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Berscheid A, Straetener J, Schilling NA, Ruppelt D, Konnerth MC, Schittek B, Krismer B, Peschel A, Steinem C, Grond S, Brötz-Oesterhelt H. The microbiome-derived antibacterial lugdunin acts as a cation ionophore in synergy with host peptides. mBio 2024:e0057824. [PMID: 39133006 DOI: 10.1128/mbio.00578-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/02/2024] [Indexed: 08/13/2024] Open
Abstract
Lugdunin is a microbiome-derived antibacterial agent with good activity against Gram-positive pathogens in vitro and in animal models of nose colonization and skin infection. We have previously shown that lugdunin depletes bacterial energy resources by dissipating the membrane potential of Staphylococcus aureus. Here, we explored the mechanism of action of lugdunin in more detail and show that lugdunin quickly depolarizes cytoplasmic membranes of different bacterial species and acidifies the cytoplasm of S. aureus within minutes due to protonophore activity. Varying the salt species and concentrations in buffers revealed that not only protons are transported, and we demonstrate the binding of the monovalent cations K+, Na+, and Li+ to lugdunin. By comparing known ionophores with various ion transport mechanisms, we conclude that the ion selectivity of lugdunin largely resembles that of 15-mer linear peptide gramicidin A. Direct interference with the main bacterial metabolic pathways including DNA, RNA, protein, and cell wall biosyntheses can be excluded. The previously observed synergism of lugdunin with dermcidin-derived peptides such as DCD-1 in killing S. aureus is mechanistically based on potentiated membrane depolarization. We also found that lugdunin was active against certain eukaryotic cells, however strongly depending on the cell line and growth conditions. While adherent lung epithelial cell lines were almost unaffected, more sensitive cells showed dissipation of the mitochondrial membrane potential. Lugdunin seems specifically adapted to its natural environment in the respiratory tract. The ionophore mechanism is refractory to resistance development and benefits from synergy with host-derived antimicrobial peptides. IMPORTANCE The vast majority of antimicrobial peptides produced by members of the microbiome target the bacterial cell envelope by many different mechanisms. These compounds and their producers have evolved side-by-side with their host and were constantly challenged by the host's immune system. These molecules are optimized to be well tolerated at their physiological site of production, and their modes of action have proven efficient in vivo. Imbalancing the cellular ion homeostasis is a prominent mechanism among antibacterial natural products. For instance, over 120 naturally occurring polyether ionophores are known to date, and antimicrobial peptides with ionophore activity have also been detected in microbiomes. In this study, we elucidated the mechanism underlying the membrane potential-dissipating activity of the thiazolidine-containing cycloheptapeptide lugdunin, the first member of the fibupeptides discovered in a commensal bacterium from the human nose, which is a promising future probiotic candidate that is not prone to resistance development.
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Affiliation(s)
- Anne Berscheid
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Dominik Ruppelt
- Georg-August-Universität Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen, Germany
| | - Martin C Konnerth
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Birgit Schittek
- Department of Dermatology, Division of Dermatooncology, University of Tübingen, Tübingen, Germany
| | - Bernhard Krismer
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Andreas Peschel
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Claudia Steinem
- Georg-August-Universität Göttingen, Institute of Organic and Biomolecular Chemistry, Göttingen, Germany
- Max-Planck-Institute for Dynamics and Self Organization, Göttingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
| | - Heike Brötz-Oesterhelt
- Interfaculty Institute of Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Microbial Bioactive Compounds, University of Tübingen, Cluster of Excellence EXC 2124-Controlling Microbes to Fight Infections, Tubingen, Germany
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2
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Ma L, Hou W, Ji Z, Sun Z, Li M, Lian B. Wearable Electrochemical Sensor for Sweat-Based Potassium Ion and Glucose Detection in Exercise Health Monitoring. ChemistryOpen 2024; 13:e202300217. [PMID: 38441499 PMCID: PMC11319218 DOI: 10.1002/open.202300217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/30/2024] [Indexed: 08/15/2024] Open
Abstract
The increasing prevalence of wearable devices has sparked a growing interest in real-time health monitoring and physiological parameter tracking. This study focuses on the development of a cost-effective sweat analysis device, utilizing microfluidic technology and selective electrochemical electrodes for non-invasive monitoring of glucose and potassium ions. The device, through real-time monitoring of glucose and potassium ion levels in sweat during physical activity, issues a warning signal when reaching experimentally set thresholds (K+ concentration at 7.5 mM, glucose concentrations at 60 μM and 120 μM). This alerts users to potential dehydration and hypoglycemic conditions. Through the integration of microfluidic devices and precise electrochemical analysis techniques, the device enables accurate and real-time monitoring of glucose and potassium ions in sweat. This advancement in wearable technology holds significant potential for personalized health management and preventive care, promoting overall well-being, and optimizing performance during physical activities.
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Affiliation(s)
- Lei Ma
- Department School of Information Science and TechnologyNantong University 9#Seyuan road, Chongchuan districtNantongChina
| | - Wenhao Hou
- Department School of Information Science and TechnologyNantong University 9#Seyuan road, Chongchuan districtNantongChina
| | - Zhi Ji
- Department School of Information Science and TechnologyNantong University 9#Seyuan road, Chongchuan districtNantongChina
| | - Ziheng Sun
- Department School of Information Science and TechnologyNantong University 9#Seyuan road, Chongchuan districtNantongChina
| | - Muxi Li
- Department School of Information Science and TechnologyNantong University 9#Seyuan road, Chongchuan districtNantongChina
| | - Bolin Lian
- Department School of Life scienceNantong University 9#Seyuan road, Chongchuan districtNantongChina
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3
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López-Corbalán V, Fuertes A, Llamas-Saiz AL, Amorín M, Granja JR. Recognition of anion-water clusters by peptide-based supramolecular capsules. Nat Commun 2024; 15:6055. [PMID: 39025854 PMCID: PMC11258365 DOI: 10.1038/s41467-024-50193-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
The biological and technological importance of anion-mediated processes has made the development of improved methods for the selective recognition of anions one of the most relevant research topics today. The hydration sphere of anions plays an important role in the functions performed by anions by forming a variety of cluster complexes. Here we describe a supramolecular capsule that recognizes hydrated anion clusters. These clusters are most likely composed of three ions that form hydrated C3 symmetry complexes that are entrapped within the supramolecular capsule of the same symmetry. The capsule is made of self-assembled α,γ-cyclic peptide containing amino acid with by five-membered rings and equipped with a tris(triazolylethyl)amine cap. To recognise the hydrated anion clusters, the hexapeptide capsule must disassemble to entrap them between its two subunits.
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Affiliation(s)
- Victoria López-Corbalán
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Organic Chemistry Department, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Fuertes
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Organic Chemistry Department, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio L Llamas-Saiz
- Unidad de Rayos X; Área de infraestructuras de Investigación, RIAIDT Edificio CACTUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Manuel Amorín
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Organic Chemistry Department, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Organic Chemistry Department, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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4
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Sidarta M, Lorente Martín AI, Monsalve A, Marinho Righetto G, Schäfer AB, Wenzel M. Lipid phase separation impairs membrane thickness sensing by the Bacillus subtilis sensor kinase DesK. Microbiol Spectr 2024; 12:e0392523. [PMID: 38717171 PMCID: PMC11237406 DOI: 10.1128/spectrum.03925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/08/2024] [Indexed: 06/06/2024] Open
Abstract
Membrane fluidity and thickness have emerged as crucial factors for the activity of and resistance to several antimicrobials. However, the lack of tools to study membrane fluidity and, in particular, thickness in living bacteria limits our understanding of this interplay. The Bacillus subtilis histidine kinase/phosphatase DesK is a molecular sensor that directly detects membrane thickness. It controls activity of DesR, which regulates expression of the lipid desaturase Des, known for its role in cold adaptation and daptomycin susceptibility. We hypothesized that this property could be exploited to develop biosensors and reporters for antibiotic-induced changes in membrane fluidity and thickness. To test this, we designed three assays based on the des system: activation of the Pdes promoter as reporter for membrane thickening, localization of DesK-GFP(green-fluorescent protein) as proxy for rigidified membrane domains, and antibiotic sensitivity of des, desK, and desR deletion mutants as readout for the importance of membrane rigidification/thickening under the tested condition. While we could not confirm the suitability of the des system as reporter for antibiotic-induced changes in membrane thickness, we did observe that des expression is only activated by mild temperature shocks, likely due to partitioning of the sensor DesK into fluid membrane domains upon phase separation, precluding effective thickness sensing under harsh cold shock and antibiotic stress conditions. Similarly, we did not observe any sensitivity of the deletion mutants to either temperature or antibiotic stress, raising the question to what extent the des system contributes to fluidity adaptation under these conditions. IMPORTANCE The B. subtilis des system is a prime model for direct molecular membrane thickness sensor and, as such, has been well studied in vitro. Our study shows that our understanding of its function in vivo and its importance under temperature and antibiotic stress is still very limited. Specifically, our results suggest that (i) the des system senses very subtle membrane fluidity changes that escape detection by established fluidity reporters like laurdan; (ii) membrane thickness sensing by DesK is impaired by phase separation due to partitioning of the protein into the fluid phase; and (iii) fluidity adaptations by Des are too subtle to elicit growth defects under rigidifying conditions, raising the question of how much the des system contributes to adaptation of overall membrane fluidity.
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Affiliation(s)
- Margareth Sidarta
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Ana I. Lorente Martín
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Anuntxi Monsalve
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Gabriela Marinho Righetto
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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5
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Chen YN, Liu YZ, Sun Q. The Molecular Mechanism of Ion Selectivity in Nanopores. Molecules 2024; 29:853. [PMID: 38398605 PMCID: PMC10891634 DOI: 10.3390/molecules29040853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/03/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Ion channels exhibit strong selectivity for specific ions over others under electrochemical potentials, such as KcsA for K+ over Na+. Based on the thermodynamic analysis, this study is focused on exploring the mechanism of ion selectivity in nanopores. It is well known that ions must lose part of their hydration layer to enter the channel. Therefore, the ion selectivity of a channel is due to the rearrangement of water molecules when entering the nanopore, which may be related to the hydrophobic interactions between ions and channels. In our recent works on hydrophobic interactions, with reference to the critical radius of solute (Rc), it was divided into initial and hydrophobic solvation processes. Additionally, the different dissolved behaviors of solutes in water are expected in various processes, such as dispersed and accumulated distributions in water. Correspondingly, as the ion approaches the nanopore, there seems to exist the "repulsive" or "attractive" forces between them. In the initial process (
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Affiliation(s)
| | | | - Qiang Sun
- Key Laboratory of Orogenic Belts and Crustal Evolution, The School of Earth and Space Sciences, Ministry of Education, Peking University, Beijing 100871, China; (Y.-N.C.); (Y.-Z.L.)
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6
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Stevens MJ, Rempe SLB. Insight into the K channel's selectivity from binding of K +, Na + and water to N-methylacetamide. Faraday Discuss 2024; 249:195-209. [PMID: 37846738 DOI: 10.1039/d3fd00110e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In potassium channels that conduct K+ selectively over Na+, which sites are occupied by K+ or water and the mechanism of selectivity are unresolved questions. The combination of the energetics and the constraints imposed by the protein structure yield the selective permeation and occupancy. To gain insight into the combination of structure and energetics, we performed density functional theory (DFT) calculations of multiple N-methyl acetamide (NMA) ligands binding to K+ and Na+, relative to hydrated K+ and Na+. NMA is an analogue of the amino acid backbone and provides the carbonyl binding to the ions that occurs in most binding sites of the K+ channel. Unconstrained optimal structures are obtained through geometry optimization calculations of the NMA ligand binding. The complexes formed by 8 NMA binding to the cations have the O atoms positioned in nearly identical locations as the O atoms in the selectivity filter. The transfer free energies between bulk water and K+ or Na+ bound to 8 NMA are almost identical, implying there is no selectivity by a single site. For water optimized with 8 NMA, binding is weak and O atoms are not positioned as in the K+ channel selectivity filter, suggesting that the ions are much more favored than water. Optimal structures of 8 NMA binding with two cations (K+ or Na+) are stable and have lower binding free energy than the optimal structures with just one cation. However, in the Na+ case, the optimal structure deforms and does not match the K+ channel; that is, two bound Na+ are destabilizing. In contrast, the two K+ structure is stabilized and the selectivity free energy favors K+. Overall, this study shows that binding site occupancy and the mechanism for K+ selectivity involves multiple K+ binding in multiple neighboring layers or sites of the K+ channel selectivity filter.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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7
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Stevens MJ, Rempe SLB. Binding of carboxylate and water to monovalent cations. Phys Chem Chem Phys 2023; 25:29881-29893. [PMID: 37889481 DOI: 10.1039/d3cp04200f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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8
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Liu Y, Ning Y, Chen Z, Han P, Zhi T, Li S, Ma A, Jia Y. Transcriptomics reveals substance biosynthesis and transport on membranes of Listeria monocytogenes affected by antimicrobial lipopeptide brevilaterin B. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Schmeltzer AJ, Harris JM, White HS. Single-Molecule Electrical Currents Associated with Valinomycin Transport of K . ACS NANO 2023; 17:8829-8836. [PMID: 37068060 DOI: 10.1021/acsnano.3c02825] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A quantitative description of ionophore-mediated ion transport is important in understanding ionophore activity in biological systems and developing ionophore applications. Herein, we describe the direct measurement of the electrical current resulting from K+ transport mediated by individual valinomycin (val) ionophores. Step fluctuations in current measured across a 1,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) bilayer suspended over a ∼400 nm radius glass nanopore result from dynamic partitioning of val between the bilayer and torus region, effectively increasing or decreasing the total number of val present in the membrane. In our studies, approximately 30 val are present in the membrane on average with a val entering or leaving the bilayer approximately every 50 s, allowing measurement of changes in electrical current associated with individual val. The single-molecule val(K+) transport current at 0.1 V applied potential is (1.3 ± 0.6) × 10-15 A, consistent with estimates of the transport kinetics based on large val ensembles. This methodology for analyzing single ionophore transport is general and can be applied to other carrier-type ionophores.
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Affiliation(s)
| | - Joel M Harris
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Henry S White
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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10
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Ives CM, Thomson NJ, Zachariae U. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels. J Gen Physiol 2023; 155:213957. [PMID: 36943243 PMCID: PMC10038842 DOI: 10.1085/jgp.202213226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.
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Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
- Biochemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee, UK
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11
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Hirata K, Sato E, Lisy JM, Ishiuchi SI, Fujii M. Cation-responsive cavity expansion of valinomycin revealed by cryogenic ion trap infrared spectroscopy. Phys Chem Chem Phys 2023; 25:1075-1080. [PMID: 36519454 DOI: 10.1039/d2cp04570b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Valinomycin (VM) is a natural K+-selective ionophore that transports K+ through the cell membrane. VM captures K+ in its central cavity with a C3-symmetric β-turn-like backbone. Although the binding affinity is drastically decreased for the VM-sodium (Na+VM) complex with respect to K+VM, VM holds relatively high affinity to Rb+ and Cs+. The high affinity for larger ions irrespective of ionic size seems to conflict with the expected optimal size matching model and raises questions on what factors determine ion selectivity. A combination of infrared spectroscopy with supporting computational calculations reveals that VM can accommodate larger Rb+ and Cs+ by flexibly changing its cavity size with the elongation of its folded β-turn-like backbone. The high affinity to Rb+ and Cs+ can be ascribed to a size-dependent cavity expansion. These findings provide a new perspective on molecular recognition and selectivity beyond the conventional size matching model.
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Affiliation(s)
- Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Eiko Sato
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - James M Lisy
- International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,International Research Frontiers Initiative (IRFI), Institute of Innovative Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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12
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Stevens MJ, Rempe SLB. Carboxylate binding prefers two cations to one. Phys Chem Chem Phys 2022; 24:22198-22205. [PMID: 36093927 DOI: 10.1039/d2cp03561h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Almost all studies of specific ion binding by carboxylates (-COO-) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs+, which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na+ and K+, and 3 for Li+ and Cs+. There is a 4-fold coordination minimum just a few kcal mol-1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. We find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective ion transport.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA. .,CBRN Defense and Energy Technologies, Sandia National Laboratories, Albuquerque, NM, 87185, USA.
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13
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Gomez DT, Pratt LR, Asthagiri DN, Rempe SB. Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory. Acc Chem Res 2022; 55:2201-2212. [PMID: 35829622 PMCID: PMC9386901 DOI: 10.1021/acs.accounts.2c00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here, we recount the foremost ab initio theory for the evaluation of the hydration free energies of ions, namely, quasi-chemical theory (QCT). We focus on anions, particularly halides but also the hydroxide anion, because they have been outstanding challenges for all theories. For example, this work supports understanding the high selectivity for F- over Cl- in fluoride-selective ion channels despite the identical charge and the size similarity of these ions. QCT is built by the identification of inner-shell clusters, separate treatment of those clusters, and then the integration of those results into the broader-scale solution environment. Recent work has focused on a close comparison with mass-spectrometric measurements of ion-hydration equilibria. We delineate how ab initio molecular dynamics (AIMD) calculations on ion-hydration clusters, elementary statistical thermodynamics, and electronic structure calculations on cluster structures sampled from the AIMD calculations obtain just the free energies extracted from the cluster experiments. That theory-experiment comparison has not been attempted before the work discussed here, but the agreement is excellent with moderate computational effort. This agreement reinforces both theory and experiment and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. Asymmetric hydration structures can be problematic for the evaluation of the QCT outer-shell contribution with the polarizable continuum model (PCM). Nevertheless, QCT provides a favorable setting for the exploitation of PCM when the inner-shell material shields the ion from the outer solution environment. For the more asymmetrically hydrated, and thus less effectively shielded, heavier halide ions clustered with waters, the PCM is less satisfactory. We therefore investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement; our final results are in close agreement with a standard tabulation of hydration free energies, and the final composite results are independent of the coordination number on the chemical energy scale of relevance, as they should be. Finally, a comparison of anion hydration structure in clusters and bulk solutions from AIMD simulations emphasize some differences: the asymmetries of bulk solution inner-shell structures are moderated compared with clusters but are still present, and inner hydration shells fill to slightly higher average coordination numbers in bulk solution than in clusters.
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Affiliation(s)
- Diego T. Gomez
- Department
of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States,
| | - Lawrence R. Pratt
- Department
of Chemical & Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States,
| | - Dilipkumar N. Asthagiri
- Department
of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States,
| | - Susan B. Rempe
- Center
for Integrated Nanotechnologies, Sandia
National Laboratories, Albuquerque, New Mexico 87185, United States,
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14
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Xue M, Qiu H, Shen C, Zhang Z, Guo W. Ion Hydration under Nanoscale Confinement: Dimensionality and Scale Effects. J Phys Chem Lett 2022; 13:4815-4822. [PMID: 35616271 DOI: 10.1021/acs.jpclett.2c00817] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
How ions are hydrated in nanoconfined spaces is crucial for understanding many natural phenomena and practical applications, such as biological functionalities and energy conversion devices. In real systems, nanoconfinement shows structural diversity, but the influence of dimensionality and scale on ion hydration remains considerably unrevealed. Here, we study ion hydration under various confinements by systematic molecular dynamics simulations. In a given dimension, the structure and dynamics of water molecules in the first hydration shell are altered to a degree inversely correlated with the confinement scale, as long as there is no central bulk-like region. Further comparison of ion hydration among different dimensional systems shows that this scale effect becomes more pronounced in systems with lower dimensionality, due to a more significant water layering effect and lower probability for ions to stay away from confining surfaces. These findings provide a qualitatively new understanding of ion transport in biological channels and are instrumental for the design of functional nanofluidic devices.
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Affiliation(s)
- Minmin Xue
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Chun Shen
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Zhuhua Zhang
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of the Ministry of Education, Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, People's Republic of China
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15
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Ribeiro SS, Castro TG, Gomes CM, Marcos JC. Hofmeister effects on protein stability are dependent on the nature of the unfolded state. Phys Chem Chem Phys 2021; 23:25210-25225. [PMID: 34730580 DOI: 10.1039/d1cp02477a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interpretation of a salt's effect on protein stability traditionally discriminates low concentration regimes (<0.3 M), dominated by electrostatic forces, and high concentration regimes, generally described by ion-specific Hofmeister effects. However, increased theoretical and experimental studies have highlighted observations of the Hofmeister phenomena at concentration ranges as low as 0.001 M. Reasonable quantitative predictions of such observations have been successfully achieved throughout the inclusion of ion dispersion forces in classical electrostatic theories. This molecular description is also on the basis of quantitative estimates obtained resorting to surface/bulk solvent partition models developed for ion-specific Hofmeister effects. However, the latter are limited by the availability of reliable structures representative of the unfolded state. Here, we use myoglobin as a model to explore how ion-dependency on the nature of the unfolded state affects protein stability, combining spectroscopic techniques with molecular dynamic simulations. To this end, the thermal and chemical stability of myoglobin was assessed in the presence of three different salts (NaCl, (NH4)2SO4 and Na2SO4), at physiologically relevant concentrations (0-0.3 M). We observed mild destabilization of the native state induced by each ion, attributed to unfavorable neutralization and hydrogen-bonding with the protein side-chains. Both effects, combined with binding of Na+, Cl- and SO42- to the thermally unfolded state, resulted in an overall destabilization of the protein. Contrastingly, ion binding was hindered in the chemically unfolded conformation, due to occupation of the binding sites by urea molecules. Such mechanistic action led to a lower degree of destabilization, promoting surface tension effects that stabilized myoglobin according to the Hofmeister series. Therefore, we demonstrate that Hofmeister effects on protein stability are modulated by the heterogeneous physico-chemical nature of the unfolded state. Altogether, our findings evidence the need to characterize the structure of the unfolded state when attempting to dissect the molecular mechanisms underlying the effects of salts on protein stability.
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Affiliation(s)
- Sara S Ribeiro
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Tarsila G Castro
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute, Faculdade de Ciências and Departamento de Química e Bioquímica, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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16
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Harris CM, Krock B, Tillmann U, Tainter CJ, Stec DF, Andersen AJC, Larsen TO, Reece KS, Harris TM. Alkali Metal- and Acid-Catalyzed Interconversion of Goniodomin A with Congeners B and C. JOURNAL OF NATURAL PRODUCTS 2021; 84:2554-2567. [PMID: 34520205 DOI: 10.1021/acs.jnatprod.1c00586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Goniodomin A (GDA, 1) is a phycotoxin produced by at least four species of Alexandrium dinoflagellates that are found globally in brackish estuaries and lagoons. It is a linear polyketide with six oxygen heterocyclic rings that is cyclized into a macrocyclic structure via lactone formation. Two of the oxygen heterocycles in 1 comprise a spiro-bis-pyran, whereas goniodomin B (GDB) contains a 2,7-dioxabicyclo[3.3.1]nonane ring system fused to a pyran. When H2O is present, 1 undergoes facile conversion to isomer GDB and to an α,β-unsaturated ketone, goniodomin C (GDC, 7). GDB and GDC can be formed from GDA by cleavage of the spiro-bis-pyran ring system. GDA, but not GDB or GDC, forms a crown ether-type complex with K+. Equilibration of GDA with GDB and GDC is observed in the presence of H+ and of Na+, but the equilibrated mixtures revert to GDA upon addition of K+. Structural differences have been found between the K+ and Na+ complexes. The association of GDA with K+ is strong, while that with Na+ is weak. The K+ complex has a compact, well-defined structure, whereas Na+ complexes are an ill-defined mixture of species. Analyses of in vitro A. monilatum and A. hiranoi cultures indicate that only GDA is present in the cells; GDB and GDC appear to be postharvest transformation products.
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Affiliation(s)
- Constance M Harris
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Urban Tillmann
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung (AWI), Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Craig J Tainter
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Donald F Stec
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Aaron J C Andersen
- Department of Biotechnology and Biomedicine, Søltofts Plads, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Søltofts Plads, Technical University of Denmark, 2800 Kgs., Lyngby, Denmark
| | - Kimberly S Reece
- Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, Virginia 23062, United States
| | - Thomas M Harris
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Virginia Institute of Marine Science (VIMS), William & Mary, Gloucester Point, Virginia 23062, United States
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17
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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18
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Xu Z, Fang N, Zhao Y. Calix[4]trap: A Bioinspired Host Equipped with Dual Selection Mechanisms. J Am Chem Soc 2021; 143:3162-3168. [PMID: 33606533 DOI: 10.1021/jacs.0c12223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Regulation of recognition events evolving in time and space is vital for living organisms. During evolution, organisms have developed distinct and orthogonal mechanisms to achieve selective recognition, avoiding mutual interference. Although the merging of multiple selection mechanisms into a single artificial host may lead to a more adaptable recognition system with unparalleled selectivity, successful implementation of this strategy is rare. Inspired by the intriguing structures and recognition properties of two well-known biological ion binders-valinomycin and K+ channels-we herein report a series of hosts equipped with dual guest selection mechanisms. These hosts simultaneously possess a preorganized binding cavity and a confined ion translocation tunnel, which are crucial to the record-setting K+/Na+ selectivity and versatile capabilities to discriminate against a wide range of ion pairs, such as K+/Rb+, K+/Ba2+, and Rb+/Cs+. Mechanistic studies verify that the host's portal is capable of discriminating cations by their size, enabling varied ion uptake rates. The confined tunnel bearing consecutive binding sites promotes complete desolvation of ions during their inclusion into the buried cavity, mimicking the ion translocation within ion channels. Our results demonstrate that the capability to manipulate guest recognition both in equilibrium and out-of-equilibrium states allows the host to effectively discriminate diverse guests via distinct mechanisms. The strategy to merge orthogonal selection mechanisms paves a new avenue to creating more robust hosts that may function in complex biological environments where many recognition events occur concurrently.
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Affiliation(s)
- Zhenchuang Xu
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Nie Fang
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
| | - Yanchuan Zhao
- Key Laboratory of Organofluorine Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China.,Key Laboratory of Energy Regulation Materials, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Ling-Ling Road, Shanghai 200032, China
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19
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Sato E, Hirata K, Lisy JM, Ishiuchi SI, Fujii M. Rethinking Ion Transport by Ionophores: Experimental and Computational Investigation of Single Water Hydration in Valinomycin-K + Complexes. J Phys Chem Lett 2021; 12:1754-1758. [PMID: 33570410 DOI: 10.1021/acs.jpclett.0c03372] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Valinomycin is a macrocyclic ionophore that transports K+ across hydrophobic membranes. Its function depends on selectivity, capture, transport, and release of the ion. While thermodynamics clearly indicate that valinomycin binds K+ preferentially over all other alkali ions, characterizing the capture/transport/release of K+ by valinomycin at the molecular level remains a challenge. The bracelet-like structure of valinomycin-K+ (K+VM) has the ion completely enveloped, facilitating transport through the cell membrane. We report that hydration by a single water molecule, (K+VM)(H2O), produces three different conformers, identified by infrared spectroscopy and supporting computational studies. For two minor conformers, the water prevents the ionophore from closing, a conformation that would inhibit diffusion through the membrane. However, the dominant conformer encloses both the ion and the water, replicating the bracelet-like K+VM and arguably enhancing diffusion through the membrane. This potential for active participation of water in transport through the hydrophobic cellular membrane has never been previously considered.
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Affiliation(s)
- Eiko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - Keisuke Hirata
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - James M Lisy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masaaki Fujii
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, 226-8503 Yokohama, Japan
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20
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Abstract
Microorganisms contend with numerous and unusual chemical threats and have evolved a catalog of resistance mechanisms in response. One particularly ancient, pernicious threat is posed by fluoride ion (F-), a common xenobiotic in natural environments that causes broad-spectrum harm to metabolic pathways. This review focuses on advances in the last ten years toward understanding the microbial response to cytoplasmic accumulation of F-, with a special emphasis on the structure and mechanisms of the proteins that microbes use to export fluoride: the CLCF family of F-/H+ antiporters and the Fluc/FEX family of F- channels.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Michal T Ruprecht
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; .,Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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21
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Carrasquel-Ursulaez W, Reeves RD, Dehghany M, Jones C, Schomaker JM, Chanda B. Re-evaluation of the mechanism of cytotoxicity of dialkylated lariat ether compounds. RSC Adv 2020; 10:40391-40394. [PMID: 33732448 PMCID: PMC7963367 DOI: 10.1039/d0ra08494h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The cytotoxicity of dialkylated lariat ethers has been previously attributed to their ionophoric properties. Herein, we provide evidence that these effects are due to loss of membrane integrity rather than ion transport, a finding with important implications for the future design of synthetic ionophores. The cytotoxicity of dialkylated lariat ethers has been previously attributed to their ionophoric properties.![]()
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Affiliation(s)
| | - Ryan D Reeves
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Mahzad Dehghany
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Corey Jones
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | | | - Baron Chanda
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63110, USA
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22
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Bondarev NV. Computer Analysis of Stability of Cation Complexes with
Ionophore Antibiotics. RUSS J GEN CHEM+ 2020. [DOI: 10.1134/s1070363220080149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Maldonado AM, Basdogan Y, Berryman JT, Rempe SB, Keith JA. First-principles modeling of chemistry in mixed solvents: Where to go from here? J Chem Phys 2020; 152:130902. [PMID: 32268733 DOI: 10.1063/1.5143207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mixed solvents (i.e., binary or higher order mixtures of ionic or nonionic liquids) play crucial roles in chemical syntheses, separations, and electrochemical devices because they can be tuned for specific reactions and applications. Apart from fully explicit solvation treatments that can be difficult to parameterize or computationally expensive, there is currently no well-established first-principles regimen for reliably modeling atomic-scale chemistry in mixed solvent environments. We offer our perspective on how this process could be achieved in the near future as mixed solvent systems become more explored using theoretical and computational chemistry. We first outline what makes mixed solvent systems far more complex compared to single-component solvents. An overview of current and promising techniques for modeling mixed solvent environments is provided. We focus on so-called hybrid solvation treatments such as the conductor-like screening model for real solvents and the reference interaction site model, which are far less computationally demanding than explicit simulations. We also propose that cluster-continuum approaches rooted in physically rigorous quasi-chemical theory provide a robust, yet practical, route for studying chemical processes in mixed solvents.
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Affiliation(s)
- Alex M Maldonado
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Yasemin Basdogan
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Joshua T Berryman
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Susan B Rempe
- Center for Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - John A Keith
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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24
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Arjes HA, Vo L, Dunn CM, Willis L, DeRosa CA, Fraser CL, Kearns DB, Huang KC. Biosurfactant-Mediated Membrane Depolarization Maintains Viability during Oxygen Depletion in Bacillus subtilis. Curr Biol 2020; 30:1011-1022.e6. [PMID: 32059765 PMCID: PMC7153240 DOI: 10.1016/j.cub.2020.01.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/09/2019] [Accepted: 01/23/2020] [Indexed: 12/26/2022]
Abstract
The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how populations adapt to shifts in oxygen availability. Here, we find that when oxygen was depleted from stationary phase B. subtilis cultures, ∼90% of cells died while the remaining cells maintained colony-forming ability. We discover that production of the antimicrobial surfactin confers two oxygen-related fitness benefits: it increases aerobic growth yield by increasing oxygen diffusion, and it maintains viability during oxygen depletion by depolarizing the membrane. Strains unable to produce surfactin exhibited an ∼50-fold reduction in viability after oxygen depletion. Surfactin treatment of these cells led to membrane depolarization and reduced ATP production. Chemical and genetic perturbations that alter oxygen consumption or redox state support a model in which surfactin-mediated membrane depolarization maintains viability through slower oxygen consumption and/or a shift to a more reduced metabolic profile. These findings highlight the importance of membrane potential in regulating cell physiology and growth, and demonstrate that antimicrobials that depolarize cell membranes can benefit cells when the terminal electron acceptor in respiration is limiting. This foundational knowledge has deep implications for environmental microbiology, clinical anti-bacterial therapy, and industrial biotechnology.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Lam Vo
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Caroline M Dunn
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Christopher A DeRosa
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Cassandra L Fraser
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Daniel B Kearns
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA.
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25
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Chaudhari MI, Vanegas JM, Pratt LR, Muralidharan A, Rempe SB. Hydration Mimicry by Membrane Ion Channels. Annu Rev Phys Chem 2020; 71:461-484. [PMID: 32155383 DOI: 10.1146/annurev-physchem-012320-015457] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ions transiting biomembranes might pass readily from water through ion-specific membrane proteins if these protein channels provide environments similar to the aqueous solution hydration environment. Indeed, bulk aqueous solution is an important reference condition for the ion permeation process. Assessment of this hydration mimicry concept depends on understanding the hydration structure and free energies of metal ions in water in order to provide a comparison for the membrane channel environment. To refine these considerations, we review local hydration structures of ions in bulk water and the molecular quasi-chemical theory that provides hydration free energies. In doing so, we note some current views of ion binding to membrane channels and suggest new physical chemical calculations and experiments that might further clarify the hydration mimicry concept.
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Affiliation(s)
- Mangesh I Chaudhari
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA;
| | - Juan M Vanegas
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA; .,Current affiliation: Department of Physics, University of Vermont, Burlington, Vermont 05405, USA
| | - L R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA
| | - Ajay Muralidharan
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, USA.,Current affiliation: Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Susan B Rempe
- Department of Computational Biology and Biophysics, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA;
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26
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Antifungal peptides produced by actinomycetes and their biological activities against plant diseases. J Antibiot (Tokyo) 2020; 73:265-282. [PMID: 32123311 DOI: 10.1038/s41429-020-0287-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/11/2020] [Accepted: 01/15/2020] [Indexed: 12/23/2022]
Abstract
Antibacterial peptides are a class of naturally occurring peptides produced by eukaryotes and prokaryotes. Some of them exhibit broad-spectrum antifungal activity. Antifungal peptides (AFPs) can be developed as antibiotic to control fungal infections in agriculture due to their different antifungal mechanisms. As actinomycetes are still one of the most important sources of novel antibiotics, in this review, the mechanisms of action of AFPs are explained. Characterization of several AFPs produced by actinomycetes and their biological activities against plant diseases are summarized. Furthermore, the pathway for total synthesis of naturally occurring cyclodepsipeptide, valinomycin, is proposed. Finally, the pathway for biosynthesis of kutzneride 2 is proposed and the structure-activity relationship of kutznerides is discussed.
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27
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Zhai Q, Yap LW, Wang R, Gong S, Guo Z, Liu Y, Lyu Q, Wang J, Simon GP, Cheng W. Vertically Aligned Gold Nanowires as Stretchable and Wearable Epidermal Ion-Selective Electrode for Noninvasive Multiplexed Sweat Analysis. Anal Chem 2020; 92:4647-4655. [DOI: 10.1021/acs.analchem.0c00274] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Qingfeng Zhai
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Lim Wei Yap
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Ren Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Shu Gong
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Zhirui Guo
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Yiyi Liu
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Quanxia Lyu
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
| | - Joseph Wang
- Department of Nanoengineering, University of California, San Diego, La Jolla, California 92093, United States
| | - George. P. Simon
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Wenlong Cheng
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
- New Horizon Research Centre, Monash University, Clayton, Victoria 3800, Australia
- The Melbourne Centre for Nanofabrication, Clayton, Victoria 3800, Australia
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28
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Basdogan Y, Groenenboom MC, Henderson E, De S, Rempe SB, Keith JA. Machine Learning-Guided Approach for Studying Solvation Environments. J Chem Theory Comput 2019; 16:633-642. [PMID: 31809056 DOI: 10.1021/acs.jctc.9b00605] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular-level understanding and characterization of solvation environments are often needed across chemistry, biology, and engineering. Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics-based cluster-continuum approach for calculating single-ion solvation free energies. This approach uses a global optimization procedure to identify low-energy molecular clusters with different numbers of explicit solvent molecules and then employs the smooth overlap for atomic positions learning kernel to quantify the similarity between different low-energy solute environments. From these data, we use sketch maps, a nonlinear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. After testing this approach on different ions having charges 2+, 1+, 1-, and 2-, we find that the solvation environment around each ion can be seen to usually become more similar in hand with its calculated single-ion solvation free energy. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies within 5% of experimental measurements for most cases, and it should be transferable for the study of other systems where dynamics simulations are not easily carried out.
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Affiliation(s)
- Yasemin Basdogan
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Mitchell C Groenenboom
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Ethan Henderson
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
| | - Sandip De
- Laboratory of Computational Science and Modelling, Institute of Materials , École Polytechnique Fédérale de Lausanne , Lausanne 1015 , Switzerland
| | - Susan B Rempe
- Department of Nanobiology , Sandia National Laboratories , Albuquerque 87185 , New Mexico , United States
| | - John A Keith
- Department of Chemical and Petroleum Engineering Swanson School of Engineering , University of Pittsburgh , Pittsburgh 15261 , Pennsylvania , United States
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29
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Selective ion transport through hydrated cation and anion exchange membranes I. The effect of specific interactions. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.117372] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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31
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Muralidharan A, Pratt L, Chaudhari M, Rempe S. Quasi-chemical theory for anion hydration and specific ion effects: Cl-(aq) vs. F-(aq). ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cpletx.2019.100037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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32
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Yang X, Cheng K, Jia GZ. Microwave heating and non-thermal effects of sodium chloride aqueous solution. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1662505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xin Yang
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
| | - Ke Cheng
- College of Optoelectronic Technology, Chengdu University of Information technology, Chengdu, People’s Republic of China
| | - Guo-zhu Jia
- College of Physical and Electronics Engineering, Sichuan Normal University, Chengdu, People’s Republic of China
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33
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Borges A, Gillespie D, Nag A. Biological applications of amide and amino acid containing synthetic macrocycles. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1650178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ariane Borges
- Department of Chemistry, Clark University, Worcester, MA, USA
| | - Dylan Gillespie
- Department of Chemistry, Clark University, Worcester, MA, USA
| | - Arundhati Nag
- Department of Chemistry, Clark University, Worcester, MA, USA
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34
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Ross EE, Hoag B, Joslin I, Johnston T. Measurements of Ion Binding to Lipid-Hosted Ionophores by Affinity Chromatography. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:9410-9421. [PMID: 31282163 DOI: 10.1021/acs.langmuir.9b01301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The binding affinity between antibiotic ionophores and alkali ions within supported lipid bilayers was evaluated using affinity chromatography. We used zonal elution and frontal analysis methods in nanovolume liquid chromatography to characterize the binding selectivity of the carrier and channel ionophores valinomycin and gramicidin A within different phosphatidylcholine bilayers. Distinct binding sensitivity to the lipid phase, both in affinity and selectivity, is observed for valinomycin, whereas gramicidin is less sensitive to changes in a membrane environment, behavior that is consistent with ion binding occurring within the interior of an established channel. There is good agreement between the chromatographic retention and the reported binding selectivity measured by other techniques. Surface potential near the binding site affects ion retention and the apparent association binding constants, but not the binding selectivity or enthalpy measurements. A model accounting for the surface potential contributions of retained ions during frontal analyses yields values close to intrinsic binding constants for gramicidin A (KA for K+ between 70 and 120 M-1) using reasonable estimates of the initial potential that is postulated to arise from the underlying silica.
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Affiliation(s)
- Eric E Ross
- Department of Chemistry & Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Bridget Hoag
- Department of Chemistry & Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Ian Joslin
- Department of Chemistry & Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
| | - Taylor Johnston
- Department of Chemistry & Biochemistry , Gonzaga University , Spokane , Washington 99258 , United States
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35
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Ahmadi S, Dabbagh HA, Ebrahimi S, Farrokhpour H. Diastereomeric discrimination by achiral substances: the effect of diverse ions in the stability of amphi-ionophore cystine-based cyclopeptide stereoisomers. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1527408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Samaneh Ahmadi
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
| | - Hossein A. Dabbagh
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
| | - Saeid Ebrahimi
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran
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36
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Ishiuchi SI, Sasaki Y, Lisy JM, Fujii M. Ion-peptide interactions between alkali metal ions and a termini-protected dipeptide: modeling a portion of the selectivity filter in K + channels. Phys Chem Chem Phys 2019; 21:561-571. [PMID: 30351321 DOI: 10.1039/c8cp05839c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Potassium channels have the unique ability to allow the selective passage of potassium ions at near diffusion-free rates while inhibiting the passage of more abundant sodium ions. Local interactions between chemical functional groups and the ions are responsible for both selectivity and transport. As an initial step in characterizing these interactions, the structures of Na+ and K+ complexed to the Ac-Tyr-NHMe peptide have been determined from infrared laser spectroscopy and supporting ab initio calculations. Ac-Tyr-NHMe, a termini-protected peptide sequence, replicates the GYG portion of one of the four peptide chains comprising the selectivity filter of a K+ channel. This peptide contains two carbonyl groups, among the eight C[double bond, length as m-dash]O groups forming the S1 binding site of the selectivity filter. Three conformations have been identified for both ions by laser IR-IR double resonance methods. Two conformations have the ion bound to the two C[double bond, length as m-dash]O groups. The third conformation has, in addition, a cation-π interaction with the aromatic ring of tyrosine, i.e. tridentate binding. The relative contributions of the three conformers are approximately the same for K+Ac-Tyr-NHMe, while the tridentate conformer is preferred for Na+Ac-Tyr-NHMe. These differences will be discussed in the context of ion mobility and selectivity.
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Affiliation(s)
- Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan.
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37
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Muralidharan A, Pratt LR, Chaudhari MI, Rempe SB. Quasi-Chemical Theory with Cluster Sampling from Ab Initio Molecular Dynamics: Fluoride (F -) Anion Hydration. J Phys Chem A 2018; 122:9806-9812. [PMID: 30475612 DOI: 10.1021/acs.jpca.8b08474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Accurate predictions of the hydration free energy for anions typically has been more challenging than that for cations. Hydrogen bond donation to the anion in hydrated clusters such as F(H2O) n - can lead to delicate structures. Consequently, the energy landscape contains many local minima, even for small clusters, and these minima present a challenge for computational optimization. Utilization of cluster experimental results for the free energies of gas-phase clusters shows that even though anharmonic effects are interesting they need not be of troublesome magnitudes for careful applications of quasi-chemical theory to ion hydration. Energy-optimized cluster structures for anions can leave the central ion highly exposed, and application of implicit solvation models to these structures can incur more serious errors than those for metal cations. Utilizing cluster structures sampled from ab initio molecular dynamics simulations substantially fixes those issues.
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Affiliation(s)
- A Muralidharan
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - L R Pratt
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - M I Chaudhari
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
| | - S B Rempe
- Center for Biological and Engineering Sciences , Sandia National Laboratories , Albuquerque , New Mexico 87185 , United States
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38
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The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations. SENSORS 2018; 18:s18093143. [PMID: 30231473 PMCID: PMC6163810 DOI: 10.3390/s18093143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGICs) to carry Na+ and K+ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently, the structure of a number of VGICs was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains (VSDs), each formed from four transmembrane (TM) segments, plus a pore domain through which ions move. Understanding the gating mechanism (how the channel opens and closes) requires structures. One TM segment (S4) has an arginine in every third position, with one such segment per domain. It is usually assumed that these arginines are all ionized, and in the resting state are held toward the intracellular side of the membrane by voltage across the membrane. They are assumed to move outward (extracellular direction) when released by depolarization of this voltage, producing a capacitive gating current and opening the channel. We suggest alternate interpretations of the evidence that led to these models. Measured gating current is the total charge displacement of all atoms in the VSD; we propose that the prime, but not sole, contributor is proton motion, not displacement of the charges on the arginines of S4. It is known that the VSD can conduct protons. Quantum calculations on the Kv1.2 potassium channel VSD show how; the key is the amphoteric nature of the arginine side chain, which allows it to transfer a proton. This appears to be the first time the arginine side chain has had its amphoteric character considered. We have calculated one such proton transfer in detail: this proton starts from a tyrosine that can ionize, transferring to the NE of the third arginine on S4; that arginine’s NH then transfers a proton to a glutamate. The backbone remains static. A mutation predicted to affect the proton transfer has been qualitatively confirmed experimentally, from the change in the gating current-voltage curve. The total charge displacement in going from a normal closed potential of −70 mV across the membrane to 0 mV (open), is calculated to be approximately consistent with measured values, although the error limits on the calculation require caution in interpretation.
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39
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Chaudhari MI, Rempe SB. Strontium and barium in aqueous solution and a potassium channel binding site. J Chem Phys 2018; 148:222831. [PMID: 29907035 DOI: 10.1063/1.5023130] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ion hydration structure and free energy establish criteria for understanding selective ion binding in potassium (K+) ion channels and may be significant to understanding blocking mechanisms as well. Recently, we investigated the hydration properties of Ba2+, the most potent blocker of K+ channels among the simple metal ions. Here, we use a similar method of combining ab initio molecular dynamics simulations, statistical mechanical theory, and electronic structure calculations to probe the fundamental hydration properties of Sr2+, which does not block bacterial K+ channels. The radial distribution of water around Sr2+ suggests a stable 8-fold geometry in the local hydration environment, similar to Ba2+. While the predicted hydration free energy of -331.8 kcal/mol is comparable with the experimental result of -334 kcal/mol, the value is significantly more favorable than the -305 kcal/mol hydration free energy of Ba2+. When placed in the innermost K+ channel blocking site, the solvation free energies and lowest energy structures of both Sr2+ and Ba2+ are nearly unchanged compared with their respective hydration properties. This result suggests that the block is not attributable to ion trapping due to +2 charge, and differences in blocking behavior arise due to free energies associated with the exchange of water ligands for channel ligands instead of free energies of transfer from water to the binding site.
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Affiliation(s)
- Mangesh I Chaudhari
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories, Albuquerque, New Mexico 87185, USA
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40
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Gerold CT, Bakker E, Henry CS. Selective Distance-Based K+ Quantification on Paper-Based Microfluidics. Anal Chem 2018; 90:4894-4900. [DOI: 10.1021/acs.analchem.8b00559] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chase T. Gerold
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Inorganic and Analytical Chemistry, The University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
| | - Eric Bakker
- Department of Inorganic and Analytical Chemistry, The University of Geneva, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland
| | - Charles S. Henry
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
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41
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Liu X, Lu B. Incorporating Born solvation energy into the three-dimensional Poisson-Nernst-Planck model to study ion selectivity in KcsA K^{+} channels. Phys Rev E 2017; 96:062416. [PMID: 29347452 DOI: 10.1103/physreve.96.062416] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Indexed: 06/07/2023]
Abstract
Potassium channels are much more permeable to potassium than sodium ions, although potassium ions are larger and both carry the same positive charge. This puzzle cannot be solved based on the traditional Poisson-Nernst-Planck (PNP) theory of electrodiffusion because the PNP model treats all ions as point charges, does not incorporate ion size information, and therefore cannot discriminate potassium from sodium ions. The PNP model can qualitatively capture some macroscopic properties of certain channel systems such as current-voltage characteristics, conductance rectification, and inverse membrane potential. However, the traditional PNP model is a continuum mean-field model and has no or underestimates the discrete ion effects, in particular the ion solvation or self-energy (which can be described by Born model). It is known that the dehydration effect (closely related to ion size) is crucial to selective permeation in potassium channels. Therefore, we incorporated Born solvation energy into the PNP model to account for ion hydration and dehydration effects when passing through inhomogeneous dielectric channel environments. A variational approach was adopted to derive a Born-energy-modified PNP (BPNP) model. The model was applied to study a cylindrical nanopore and a realistic KcsA channel, and three-dimensional finite element simulations were performed. The BPNP model can distinguish different ion species by ion radius and predict selectivity for K^{+} over Na^{+} in KcsA channels. Furthermore, ion current rectification in the KcsA channel was observed by both the PNP and BPNP models. The I-V curve of the BPNP model for the KcsA channel indicated an inward rectifier effect for K^{+} (rectification ratio of ∼3/2) but indicated an outward rectifier effect for Na^{+} (rectification ratio of ∼1/6).
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Affiliation(s)
- Xuejiao Liu
- State Key Laboratory of Scientific and Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Benzhuo Lu
- State Key Laboratory of Scientific and Engineering Computing, National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China and School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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42
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Sahu S, Di Ventra M, Zwolak M. Dehydration as a Universal Mechanism for Ion Selectivity in Graphene and Other Atomically Thin Pores. NANO LETTERS 2017; 17:4719-4724. [PMID: 28678508 PMCID: PMC5614503 DOI: 10.1021/acs.nanolett.7b01399] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ion channels play a key role in regulating cell behavior and in electrical signaling. In these settings, polar and charged functional groups, as well as protein response, compensate for dehydration in an ion-dependent way, giving rise to the ion selective transport critical to the operation of cells. Dehydration, though, yields ion-dependent free-energy barriers and thus is predicted to give rise to selectivity by itself. However, these barriers are typically so large that they will suppress the ion currents to undetectable levels. Here, we establish that graphene displays a measurable dehydration-only mechanism for selectivity of K+ over Cl-. This fundamental mechanism, one that depends only on the geometry and hydration, is the starting point for selectivity for all channels and pores. Moreover, while we study selectivity of K+ over Cl- we find that dehydration-based selectivity functions for all ions, that is, cation over cation selectivity (e.g., K+ over Na+). Its likely detection in graphene pores resolves conflicting experimental results, as well as presents a new paradigm for characterizing the operation of ion channels and engineering molecular/ionic selectivity in filtration and other applications.
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Affiliation(s)
- Subin Sahu
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
- Maryland Nanocenter, University of Maryland , College Park, Maryland 20742, United States
- Department of Physics, Oregon State University , Corvallis, Oregon 97331, United States
| | - Massimiliano Di Ventra
- Department of Physics, University of California , San Diego, California 92093, United States
| | - Michael Zwolak
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
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43
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Ahmed M, Jalily Hasani H, Ganesan A, Houghton M, Barakat K. Modeling the human Na v1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. Drug Des Devel Ther 2017; 11:2301-2324. [PMID: 28831242 PMCID: PMC5552146 DOI: 10.2147/dddt.s133944] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer. Our model was comprehensively validated by using reported mutagenesis data, comparisons with previous models, and binding to a panel of known hNav1.5 blockers. The relatively long classical MD simulation was sufficient to observe a natural sodium permeation event across the channel's selectivity filters to reach the channel's central cavity, together with the identification of a unique role of the lysine residue. Electrostatic potential calculations revealed the existence of two potential binding sites for the sodium ion at the outer selectivity filters. To obtain further mechanistic insight into the permeation event from the central cavity to the intracellular region of the channel, we further employed "state-of-the-art" steered molecular dynamics (SMD) simulations. Our SMD simulations revealed two different pathways through which a sodium ion can be expelled from the channel. Further, the SMD simulations identified the key residues that are likely to control these processes. Finally, we discuss the potential binding modes of a panel of known hNav1.5 blockers to our structural model of hNav1.5. We believe that the data presented here will enhance our understanding of the structure-property relationships of the hNav1.5 ion channel and the underlying molecular mechanisms in sodium ion permeation and drug interactions. The results presented here could be useful for designing safer drugs that do not block the hNav1.5 channel.
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Affiliation(s)
| | | | | | - Michael Houghton
- Li Ka Shing Institute of Virology
- Li Ka Shing Applied Virology Institute
- Department of Medical Microbiology and Immunology, Katz Centre for Health Research, University of Alberta, Edmonton, AB, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences
- Li Ka Shing Institute of Virology
- Li Ka Shing Applied Virology Institute
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44
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Okur HI, Hladílková J, Rembert KB, Cho Y, Heyda J, Dzubiella J, Cremer PS, Jungwirth P. Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions. J Phys Chem B 2017; 121:1997-2014. [PMID: 28094985 DOI: 10.1021/acs.jpcb.6b10797] [Citation(s) in RCA: 411] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting out/salting in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood. This situation could have been summarized as follows: Many chemists used the Hofmeister series as a mantra to put a label on ion-specific behavior in various environments, rather than to reach a molecular level understanding and, consequently, an ability to predict a particular effect of a given salt ion on proteins in solutions. In this Feature Article we show that the cationic and anionic Hofmeister series can now be rationalized primarily in terms of specific interactions of salt ions with the backbone and charged side chain groups at the protein surface in solution. At the same time, we demonstrate the limitations of separating Hofmeister effects into independent cationic and anionic contributions due to the electroneutrality condition, as well as specific ion pairing, leading to interactions of ions of opposite polarity. Finally, we outline the route beyond Hofmeister chemistry in the direction of understanding specific roles of ions in various biological functionalities, where generic Hofmeister-type interactions can be complemented or even overruled by particular steric arrangements in various ion binding sites.
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Affiliation(s)
- Halil I Okur
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
| | - Jana Hladílková
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic.,Division of Theoretical Chemistry, Lund University , P.O.B. 124, SE-22100 Lund, Sweden
| | | | - Younhee Cho
- Department of Chemistry, Texas A&M University , College Station 77843, Texas, United States
| | - Jan Heyda
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Department of Physical Chemistry, University of Chemistry and Technology, Prague , Technická 5, 16628 Prague 6, Czech Republic
| | - Joachim Dzubiella
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner Platz 1, 14109 Berlin, Germany.,Institut für Physik, Humboldt-Universität zu Berlin , Newtonstrasse 15, 12489 Berlin, Germany
| | | | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
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Abstract
Specific ion binding by carboxylates (-COO-) is a broadly important topic because -COO- is one of the most common functional groups coordinated to metal ions in metalloproteins and synthetic polymers. We apply quantum chemical methods and the quasi-chemical free-energy theory to investigate how variations in the number of -COO- ligands in a binding site determine ion-binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) and divalent (Zn2+, Ca2+) ions relevant to experimental work on ion channels and ionomers. Of two competing hypotheses, our results support the ligand field strength hypothesis and follow the reverse Hofmeister series for ion solvation and ion transfer from aqueous solution to binding sites with the preferred number of ligands. New insight arises from the finding that ion-binding sequences can be manipulated and even reversed just by constraining the number of carboxylate ligands in the binding sites. Our results help clarify the discrepancy in ion association between molecular ligands in aqueous solutions and ionomers, and their chemical analogues in ion-channel binding sites.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies and ‡Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87185, United States
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46
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Soniat M, Rogers DM, Rempe SB. Dispersion- and Exchange-Corrected Density Functional Theory for Sodium Ion Hydration. J Chem Theory Comput 2016; 11:2958-67. [PMID: 26575733 DOI: 10.1021/acs.jctc.5b00357] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A challenge in density functional theory is developing functionals that simultaneously describe intermolecular electron correlation and electron delocalization. Recent exchange-correlation functionals address those two issues by adding corrections important at long ranges: an atom-centered pairwise dispersion term to account for correlation and a modified long-range component of the electron exchange term to correct for delocalization. Here we investigate how those corrections influence the accuracy of binding free energy predictions for sodium-water clusters. We find that the dual-corrected ωB97X-D functional gives cluster binding energies closest to high-level ab initio methods (CCSD(T)). Binding energy decomposition shows that the ωB97X-D functional predicts the smallest ion-water (pairwise) interaction energy and larger multibody contributions for a four-water cluster than most other functionals - a trend consistent with CCSD(T) results. Also, ωB97X-D produces the smallest amounts of charge transfer and the least polarizable waters of the density functionals studied, which mimics the lower polarizability of CCSD. When compared with experimental binding free energies, however, the exchange-corrected CAM-B3LYP functional performs best (error <1 kcal/mol), possibly because of its parametrization to experimental formation enthalpies. For clusters containing more than four waters, "split-shell" coordination must be considered to obtain accurate free energies in comparison with experiment.
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Affiliation(s)
- Marielle Soniat
- Department of Chemistry, University of New Orleans , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, United States
| | - David M Rogers
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States.,Department of Chemistry, University of South Florida , Tampa, Florida 33620, United States
| | - Susan B Rempe
- Center for Biological and Engineering Sciences, Sandia National Laboratories , Albuquerque, New Mexico 87123, United States
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Štěpánová S, Kašička V. Affinity Capillary Electrophoresis Applied to Investigation of Valinomycin Complexes with Ammonium and Alkali Metal Ions. Methods Mol Biol 2016; 1466:219-232. [PMID: 27473493 DOI: 10.1007/978-1-4939-4014-1_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This chapter deals with the application of affinity capillary electrophoresis (ACE) to investigation of noncovalent interactions (complexes) of valinomycin, a macrocyclic dodecadepsipeptide antibiotic ionophore, with ammonium and alkali metal ions (lithium, sodium, potassium, rubidium, and cesium). The strength of these interactions was characterized by the apparent binding (stability, association) constants (K b) of the above valinomycin complexes using the mobility shift assay mode of ACE. The study involved measurements of effective electrophoretic mobility of valinomycin at variable concentrations of ammonium or alkali metal ions in the background electrolyte (BGE). The effective electrophoretic mobilities of valinomycin measured at ambient temperature and variable ionic strength were first corrected to the reference temperature 25 °C and constant ionic strength (10 or 25 mM). Then, from the dependence of the corrected valinomycin effective mobility on the ammonium or alkali metal ion concentration in the BGE, the apparent binding constants of the valinomycin-ammonium or valinomycin-alkali metal ion complexes were determined using a nonlinear regression analysis. Logarithmic form of the binding constants (log K b) were found to be in the range of 1.50-4.63, decreasing in the order Rb(+) > K(+) > Cs(+) > > Na(+) > NH4 (+) ~ Li(+).
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Affiliation(s)
- Sille Štěpánová
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo 2, Prague 6, 166 10, Czech Republic
| | - Václav Kašička
- Academy of Sciences of the Czech Republic, Institute of Organic Chemistry and Biochemistry, Flemingovo 2, Prague 6, 166 10, Czech Republic.
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Sadhu B, Sundararajan M, Bandyopadhyay T. Selectivity of a Singly Permeating Ion in Nonselective NaK Channel: Combined QM and MD Based Investigations. J Phys Chem B 2015; 119:12783-97. [DOI: 10.1021/acs.jpcb.5b05996] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Biswajit Sadhu
- Radiation Safety Systems Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Mahesh Sundararajan
- Radiation Safety Systems Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Radiation Safety Systems Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S. Crystal structures of a double-barrelled fluoride ion channel. Nature 2015; 525:548-51. [PMID: 26344196 PMCID: PMC4876929 DOI: 10.1038/nature14981] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/20/2015] [Indexed: 11/30/2022]
Abstract
To contend with hazards posed by environmental fluoride, microorganisms export this anion through F(-)-specific ion channels of the Fluc family. Since the recent discovery of Fluc channels, numerous idiosyncratic features of these proteins have been unearthed, including strong selectivity for F(-) over Cl(-) and dual-topology dimeric assembly. To understand the chemical basis for F(-) permeation and how the antiparallel subunits convene to form a F(-)-selective pore, here we solve the crystal structures of two bacterial Fluc homologues in complex with three different monobody inhibitors, with and without F(-) present, to a maximum resolution of 2.1 Å. The structures reveal a surprising 'double-barrelled' channel architecture in which two F(-) ion pathways span the membrane, and the dual-topology arrangement includes a centrally coordinated cation, most likely Na(+). F(-) selectivity is proposed to arise from the very narrow pores and an unusual anion coordination that exploits the quadrupolar edges of conserved phenylalanine rings.
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Affiliation(s)
- Randy B Stockbridge
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Ludmila Kolmakova-Partensky
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Tania Shane
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454, USA
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QU, UK
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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50
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Lockless SW. Determinants of cation transport selectivity: Equilibrium binding and transport kinetics. J Gen Physiol 2015; 146:3-13. [PMID: 26078056 PMCID: PMC4485025 DOI: 10.1085/jgp.201511371] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/11/2015] [Indexed: 01/13/2023] Open
Abstract
The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K(+)-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules.
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Affiliation(s)
- Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843
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