Simple Membrane System Research Articles

On evolving environment of 2D P colonies: ant colony simulation

P colonies are very simple membrane systems originally derived from the P systems. The 2D P colonies, as a version of P colonies with a two-dimensional environment, were introduced as a theoretical model of the multi-agent system for observing the behavior of a community of very simple agents living in a shared environment. Each agent is equipped with a set of programs consisting of a small number of simple rules. These programs allow the agent to act and move in the environment. Although, the 2D P colonies proved to be suitable for the simulations of various (not only) multi-agent systems, and natural phenomena, like the flash floods, there are phenomena which they are not able to simulate without some additional features or characteristics. One of the ways the agents can share the information is to use the stigmergy, which means to leave some special symbols in the environment. In this paper, we follow our previous research on the 2D P colony. We present a model of the 2D P colony with evolving environment, which allows us to simulate phenomena like the stigmergy, hence to simulate an ant colony.

Investigating Structural Property Relationships to Enable Repurposing of Pharmaceuticals as Zinc Ionophores

The importance of zinc in biology has gained greater recognition in recent years due to its essential contributions to the function of many endogenous enzymes. Disruption of zinc homeostasis may be useful in treating pathological conditions, such as Alzheimer’s, and for antiviral purposes. Despite the growth of knowledge and increased interest in zinc, little is known about the structure and function of zinc ionophores. In this study we analyse the Cambridge Structural Database and solution complexation studies found in the literature to identify key functional groups which may confer zinc ionophorism. Pharmaceuticals, nutraceuticals and amino acids with these functionalities were selected to enable us to explore the translatability of ionophoric activity from in vitro assays to cellular systems. We find that although certain species may complex to zinc in the solid and solution states, and may carry ions across simple membrane systems, this does not necessarily translate into ionophoric activity. We propose that the CSD can help refine key functionalities but that ionophoric activity must be confirmed in cellular systems.

Spatial organization of thylakoid network in higher plants

ABSTRACTAn intricate network of internal plastid membrane is formed in chloroplasts during plant ontogenesis. The network develops directly from a simple membrane system in proplastids or through a paracrystalline tubular prolamellar body (PLB) in etioplasts. A complex spatial structure of PLB interconnected with porous prothylakoids (PTs) is formed when the seedling growth proceeds without light. Upon illumination, PLB transforms through a multistage process into a lamellar system of stacked (grana) and loosely arranged (stroma) thylakoids. The chloroplast thylakoid network, the site of photochemical reactions, is one of the most important as well as most complicated membrane systems in nature. Thus, extensive studies on its possible spatial rearrangements are important for a better understanding of the crucial role of the thylakoid structure in the regulation of photosynthesis. Complementary structural methods are necessary to provide a complex image of spatial thylakoid arrangement. Therefore, in this review, we describe the results obtained by methods using both fixed and in vivo samples. The main goal of this review is to present the state of research on the three-dimensional (3D) structure of internal plastid membrane network, its spatial arrangement during plant ontogenesis and its modifications caused by different factors. Influence of different membrane components on the formation of the thylakoid network shape is also described. Additionally, we summarize recent 3D structural results in the field of thylakoid dynamics induced by environmental factors, especially of light-triggered changes related to rearrangements of the photosynthetic complexes.

Analysis of the Area Per Lipid in Protein-Membrane Systems

Molecular dynamics (MD) simulation is a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems the complexity of protein-lipid interactions makes investigation of lipid structure more difficult. Although the area per lipid is one of the important structural properties of membranes, the area in protein-membrane systems cannot be calculated easily by conventional approaches like Voronoi tessellation method. Here, we developed a new method, based on a combination of the two-dimensional Voronoi tessellation and Monte Carlo integration methods. Monte Carlo integration enables us to estimate the cross-sectional area of arbitrary-shaped target molecules. We applied the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca2+-pump and the SecY protein-conducting channel. The calculated lipid surface area was in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observed a response of lipid bilayers to the conformational transition of SecY. We believe that our method is useful to analyze time courses of protein-lipid interactions in MD simulations of membrane proteins.

Analysis of lipid surface area in protein–membrane systems combining voronoi tessellation and monte carlo integration methods

All-atom molecular dynamics (MD) simulation has become a powerful research tool to investigate structural and dynamical properties of biological membranes and membrane proteins. The lipid structures of simple membrane systems in recent MD simulations are in good agreement with those obtained by experiments. However, for protein-membrane systems, the complexity of protein-lipid interactions makes investigation of lipid structure difficult. Although the area per lipid is one of the essential structural properties in membrane systems, the area in protein-membrane systems cannot be computed easily by conventional approaches like the Voronoi tessellation method. To overcome this limitation, we propose a new method combining the two-dimensional Voronoi tessellation and Monte Carlo integration methods. This approach computes individual surface areas of lipid molecules not only in bulk lipids but also in proximity to membrane proteins. We apply the method to all-atom MD trajectories of the sarcoplasmic reticulum Ca(2+)-pump and the SecY protein-conducting channel. The calculated lipid surface area is in agreement with experimental values and consistent with other structural parameters of lipid bilayers. We also observe changes in the average area per lipid induced by the conformational transition of the SecY channel. Our method is particularly useful for examining equilibration of lipids around membrane proteins and for analyzing the time course of protein-lipid interactions.

A Survey of Membrane Computing as a New Branch of Natural Computing

As a new branch of natural computing,membrane computing is a hot cross-discipline topic,which involves computer science,mathematics,biology and artificial intelligence,etc..This paper outlines the recent development of membrane computing.A simple membrane system is taken for an example to introduce basic concepts and fundamental principles of this area.The theoretical development is surveyed from cell-like,tissue-like,neural-like P systems and their computational power and efficiency.The prospect and directions are discussed by summarizing research fruits of applications in the literature.The software/hardware implementation for P systems is analyzed to generalize the research advance.Finally,some important online resources,hot topics and further research paths are provided.

Molecular Dynamics Simulations of Na+/Cl−‐Dependent Neurotransmitter Transporters in a Membrane‐Aqueous System

We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate 5-HT or the selective serotonin reuptake inhibitor escitalopram. We have also included a transporter homologue, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystallographic B factors. Furthermore, key interactions identified in the X-ray structure of LeuT are maintained throughout the simulations indicating that our simple membrane system is suitable for studying the transmembrane protein hSERT in complex with 5-HT or escitalopram. For these transporter complexes, only relatively small fluctuations are observed in the ligand-binding cleft. Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitalopram complexes. Our findings are in good agreement with predictions from mutagenesis studies.

Membrane structure and radiation and hyperthermic damage

The general structure of the biological membrane and its involvement in cell damage from radiation and hyperthermic insults are discussed using bacterial cells as an example. Bacterial cells are useful models for these types of studies because they possess a simple membrane system whose composition can be readily altered. Also, various strains exist having different sensitivities to radiation and heat. For example, the response of Escherichia coli cells to ionizing radiation is found to be related to the degree of association between its DNA and membrane. Likewise, membrane lipids reportedly are important components in the cellular response to radiation. For example, radiation-induced lipid peroxidation leads to both structural and functional alterations in the membranes which must be considered to fully comprehend the biological effects of radiation. The physical state of the membrane during radiation exposure also is involved in the cellular response to radiation. Functional changes during radiation have been ascribed to changes in the protein component of the membrane. Other alterations which may play a role in radiation-induced cell damage include electrophoretic mobility of cells, membrane transport mechanisms, and membrane polysaccharide content. The cell membrane, particularly the lipid component, is an important target in hyperthermic cell killing. The composition and organization of the membrane lipids can influence a cell's response to heat. Heat-induced changes in membrane lipids lead to altered distribution of E. coli proteins, particularly their translocation to the outer membrane. These and other aspects are discussed in this review.

Anomalous properties of a simple small-volume membrane transport system at steady state

We investigate the transport of a single ligand L, between two macroscopic baths with different concentrations of L, by a simple membrane system. The center of this system is a very small volume V that might contain N = 0, 1, 2,... molecules of L. Access to V from either bath is by means of a single binding site for L. The steady-state properties of this simple system are studied exactly by a discrete-N master-equation approach. It is found that the mean concentration of L in V, c = N/V, is not a significant quantity either kinetically or thermodynamically. Further, the chemical potential of L in V is not defined and hence the overall thermodynamic force on L between the two baths cannot be subdivided at V. In fact, because V is small, the transport system must be treated as an indivisible system with interdependent parts. In the limit when V and N are very large, V becomes in effect a third macroscopic bath and two well-defined transport subsystems emerge (between V and either bath).

Interpretation of 100- and 360-MHz proton magnetic resonance spectra of retinal rod outer segment disk membranes.

Well resolved proton nuclear magnetic resonance ('H NMR) spectra of bovine retinal rod outer segment (ROS) disk membranes have been obtained at 100 and 360 MHz. The resolved IH resonances of the ROS membranes are due to phospholipids, with little contribution from rhodopsin. The spectra of both the ROS membranes and bilayer vesicles pre- pared from purified ROS phospholipids (liposomes) appear to represent a superposition of relatively sharp resonance components and a broad, underlying background. The distri- bution between sharp and broad spectral components is sen- sitive to sonication and temperature. The percentage of choline methyl protons which are resolved in the ROS membrane spectra as sharp resonance components increases from ap- proximately 35 to 100% and the average of the lipid hydro- carbon chain protons from approximately 20 to 40% over the Nuclear magnetic resonanie (NMR)~ has been used to elucidate details of motion (Horwitz et al., 1972; 1973b; Levine et al., 1972), phase behavior (Chapman, 1975), and asymmetry (Michaelson et al., 1974) in pure and mixed phospholipid bi- layer membranes. In addition, well resolved NMR spectra have been obtained of several natural membranes (see, e.g., Lee et al., 1974a; Davis et al., 1976). A relatively simple membrane system which appears to be particularly amenable to magnetic resonance studies is the rod outer segment (ROS) disk mem- brane from the vertebrate retina (for reviews see Hagins, 1972; Daemen, 1973; Hubbell, 1975; Ebrey and Honig, 1975; Dratz, 1977). A single protein, rhodopsin, comprises at least 85% of the total protein content. The ROS phospholipids are partic- ularly rich in polyunsaturated fatty acids, with docosahexenoic acid (C22:6w3) comprising at least 3 1-37% of the total fatty acid composition of bovine ROS disk membranes* (Nielson et al., 1970; Anderson and Sperling, 1971). The visual pigment rhodopsin rotates and translates freely in the ROS disk