and size of treated monomers and complexes. Knowledge on side chain flexibility is extracted by means of an exhaustive analysis of crystallographic data on proteins and protein complexes. Results demonstrate the competency of the algorithm since comparison of calculated and crystallographic data accounts for a maximum of 2.5A in RMS difference, including side chain conformation. The system allows routine analysis of this fundamental molecular biology problem important to elucidate bio-macromolecular function in biophysical and biochemical mechanisms involving molecular recognition and interaction, yielding simultaneously clues for designing new proteins and enzymes directed to different purposes.

Algorithms↗