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International Journal of Molecular... Mar 2021In this book, the papers published in the second issue, "Ion and Molecule Transport in Membrane Systems 2 [...].
In this book, the papers published in the second issue, "Ion and Molecule Transport in Membrane Systems 2 [...].
Topics: Animals; Biological Transport; Cell Membrane; Ions; Membranes, Artificial; Water
PubMed: 33805500
DOI: 10.3390/ijms22073533 -
The Journal of Membrane Biology Jun 2018Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure,...
Biomembranes assemble and operate at the interface with electrolyte solutions. Interactions between ions in solutions and the lipid affect the membrane structure, dynamics and electrostatic potential. In this article, I review some of the experimental and computational methods that are used to study membrane-ions interactions. Experimental methods that account for membrane-ion interactions directly and indirectly are presented first. Then, studies in which molecular dynamics simulations were used to gain an understanding of membrane-ion interactions are surveyed. Finally, the current view on membrane-ion interactions and their significance is briefly discussed.
Topics: Ions; Magnetic Resonance Spectroscopy; Membranes; Molecular Dynamics Simulation
PubMed: 29330605
DOI: 10.1007/s00232-017-0010-y -
Chemical Reviews Oct 2021Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical... (Review)
Review
Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical and electrochemical measurements. The heart of the SICM is a nanometer-scale electrolyte filled glass pipette that serves as a scanning probe. In the initial conception, manipulations of ion currents through the tip of the pipette and appropriate positioning hardware provided a route to recording micro- and nanoscopic mapping of the topography of surfaces. Subsequent advances in instrumentation, probe design, and methods significantly increased opportunities for SICM beyond recording topography. Hybridization of SICM with coincident characterization techniques such as optical microscopy and faradaic electrodes have brought SICM to the forefront as a tool for nanoscale chemical measurement for a wide range of applications. Modern approaches to SICM realize an important tool in analytical, bioanalytical, biophysical, and materials measurements, where significant opportunities remain for further exploration. In this review, we chronicle the development of SICM from the perspective of both the development of instrumentation and methods and the breadth of measurements performed.
Topics: Electrodes; Electrolytes; Ions; Microscopy
PubMed: 33295182
DOI: 10.1021/acs.chemrev.0c00962 -
International Journal of Molecular... Dec 2022Artificial ion-exchange and other charged membranes, such as biomembranes, are self-organizing nanomaterials built from macromolecules. The interactions of fragments of... (Review)
Review
Artificial ion-exchange and other charged membranes, such as biomembranes, are self-organizing nanomaterials built from macromolecules. The interactions of fragments of macromolecules results in phase separation and the formation of ion-conducting channels. The properties conditioned by the structure of charged membranes determine their application in separation processes (water treatment, electrolyte concentration, food industry and others), energy (reverse electrodialysis, fuel cells and others), and chlore-alkali production and others. The purpose of this review is to provide guidelines for modeling the transport of ions and water in charged membranes, as well as to describe the latest advances in this field with a focus on power generation systems. We briefly describe the main structural elements of charged membranes which determine their ion and water transport characteristics. The main governing equations and the most commonly used theories and assumptions are presented and analyzed. The known models are classified and then described based on the information about the equations and the assumptions they are based on. Most attention is paid to the models which have the greatest impact and are most frequently used in the literature. Among them, we focus on recent models developed for proton-exchange membranes used in fuel cells and for membranes applied in reverse electrodialysis.
Topics: Membranes, Artificial; Ions; Biological Transport; Ion Exchange; Protons
PubMed: 36613476
DOI: 10.3390/ijms24010034 -
Protein Science : a Publication of the... Jul 2015Ion-dipole interactions in biological macromolecules are formed between atomic or molecular ions and neutral protein dipolar groups through either hydrogen bond or... (Review)
Review
Ion-dipole interactions in biological macromolecules are formed between atomic or molecular ions and neutral protein dipolar groups through either hydrogen bond or coordination. Since their discovery 30 years ago, these interactions have proven to be a frequent occurrence in protein structures, appearing in everything from transporters and ion channels to enzyme active sites to protein-protein interfaces. However, their significance and roles in protein functions are largely underappreciated. We performed PDB data mining to identify a sampling of proteins that possess these interactions. In this review, we will define the ion-dipole interaction and discuss several prominent examples of their functional roles in nature.
Topics: Allosteric Regulation; Animals; Humans; Ions; Models, Molecular; Protein Binding; Protein Conformation; Protein Stability; Proteins
PubMed: 25866296
DOI: 10.1002/pro.2685 -
Biophysical Journal Sep 2016The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects... (Review)
Review
The inside of the cell is full of important, yet invisible species of molecules and proteins that interact weakly but couple together to have huge and important effects in many biological processes. Such "dark matter" inside cells remains mostly hidden, because our tools were developed to investigate strongly interacting species and folded proteins. Example dark-matter species include intrinsically disordered proteins, posttranslational states, ion species, and rare, transient, and weak interactions undetectable by biochemical assays. The dark matter of biology is likely to have multiple, vital roles to regulate signaling, rates of reactions, water structure and viscosity, crowding, and other cellular activities. We need to create new tools to image, detect, and understand these dark-matter species if we are to truly understand fundamental physical principles of biology.
Topics: Animals; Biophysical Phenomena; Humans; Intracellular Space; Ions; Protein Processing, Post-Translational; Proteins; Thermodynamics
PubMed: 27602719
DOI: 10.1016/j.bpj.2016.07.037 -
Annual Review of Biochemistry 2014Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with... (Review)
Review
Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
Topics: Algorithms; Binding Sites; Cations; Crystallography, X-Ray; DNA; Ions; Magnesium; Metals; Models, Theoretical; Nucleic Acid Conformation; Nucleic Acids; Poisson Distribution; RNA; Software; Static Electricity; Thermodynamics
PubMed: 24606136
DOI: 10.1146/annurev-biochem-060409-092720 -
Biotechnology and Applied Biochemistry Jan 2020Cell-free metabolic engineering is an emerging and promising alternative platform for the production of fuels and chemicals. In recent years, macromolecular crowding...
Cell-free metabolic engineering is an emerging and promising alternative platform for the production of fuels and chemicals. In recent years, macromolecular crowding effect, which is an important function in living cells but ignored in cell-free systems, has been transferred to cell-free protein synthesis (CFPS). However, inhibitory effects of crowding agents on CFPS were frequently observed, and the mechanism is unclear. In this study, free Mg was found to be a key factor that can regulate the macromolecular crowding effect on in vitro transcription, in vitro translation, and coupled transcript/translation. Addition of crowding agents (20% of Ficoll-70 or Ficoll-400) enhanced in vitro transcription at an index of free Mg concentration (IFMC) below 2 mM but inhibited the transcription when the IFMC was higher than 2 mM. Similarly, Ficoll-400 enhanced in vitro translation and coupled transcription/translation at a lower IFMC (0.1-2 mM) and inhibited the reactions at higher IFMC (>2 mM). Based on the results, CFPS systems could be further optimized by adjusting the content of crowding agents and the IFMC. Besides, the results also indicate that macromolecular crowding effect is important for maintaining the efficiency of in vivo transcription and translation which occur at a low intracellular IFMC (<1 mM).
Topics: Ions; Macromolecular Substances; Magnesium; Proteins
PubMed: 31576614
DOI: 10.1002/bab.1827 -
Sensors (Basel, Switzerland) Aug 2020In high concentrations, ionic species can be toxic in the body, catalyzing unwanted bioreactions, inhibiting enzymes, generating free radicals, in addition to having... (Review)
Review
In high concentrations, ionic species can be toxic in the body, catalyzing unwanted bioreactions, inhibiting enzymes, generating free radicals, in addition to having been associated with diseases like Alzheimer's and cancer. Although ionic species are ubiquitous in the environment in trace amounts, high concentrations of these metals are often found within industrial and agricultural waste runoff. Therefore, it remains a global interest to develop technologies capable of quickly and accurately detecting trace levels of ionic species, particularly in aqueous environments that naturally contain other competing/inhibiting ions. Herein, we provide an overview of the technologies that have been developed, including the general theory, design, and benefits/challenges associated with ion-selective electrode technologies (carrier-doped membranes, carbon-based varieties, enzyme inhibition electrodes). Notable variations of these electrodes will be highlighted, and a brief overview of associated electrochemical techniques will be given.
Topics: Biosensing Techniques; Carbon; Electrochemical Techniques; Electrodes; Ion-Selective Electrodes; Ions
PubMed: 32823973
DOI: 10.3390/s20164568 -
Journal of Mass Spectrometry : JMS May 2022This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the... (Review)
Review
This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.
Topics: Ions; Mass Spectrometry; Spectrum Analysis
PubMed: 35434805
DOI: 10.1002/jms.4826