scholarly journals Ion Channels in Microbes

2008 ◽  
Vol 88 (4) ◽  
pp. 1449-1490 ◽  
Author(s):  
Boris Martinac ◽  
Yoshiro Saimi ◽  
Ching Kung
Keyword(s):  
Ion Channels ◽  
Biological Macromolecules ◽  
Structural Studies ◽  
Cellular Membranes ◽  
Genome Sequences ◽  
Microbial Cells ◽  
Laboratory Environment ◽  
Evolutionary Relatedness ◽  
Living Organisms ◽  
Multicellular Organisms

Studies of ion channels have for long been dominated by the animalcentric, if not anthropocentric, view of physiology. The structures and activities of ion channels had, however, evolved long before the appearance of complex multicellular organisms on earth. The diversity of ion channels existing in cellular membranes of prokaryotes is a good example. Although at first it may appear as a paradox that most of what we know about the structure of eukaryotic ion channels is based on the structure of bacterial channels, this should not be surprising given the evolutionary relatedness of all living organisms and suitability of microbial cells for structural studies of biological macromolecules in a laboratory environment. Genome sequences of the human as well as various microbial, plant, and animal organisms unambiguously established the evolutionary links, whereas crystallographic studies of the structures of major types of ion channels published over the last decade clearly demonstrated the advantage of using microbes as experimental organisms. The purpose of this review is not only to provide an account of acquired knowledge on microbial ion channels but also to show that the study of microbes and their ion channels may also hold a key to solving unresolved molecular mysteries in the future.

scholarly journals Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing

2017 ◽  
Vol 2017 ◽  
pp. 1-23 ◽  
Author(s):  
H. E. White ◽  
A. Ignatiou ◽  
D. K. Clare ◽  
E. V. Orlova
Keyword(s):  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Structural Studies ◽  
Structural Variations ◽  
Conformational States ◽  
Basic Principles ◽  
Computing Power ◽  
Living Organisms ◽  
Multiple Conformations

In living organisms, biological macromolecules are intrinsically flexible and naturally exist in multiple conformations. Modern electron microscopy, especially at liquid nitrogen temperatures (cryo-EM), is able to visualise biocomplexes in nearly native conditions and in multiple conformational states. The advances made during the last decade in electronic technology and software development have led to the revelation of structural variations in complexes and also improved the resolution of EM structures. Nowadays, structural studies based on single particle analysis (SPA) suggests several approaches for the separation of different conformational states and therefore disclosure of the mechanisms for functioning of complexes. The task of resolving different states requires the examination of large datasets, sophisticated programs, and significant computing power. Some methods are based on analysis of two-dimensional images, while others are based on three-dimensional studies. In this review, we describe the basic principles implemented in the various techniques that are currently used in the analysis of structural conformations and provide some examples of successful applications of these methods in structural studies of biologically significant complexes.

Epigenetic Mechanisms of Maternal Dietary Protein and Amino Acids Affecting Growth and Development of Offspring

2019 ◽  
Vol 20 (7) ◽  
pp. 727-735 ◽  
Author(s):  
Yi Wu ◽  
Zhibin Cheng ◽  
Yueyu Bai ◽  
Xi Ma
Keyword(s):  
Amino Acids ◽  
Dna Methylation ◽  
Dietary Protein ◽  
Growth And Development ◽  
Later Life ◽  
Biological Macromolecules ◽  
Epigenetic Mechanisms ◽  
Maternal Circulation ◽  
Energy Processing ◽  
Living Organisms

Nutrients can regulate metabolic activities of living organisms through epigenetic mechanisms, including DNA methylation, histone modification, and RNA regulation. Since the nutrients required for early embryos and postpartum lactation are derived in whole or in part from maternal and lactating nutrition, the maternal nutritional level affects the growth and development of fetus and creates a profound relationship between disease development and early environmental exposure in the offspring’s later life. Protein is one of the most important biological macromolecules, involved in almost every process of life, such as information transmission, energy processing and material metabolism. Maternal protein intake levels may affect the integrity of the fetal genome and alter DNA methylation and gene expression. Most amino acids are supplied to the fetus from the maternal circulation through active transport of placenta. Some amino acids, such as methionine, as dietary methyl donor, play an important role in DNA methylation and body’s one-carbon metabolism. The purpose of this review is to describe effects of maternal dietary protein and amino acid intake on fetal and neonatal growth and development through epigenetic mechanisms, with examples in humans and animals.

scholarly journals Analysis of site and structure specific core fucosylation in liver disease progression using exoglycosidase-assisted data-independent LC-MS/MS

2020 ◽  
Author(s):  
Miloslav Sanda ◽  
Jaeil Ahn ◽  
Petr Kozlik ◽  
Radoslav Goldman
Keyword(s):  
Liver Disease ◽  
Disease Progression ◽  
Serum Proteins ◽  
Receptor Activation ◽  
Biological Macromolecules ◽  
The Core ◽  
Liver Disease Progression ◽  
Living Organisms ◽  
Protein Attachment ◽  
Core Fucosylation

ABSTRACTCarbohydrates form one of the major groups of biological macromolecules in living organisms. Many biological processes including protein folding, stability, immune response, and receptor activation are regulated by glycosylation. Fucosylation of proteins regulates such processes and is associated with various diseases including autoimmunity and cancer. Mass spectrometry efficiently identifies structures of fucosylated glycans or sites of core fucosylated N-glycopeptides but quantification of the glycopeptides remains less explored. We performed experiments that facilitate quantitative analysis of the core fucosylation of proteins with partial structural resolution of the glycans and we present results of the mass spectrometric SWATH-type DIA analysis of relative abundances of the core fucosylated glycoforms of 45 glycopeptides derived from 18 serum proteins in liver disease of different etiologies. Our results show that a combination of soft fragmentation with exoglycosidases is efficient at the assignment and quantification of the core fucosylated N-glycoforms at specific sites of protein attachment. In addition, our results show that disease-associated changes in core fucosylation are peptide-dependent and further differ by branching of the core fucosylated glycans. Further studies are needed to verify whether tri- and tetra-antennary core fucosylated glycopeptides could be used as markers of liver disease progression.

The biological impact of superflares on planets in the Habitable Zone

2018 ◽  
Vol 14 (S345) ◽  
pp. 176-180
Author(s):  
Adriana Valio ◽  
Raissa Estrela ◽  
Luisa Cabral ◽  
Abel Grangeiro
Keyword(s):  
Survival Rates ◽  
Shallow Waters ◽  
The Sun ◽  
Habitable Zone ◽  
Biological Impact ◽  
Solar Type ◽  
Living Organisms ◽  
Multicellular Organisms ◽  
The Impact ◽  
M Dwarf

AbstractYounger and fully convective stars are much more active than our Sun, producing many superflares. Here we estimate the impact of the superflares UV radiation on living organisms on the surface of orbiting planets in the habitable zone of the star. For this we study two active stars, Kepler-96 (solar type) and TRAPPIST-1 (M dwarf). Kepler-96, with an age of 2.4 Gyr, is at the same stage of the Sun when the first multicellular organisms appeared on Earth. The biological impact of super flares are studied on a hypothetical Earth at 1AU of Kepler-96 and on planets TRAPPIST-1e, f, and g for three atmospheres scenarios: an Archean and Present-day atmospheres with and without ozone. We estimated the survival rates of two bacteria and concluded that life would only survive on the surface of these planets if their atmosphere had an ozone layer, or in shallow waters of an ocean.

Article Commentary: Regulation of Protein Function by Residue Oxidation

2010 ◽  
Vol 3 ◽  
pp. PRI.S3327 ◽  
Author(s):  
Xing-Hai Zhang
Keyword(s):  
Protein Function ◽  
Regulatory Mechanism ◽  
Cellular Metabolism ◽  
Life Forms ◽  
Biological Macromolecules ◽  
Oxygen Species ◽  
Cellular Processes ◽  
Methionine Residues ◽  
Living Organisms ◽  
Face Generation

A majority of extant life forms require O2 to survive and thrive. Oxidation is inevitably one of the most active cellular processes and one constant challenge that living organisms must face. Generation of oxidants including reactive oxygen species is a natural consequence of cellular metabolism of all biological systems during normal life cycle under different environments. These oxidants oxidize many biological macromolecules such as proteins and affect their functions. Oxidation of specific amino acids in proteins may cause damage to protein structure and impair function, or may also activate protein activities and promote cellular metabolism. As an example, the reversible oxidation of cysteine and methionine residues has a profound impact on protein function and cellular process. A recent study that examines the effect of Met oxidation on Ser phosphorylation in a mitochondrial enzyme, pyruvate dehydrogenase, provides another demonstration that protein oxidation is an important regulatory mechanism for organisms to deal with developmental and environmental challenges throughout life processes.

Generic tools for conditionally altering protein abundance and phenotypes on demand

2014 ◽  
Vol 395 (7-8) ◽  
pp. 737-762 ◽  
Author(s):  
Frederik Faden ◽  
Stefan Mielke ◽  
Dieter Lange ◽  
Nico Dissmeyer
Keyword(s):  
Protein Stability ◽  
Active Form ◽  
Protein Abundance ◽  
Physiological Conditions ◽  
On Demand ◽  
Conditional Gene Expression ◽  
Tissue Specific Promoter ◽  
Living Organisms ◽  
Multicellular Organisms

Abstract Conditional gene expression and modulating protein stability under physiological conditions are important tools in biomedical research. They led to a thorough understanding of the roles of many proteins in living organisms. Current protocols allow for manipulating levels of DNA, mRNA, and of functional proteins. Modulating concentrations of proteins of interest, their post-translational processing, and their targeted depletion or accumulation are based on a variety of underlying molecular modes of action. Several available tools allow a direct as well as rapid and reversible variation right on the spot, i.e., on the level of the active form of a gene product. The methods and protocols discussed here include inducible and tissue-specific promoter systems as well as portable degrons derived from instable donor sequences. These are either constitutively active or dormant so that they can be triggered by exogenous or developmental cues. Many of the described techniques here directly influencing the protein stability are established in yeast, cell culture and in vitro systems only, whereas the indirectly working promoter-based tools are also commonly used in higher eukaryotes. Our major goal is to link current concepts of conditionally modulating a protein of interest’s activity and/or abundance and approaches for generating cell and tissue types on demand in living, multicellular organisms with special emphasis on plants.

scholarly journals Electron Microscopy Analysis of Multilamellar Vesicles Prepared from Synthetic Lipids: A Model System for Studying Membrane Structure in the Molecular Cell Biology Classroom and Laboratory

2004 ◽  
Vol 12 (5) ◽  
pp. 40-45
Author(s):  
Russell R. Camp ◽  
Jungsoo Byun ◽  
Robert Jacob
Keyword(s):  
Cell Biology ◽  
Model System ◽  
Signaling Cascades ◽  
Considerable Research ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis ◽  
Molecular Cell Biology ◽  
Living Organisms ◽  
Multicellular Organisms ◽  
Flow Of Information

The cell is the fundamental unit of all living organisms, ranging from the unicellular archaea and bacteria (prokaryotes) to higher multicellular plants and animals (eukaryotes). All cells are bounded by a complex and dynamic plasma membrane, which functions principally to maintain cellular and organismal steady state by performing complex energy transformations and regulating the flow of information for the cell. The cell membrane also performs a number of vital housekeeping functions, which include control of the transport of substances between extracellular and intracellular environments, participation in cell signaling cascades by hosting receptors of extracellular ligands, and facilitating critical cell-to-cell communications in multicellular organisms (Karp, 2005).Considerable research over the last fifty years has significantly increased our understanding of cell membranes and their structural organization. Every membrane is fundamentally comprised of a dynamic lipid bilayer that supports a variety of transmembrane and membraneassociated proteins.

Transient receptor potential ion channels as participants in thermosensation and thermoregulation

2007 ◽  
Vol 292 (1) ◽  
pp. R64-R76 ◽  
Author(s):  
Michael J. Caterina
Keyword(s):  
Ion Channels ◽  
Molecular Mechanisms ◽  
Transient Receptor Potential ◽  
Trp Channels ◽  
Core Body Temperature ◽  
Expression Patterns ◽  
Receptor Potential ◽  
Genetic Ablation ◽  
Transient Receptor ◽  
Living Organisms

Living organisms must evaluate changes in environmental and internal temperatures to mount appropriate physiological and behavioral responses conducive to survival. Classical physiology has provided a wealth of information regarding the specialization of thermosensory functions among subclasses of peripheral sensory neurons and intrinsically thermosensitive neurons within the hypothalamus. However, until recently, the molecular mechanisms by which these cells carry out thermometry have remained poorly understood. The demonstration that certain ion channels of the transient receptor potential (TRP) family can be activated by increases or decreases in ambient temperature, along with the recognition of their heterogeneous expression patterns and heterogeneous temperature sensitivities, has led investigators to evaluate these proteins as candidate endogenous thermosensors. Much of this work has involved one specific channel, TRP vanilloid 1 (TRPV1), which is both a receptor for capsaicin and related pungent vanilloid compounds and a “heat receptor,” capable of directly depolarizing neurons in response to temperatures >42°C. Evidence for a contribution of TRPV1 to peripheral thermosensation has come from pharmacological, physiological, and genetic approaches. In contrast, although capsaicin-sensitive mechanisms clearly influence core body temperature regulation, the specific contribution of TRPV1 to this process remains a matter of debate. Besides TRPV1, at least six additional thermally sensitive TRP channels have been identified in mammals, and many of these also appear to participate in thermosensation. Moreover, the identification of invertebrate TRP channels, whose genetic ablation alters thermally driven behaviors, makes it clear that thermosensation represents an evolutionarily conserved role of this ion channel family.

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