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Sudnitsyna J, Ruzhnikova TO, Panteleev MA, Kharazova A, Gambaryan S, Mindukshev IV. Chloride Gradient Is Involved in Ammonium Influx in Human Erythrocytes. Int J Mol Sci 2024; 25:7390. [PMID: 39000500 PMCID: PMC11242273 DOI: 10.3390/ijms25137390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/16/2024] Open
Abstract
The ammonia/ammonium (NH3/NH4+, AM) concentration in human erythrocytes (RBCs) is significantly higher than in plasma. Two main possible mechanisms for AM transport, including simple and facilitated diffusion, are described; however, the driving force for AM transport is not yet fully characterized. Since the erythroid ammonium channel RhAG forms a structural unit with anion exchanger 1 (eAE1) within the ankyrin core complex, we hypothesized the involvement of eAE1 in AM transport. To evaluate the functional interaction between eAE1 and RhAG, we used a unique feature of RBCs to swell and lyse in isotonic NH4+ buffer. The kinetics of cell swelling and lysis were analyzed by flow cytometry and an original laser diffraction method, adapted for accurate volume sensing. The eAE1 role was revealed according to (i) the changes in cell swelling and lysis kinetics, and (ii) changes in intracellular pH, triggered by eAE1 inhibition or the modulation of eAE1 main ligand concentrations (Cl- and HCO3-). Additionally, the AM import kinetics was analyzed enzymatically and colorimetrically. In NH4+ buffer, RBCs concentration-dependently swelled and lysed when [NH4+] exceeded 100 mM. Cell swelling and hemolysis were tightly regulated by chloride concentration. The complete substitution of chloride with glutamate prevented NH4+-induced cell swelling and hemolysis, and the restoration of [Cl-] dose-dependently amplified the rates of RBC swelling and lysis and the percentage of hemolyzed cells. Similarly, eAE1 inhibition impeded cell swelling and completely prevented hemolysis. Accordingly, eAE1 inhibition, or a lack of chloride anions in the buffer, significantly decreased NH4+ import. Our data indicate that the eAE1-mediated chloride gradient is required for AM transport. Taken together, our data reveal a new player in AM transport in RBCs.
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Affiliation(s)
- Julia Sudnitsyna
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya St., 109029 Moscow, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Ave., 194223 Saint Petersburg, Russia
| | - Tamara O Ruzhnikova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Ave., 194223 Saint Petersburg, Russia
- Department of Cytology and Histology, Saint Petersburg State University, 7/9 Universitetskaya Emb., 199034 Saint Petersburg, Russia
| | - Mikhail A Panteleev
- Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 30 Srednyaya Kalitnikovskaya St., 109029 Moscow, Russia
| | - Alexandra Kharazova
- Department of Cytology and Histology, Saint Petersburg State University, 7/9 Universitetskaya Emb., 199034 Saint Petersburg, Russia
| | - Stepan Gambaryan
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Ave., 194223 Saint Petersburg, Russia
| | - Igor V Mindukshev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 44 Thorez Ave., 194223 Saint Petersburg, Russia
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2
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Espada‐Hinojosa S, Karthäuser C, Srivastava A, Schuster L, Winter T, de Oliveira AL, Schulz F, Horn M, Sievert S, Bright M. Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative. Mol Ecol Resour 2024; 24:e13889. [PMID: 38010882 PMCID: PMC10952691 DOI: 10.1111/1755-0998.13889] [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: 01/09/2023] [Revised: 08/31/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.
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Affiliation(s)
| | - Clarissa Karthäuser
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Abhishek Srivastava
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Lukas Schuster
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Deakin UniversityBurwoodAustralia
| | - Teresa Winter
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - André Luiz de Oliveira
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Frederik Schulz
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Present address:
DOE Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Matthias Horn
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Stefan Sievert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Monika Bright
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
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3
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Sebastiana M, Serrazina S, Monteiro F, Wipf D, Fromentin J, Teixeira R, Malhó R, Courty PE. Nitrogen Acquisition and Transport in the Ectomycorrhizal Symbiosis-Insights from the Interaction between an Oak Tree and Pisolithus tinctorius. PLANTS (BASEL, SWITZERLAND) 2022; 12:10. [PMID: 36616139 PMCID: PMC9823632 DOI: 10.3390/plants12010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/04/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
In temperate forests, the roots of various tree species are colonized by ectomycorrhizal fungi, which have a key role in the nitrogen nutrition of their hosts. However, not much is known about the molecular mechanisms related to nitrogen metabolism in ectomycorrhizal plants. This study aimed to evaluate the nitrogen metabolic response of oak plants when inoculated with the ectomycorrhizal fungus Pisolithus tinctorius. The expression of candidate genes encoding proteins involved in nitrogen uptake and assimilation was investigated in ectomycorrhizal roots. We found that three oak ammonium transporters were over-expressed in root tissues after inoculation, while the expression of amino acid transporters was not modified, suggesting that inorganic nitrogen is the main form of nitrogen transferred by the symbiotic fungus into the roots of the host plant. Analysis by heterologous complementation of a yeast mutant defective in ammonium uptake and GFP subcellular protein localization clearly confirmed that two of these genes encode functional ammonium transporters. Structural similarities between the proteins encoded by these ectomycorrhizal upregulated ammonium transporters, and a well-characterized ammonium transporter from E. coli, suggest a similar transport mechanism, involving deprotonation of NH4+, followed by diffusion of uncharged NH3 into the cytosol. This view is supported by the lack of induction of NH4+ detoxifying mechanisms, such as the GS/GOGAT pathway, in the oak mycorrhizal roots.
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Affiliation(s)
- Mónica Sebastiana
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Susana Serrazina
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Filipa Monteiro
- Linking Landscape, Environment, Agriculture and Food (LEAF), Associated Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, 1349-017 Lisbon, Portugal
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE—Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Daniel Wipf
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Jérome Fromentin
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Rita Teixeira
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Rui Malhó
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pierre-Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, University Bourgogne Franche-Comté, F-21000 Dijon, France
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4
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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5
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Sanchez-Andrada P, Vidal-Vidal A, Prieto T, Elguero J, Alkorta I, Marin-Luna M. Alkylammonium Cation Affinities of Nitrogenated Organobases: The Roles of Hydrogen Bonding and Proton Transfer. Chempluschem 2021; 86:1097-1105. [PMID: 34251758 DOI: 10.1002/cplu.202100235] [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: 05/26/2021] [Revised: 06/29/2021] [Indexed: 11/06/2022]
Abstract
Alkylammonium cation affinities of 64 nitrogen-containing organobases, as well as the respective proton transfer processes from the alkylammonium cations to the base, have been computed in the gas phase by using DFT methods. The guanidine bases show the highest proton transfer values (191.9-233 kJ mol-1 ) whereas the cis-2,2'-biimidazole presents the largest affinity towards the alkylammonium cations (>200 kJ mol-1 ) values. The resulting data have been compared with the experimentally reported proton affinities of the studied nitrogen-containing organobases revealing that the propensity of an organobase for the proton transfer process increases linearly with its proton affinity. This work can provide a tool for designing senors for bioactive compounds containing amino groups that are protonated at physiological pH.
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Affiliation(s)
- Pilar Sanchez-Andrada
- Departamento de Química Orgánica Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia Facultad de Química, Campus de Espinardo, E-30100, Murcia, Spain
| | - Angel Vidal-Vidal
- Departamento de Química Orgánica, Universidade de Vigo Campus Lagoas-Marcosende, Vigo, Spain
| | - Tania Prieto
- Departamento de Química Orgánica, Universidade de Vigo Campus Lagoas-Marcosende, Vigo, Spain
| | - José Elguero
- Instituto de Química Médica, Centro Superior de Investigaciones Científicas (CSIC), Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, Centro Superior de Investigaciones Científicas (CSIC), Juan de la Cierva, 3, E-28006, Madrid, Spain
| | - Marta Marin-Luna
- Departamento de Química Orgánica Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia Facultad de Química, Campus de Espinardo, E-30100, Murcia, Spain
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6
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Perin G, Fletcher T, Sagi-Kiss V, Gaboriau DCA, Carey MR, Bundy JG, Jones PR. Calm on the surface, dynamic on the inside. Molecular homeostasis of Anabaena sp. PCC 7120 nitrogen metabolism. PLANT, CELL & ENVIRONMENT 2021; 44:1885-1907. [PMID: 33608943 DOI: 10.1111/pce.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen sources are all converted into ammonium/ia as a first step of assimilation. It is reasonable to expect that molecular components involved in the transport of ammonium/ia across biological membranes connect with the regulation of both nitrogen and central metabolism. We applied both genetic (i.e., Δamt mutation) and environmental treatments to a target biological system, the cyanobacterium Anabaena sp PCC 7120. The aim was to both perturb nitrogen metabolism and induce multiple inner nitrogen states, respectively, followed by targeted quantification of key proteins, metabolites and enzyme activities. The absence of AMT transporters triggered a substantial whole-system response, affecting enzyme activities and quantity of proteins and metabolites, spanning nitrogen and carbon metabolisms. Moreover, the Δamt strain displayed a molecular fingerprint indicating nitrogen deficiency even under nitrogen replete conditions. Contrasting with such dynamic adaptations was the striking near-complete lack of an externally measurable altered phenotype. We conclude that this species evolved a highly robust and adaptable molecular network to maintain homeostasis, resulting in substantial internal but minimal external perturbations. This analysis provides evidence for a potential role of AMT transporters in the regulatory/signalling network of nitrogen metabolism and the existence of a novel fourth regulatory mechanism controlling glutamine synthetase activity.
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Affiliation(s)
- Giorgio Perin
- Department of Life Sciences, Imperial College London, London, UK
| | - Tyler Fletcher
- Complex Carbohydrate Research Center and Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Virag Sagi-Kiss
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - David C A Gaboriau
- Facility for Imaging by Light Microscopy, NHLI, Imperial College London, London, UK
| | - Mathew R Carey
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jacob G Bundy
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Patrik R Jones
- Department of Life Sciences, Imperial College London, London, UK
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7
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Orabi EA. Molecular dynamics investigation of the structural flexibility of H2O2 and H2S2 in response to medium polarity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Orabi EA, English AM. Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H 2O 2 and H 2O. J Phys Chem B 2020; 125:137-147. [PMID: 33356279 DOI: 10.1021/acs.jpcb.0c10326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Long associated with cell death, hydrogen peroxide (H2O2) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H2O2 (ϕHOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (Vs,min) and 36.5 (Vs,max), respectively. Transition-state, nonpolar trans rotamers (ϕHOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (Vs,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕHOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (Vs,max = 52.7). Modeling H2O2 association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕHOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (ECP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H2O exhibit a similar range of stabilities (ECP ∼ -1 to -18). However, considerably higher energies (ECP ∼ -14 to -36) are found for the H2O2 complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕHOOH = 0-60°). H2O is a much poorer H-bond donor (Vs,max = 33.4) than cis-H2O2, so its anionic complexes are significantly weaker (ECP ∼ -11 to -20). Thus, by dictating the rotamer preference of H2O2, functional groups in biomolecules can discriminate between H2O2 and H2O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H2O2 (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H2O2 in biology.
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Center for Research in Molecular Modeling (CERMM) and Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Concordia University, Montreal, Quebec H4B 1R6, Canada
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9
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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10
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Williamson G, Tamburrino G, Bizior A, Boeckstaens M, Dias Mirandela G, Bage MG, Pisliakov A, Ives CM, Terras E, Hoskisson PA, Marini AM, Zachariae U, Javelle A. A two-lane mechanism for selective biological ammonium transport. eLife 2020; 9:57183. [PMID: 32662768 PMCID: PMC7447429 DOI: 10.7554/elife.57183] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
The transport of charged molecules across biological membranes faces the dual problem of accommodating charges in a highly hydrophobic environment while maintaining selective substrate translocation. This has been the subject of a particular controversy for the exchange of ammonium across cellular membranes, an essential process in all domains of life. Ammonium transport is mediated by the ubiquitous Amt/Mep/Rh transporters that includes the human Rhesus factors. Here, using a combination of electrophysiology, yeast functional complementation and extended molecular dynamics simulations, we reveal a unique two-lane pathway for electrogenic NH4+ transport in two archetypal members of the family, the transporters AmtB from Escherichia coli and Rh50 from Nitrosomonas europaea. The pathway underpins a mechanism by which charged H+ and neutral NH3 are carried separately across the membrane after NH4+ deprotonation. This mechanism defines a new principle of achieving transport selectivity against competing ions in a biological transport process.
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Affiliation(s)
- Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Mélanie Boeckstaens
- Biology of Membrane Transport Laboratory, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Gaëtan Dias Mirandela
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Marcus G Bage
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Andrei Pisliakov
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Eilidh Terras
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Anna Maria Marini
- Biology of Membrane Transport Laboratory, Department of Molecular Biology, Université Libre de Bruxelles, Gosselies, Belgium
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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11
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Brito AS, Neuhäuser B, Wintjens R, Marini AM, Boeckstaens M. Yeast filamentation signaling is connected to a specific substrate translocation mechanism of the Mep2 transceptor. PLoS Genet 2020; 16:e1008634. [PMID: 32069286 PMCID: PMC7048316 DOI: 10.1371/journal.pgen.1008634] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 02/28/2020] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
The dimorphic transition from the yeast to the filamentous form of growth allows cells to explore their environment for more suitable niches and is often crucial for the virulence of pathogenic fungi. In contrast to their Mep1/3 paralogues, fungal Mep2-type ammonium transport proteins of the conserved Mep-Amt-Rh family have been assigned an additional receptor role required to trigger the filamentation signal in response to ammonium scarcity. Here, genetic, kinetic and structure-function analyses were used to shed light on the poorly characterized signaling role of Saccharomyces cerevisiae Mep2. We show that Mep2 variants lacking the C-terminal tail conserve the ability to induce filamentation, revealing that signaling can proceed in the absence of exclusive binding of a putative partner to the largest cytosolic domain of the protein. Our data support that filamentation signaling requires the conformational changes accompanying substrate translocation through the pore crossing the hydrophobic core of Mep2. pHluorin reporter assays show that the transport activity of Mep2 and of non-signaling Mep1 differently affect yeast cytosolic pH in vivo, and that the unique pore variant Mep2H194E, with apparent uncoupling of transport and signaling functions, acquires increased ability of acidification. Functional characterization in Xenopus oocytes reveals that Mep2 mediates electroneutral substrate translocation while Mep1 performs electrogenic transport. Our findings highlight that the Mep2-dependent filamentation induction is connected to its specific transport mechanism, suggesting a role of pH in signal mediation. Finally, we show that the signaling process is conserved for the Mep2 protein from the human pathogen Candida albicans. Fungal Mep2-type ammonium transport proteins of the conserved Mep-Amt-Rh family that includes human Rhesus factors are specifically required to allow filamentation in response to ammonium limitation. These proteins were therefore assigned a receptor role while the underlying mechanism of signal transduction remains poorly understood. The “transceptor” property has subsequently been proposed to concern transporters of all kind of micro- and macro- nutrients in eukaryotes, from fungi to human. However, bringing the firm demonstration of their existence remains challenging as variants with full uncoupling of transport and receptor functions are difficult to obtain. Our data question the involvement of the C-terminal extremity of Saccharomyces cerevisiae Mep2 in the signal mediation leading to filamentation. If signaling partners exist, they should also bind to cytosolic loops and/or membrane-embedded domains. The capacity of Mep2 to enable filamentation is closely intertwined to the mechanism of substrate translocation through the pore of the hydrophobic core of the protein. In Xenopus oocytes, the transport activity of non-signaling Mep1 is electrogenic while it is electroneutral for Mep2, the latter likely translocating the weak base NH3, but not the proton released after NH4+ recognition and depronotation. We propose that given consequences of a Mep2-specific transport process, such as an intracellular pH modification, could be the underlying cause of the filamentation signal ensured by Mep2-type proteins.
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Affiliation(s)
- Ana Sofia Brito
- Biology of Membrane Transport Laboratory, Molecular Biology Department, Université Libre de Bruxelles, Gosselies, Belgium
| | - Benjamin Neuhäuser
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire, Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, Brussels, Belgium
| | - Anna Maria Marini
- Biology of Membrane Transport Laboratory, Molecular Biology Department, Université Libre de Bruxelles, Gosselies, Belgium
- * E-mail: (AMM); (MB)
| | - Mélanie Boeckstaens
- Biology of Membrane Transport Laboratory, Molecular Biology Department, Université Libre de Bruxelles, Gosselies, Belgium
- * E-mail: (AMM); (MB)
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12
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Affiliation(s)
- Bert van den Berg
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Siobhan Lister
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Julian C. Rutherford
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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13
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Orabi EA, Davis RL, Lamoureux G. Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. J Comput Chem 2019; 41:472-481. [DOI: 10.1002/jcc.26084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Esam A. Orabi
- Department of ChemistryFaculty of Science, Assiut University Assiut 71516 Egypt
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Rebecca L. Davis
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Center for Computational and Integrative Biology (CCIB)Rutgers University Camden New Jersey 08102
- Centre for Research in Molecular Modeling (CERMM), Concordia University Montréal Québec H4B 1R6 Canada
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14
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Wang AH, Zhang ZC, Li GH. Advances in enhanced sampling molecular dynamics simulations for biomolecules. CHINESE J CHEM PHYS 2019. [DOI: 10.1063/1674-0068/cjcp1905091] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- An-hui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, China
| | - Zhi-chao Zhang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116024, China
| | - Guo-hui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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15
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Maeda K, Westerhoff HV, Kurata H, Boogerd FC. Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network. NPJ Syst Biol Appl 2019; 5:14. [PMID: 30993002 PMCID: PMC6461619 DOI: 10.1038/s41540-019-0091-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/12/2019] [Indexed: 11/17/2022] Open
Abstract
The complex ammonium transport and assimilation network of E. coli involves the ammonium transporter AmtB, the regulatory proteins GlnK and GlnB, and the central N-assimilating enzymes together with their highly complex interactions. The engineering and modelling of such a complex network seem impossible because functioning depends critically on a gamut of data known at patchy accuracy. We developed a way out of this predicament, which employs: (i) a constrained optimization-based technology for the simultaneous fitting of models to heterogeneous experimental data sets gathered through diverse experimental set-ups, (ii) a 'rubber band method' to deal with different degrees of uncertainty, both in experimentally determined or estimated parameter values and in measured transient or steady-state variables (training data sets), (iii) integration of human expertise to decide on accuracies of both parameters and variables, (iv) massive computation employing a fast algorithm and a supercomputer, (v) an objective way of quantifying the plausibility of models, which makes it possible to decide which model is the best and how much better that model is than the others. We applied the new technology to the ammonium transport and assimilation network, integrating recent and older data of various accuracies, from different expert laboratories. The kinetic model objectively ranked best, has E. coli's AmtB as an active transporter of ammonia to be assimilated with GlnK minimizing the futile cycling that is an inevitable consequence of intracellular ammonium accumulation. It is 130 times better than a model with facilitated passive transport of ammonia.
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Affiliation(s)
- Kazuhiro Maeda
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Kitakyushu, Fukuoka, Japan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka Japan
| | - Hans V. Westerhoff
- Department of Molecular Cell Biology, Faculty of Science, VU University Amsterdam, O|2 building, Amsterdam, Netherlands
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science, The University of Manchester, Manchester, UK
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka Japan
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Fukuoka Japan
| | - Fred C. Boogerd
- Department of Molecular Cell Biology, Faculty of Science, VU University Amsterdam, O|2 building, Amsterdam, Netherlands
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16
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Pieńko T, Trylska J. Computational Methods Used to Explore Transport Events in Biological Systems. J Chem Inf Model 2019; 59:1772-1781. [DOI: 10.1021/acs.jcim.8b00974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, S. Banacha 1a, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
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17
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Mirandela GD, Tamburrino G, Hoskisson PA, Zachariae U, Javelle A. The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB. FASEB J 2019; 33:1989-1999. [PMID: 30211659 PMCID: PMC6338640 DOI: 10.1096/fj.201800782r] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022]
Abstract
The movement of ammonium across biologic membranes is a fundamental process in all living organisms and is mediated by the ubiquitous ammonium transporter/methylammonium permease/rhesus protein (Amt/Mep/Rh) family of transporters. Recent structural analysis and coupled mass spectrometry studies have shown that the Escherichia coli ammonium transporter AmtB specifically binds 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG). Upon POPG binding, several residues of AmtB undergo a small conformational change, which stabilizes the protein against unfolding. However, no studies have so far been conducted, to our knowledge, to explore whether POPG binding to AmtB has functional consequences. Here, we used an in vitro experimental assay with purified components, together with molecular dynamics simulations, to characterize the relation between POPG binding and AmtB activity. We show that the AmtB activity is electrogenic. Our results indicate that the activity, at the molecular level, of Amt in archaebacteria and eubacteria may differ. We also show that POPG is an important cofactor for AmtB activity and that, in the absence of POPG, AmtB cannot complete the full translocation cycle. Furthermore, our simulations reveal previously undiscovered POPG binding sites on the intracellular side of the lipid bilayer between the AmtB subunits. Possible molecular mechanisms explaining the functional role of POPG are discussed.-Mirandela, G. D., Tamburrino, G., Hoskisson, P. A., Zachariae, U., Javelle, A. The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB.
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Affiliation(s)
- Gaëtan Dias Mirandela
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Physics, School of Science and Engineering, University of Dundee, Dundee, United Kingdom
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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18
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Zhang Q, Du Y, Chen C, Zhuang W. Rotational mechanism of ammonium ion in water and methanol. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1806144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Qiang Zhang
- Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Yang Du
- Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Chen Chen
- Department of Chemistry, Bohai University, Jinzhou 121013, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
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19
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Zhu Y, Hao Y, Liu H, Sun G, Chen R, Song S. Identification and characterization of two ammonium transporter genes in flowering Chinese cabbage ( Brassica campestris). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:59-70. [PMID: 31275038 PMCID: PMC6543737 DOI: 10.5511/plantbiotechnology.18.0202a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/02/2018] [Indexed: 06/09/2023]
Abstract
Ammonium transporters (AMTs), which include AMT1 and AMT2 subfamilies, have been identified and partially characterized in many plants. In this study, two AMT2-type genes from Brassica campestris, namely BcAMT2 and BcAMT2like, were identified and characterized. BcAMT2 and BcAMT2like are 2666 bp and 2952 bp, encode proteins of 490 and 489 amino acids, respectively, and contain five exons and four introns. Transient expression of these proteins labelled with green fluorescence protein in onion epidermal cells indicated that both are located on the plasma membrane. When expressing BcAMT2 or BcAMT2like, the mutant yeast strain 31019b could grow on medium containing 2 mM ammonium as the only nitrogen source when expressing BcAMT2 or BcAMT2like, indicating that both are functional AMT genes. Quantitative PCR results showed that BcAMT2 and BcAMT2like were expressed in all tissues, but they displayed different expression patterns in the reproductive stages. BcAMT2s transcript levels in leaves were positively correlated with ammonium concentration and external pH. Moreover, the expression BcAMT2s responded to diurnal change. Furthermore, the uncharged form of ammonium, i.e., ammonia, might also be transported by BcAMT2s. These results provide new insights into the molecular mechanisms underlying ammonium absorption and transportation by the AMT2 subfamily in B. campestris.
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Affiliation(s)
- Yunna Zhu
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
| | - Yanwei Hao
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
| | - Houcheng Liu
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
| | - Guangwen Sun
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
| | - Riyuan Chen
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
| | - Shiwei Song
- College of Horticulture, South China Agricultural University, 510642, Guangzhou, People’s Republic of China
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20
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Wang CH, Duster AW, Aydintug BO, Zarecki MG, Lin H. Chloride Ion Transport by the E. coli CLC Cl -/H + Antiporter: A Combined Quantum-Mechanical and Molecular-Mechanical Study. Front Chem 2018; 6:62. [PMID: 29594103 PMCID: PMC5859129 DOI: 10.3389/fchem.2018.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 02/26/2018] [Indexed: 01/05/2023] Open
Abstract
We performed steered molecular dynamics (SMD) and umbrella sampling simulations of Cl- ion migration through the transmembrane domain of a prototypical E. coli CLC Cl-/H+ antiporter by employing combined quantum-mechanical (QM) and molecular-mechanical (MM) calculations. The SMD simulations revealed interesting conformational changes of the protein. While no large-amplitude motions of the protein were observed during pore opening, the side chain rotation of the protonated external gating residue Glu148 was found to be critical for full access of the channel entrance by Cl-. Moving the anion into the external binding site (Sext) induced small-amplitude shifting of the protein backbone at the N-terminal end of helix F. As Cl- traveled through the pore, rigid-body swinging motions of helix R separated it from helix D. Helix R returned to its original position once Cl- exited the channel. Population analysis based on polarized wavefunction from QM/MM calculations discovered significant (up to 20%) charge loss for Cl- along the ion translocation pathway inside the pore. The delocalized charge was redistributed onto the pore residues, especially the functional groups containing π bonds (e.g., the Tyr445 side chain), while the charges of the H atoms coordinating Cl- changed almost negligibly. Potentials of mean force computed from umbrella sampling at the QM/MM and MM levels both displayed barriers at the same locations near the pore entrance and exit. However, the QM/MM PMF showed higher barriers (~10 kcal/mol) than the MM PMF (~2 kcal/mol). Binding energy calculations indicated that the interactions between Cl- and certain pore residues were overestimated by the semi-empirical PM3 Hamiltonian and underestimated by the CHARMM36 force fields, both of which were employed in the umbrella sampling simulations. In particular, CHARMM36 underestimated binding interactions for the functional groups containing π bonds, missing the stabilizations of the Cl- ion due to electron delocalization. The results suggested that it is important to explore these quantum effects for accurate descriptions of the Cl- transport.
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Affiliation(s)
- Chun-Hung Wang
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Adam W Duster
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Baris O Aydintug
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - MacKenzie G Zarecki
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
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21
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Orabi EA, Lamoureux G. Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J Phys Chem B 2018; 122:2251-2260. [PMID: 29397727 DOI: 10.1021/acs.jpcb.7b11983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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22
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Manjari SR, Banavali NK. Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. J Chem Inf Model 2018; 58:453-463. [PMID: 29357231 DOI: 10.1021/acs.jcim.7b00699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A strategy named "restrained geometries and topology switching" (RGATS) is presented to obtain detailed trajectories for complex biochemical reactions using molecular mechanics (MM) methods. It enables prediction of realistic dynamical pathways for chemical reactions, especially for accurately characterizing the structural adjustments of highly complex environments to any proximal biochemical reaction. It can be used to generate reactive conformations, model stepwise or concerted reactions in complex environments, and probe the influence of changes in the environment. Its ability to take reactively nonoptimal conformations and generate favorable starting conformations for a biochemical reaction is illustrated for a proton transfer between two model compounds. Its ability to study concerted reactions in explicit solvent is illustrated using proton transfers between an ammonium ion and two conserved histidines in an ammonia transporter channel embedded in a lipid membrane. Its ability to characterize the changes induced by subtle differences in the active site environment is illustrated using nucleotide addition by a DNA polymerase in the presence of two versus three Mg2+ ions. RGATS can be employed within any MM program and requires no additional software implementation. This allows the full assortment of computational methods implemented in all available MM programs to be used to tackle virtually any question about biochemical reactions that is answerable without using a quantum mechanical (QM) model. It can also be applied to generate reasonable starting structures for more detailed and expensive QM or QM/MM methods. In particular, this strategy enables rapid prediction of reactant, intermediary, or product state structures in any macromolecular context, with the only requirement being that the structure in any one of these states is either known or can be accurately modeled.
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Affiliation(s)
- Swati R Manjari
- Laboratory of Computational and Structural Biology, Division of Genetics, NYS Department of Health , CMS 2008, Biggs Laboratory, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, United States
| | - Nilesh K Banavali
- Laboratory of Computational and Structural Biology, Division of Genetics, NYS Department of Health , CMS 2008, Biggs Laboratory, Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, United States.,Department of Biomedical Sciences, School of Public Health, State University of New York at Albany , Albany, New York 12222, United States
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23
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Koegel S, Mieulet D, Baday S, Chatagnier O, Lehmann MF, Wiemken A, Boller T, Wipf D, Bernèche S, Guiderdoni E, Courty PE. Phylogenetic, structural, and functional characterization of AMT3;1, an ammonium transporter induced by mycorrhization among model grasses. MYCORRHIZA 2017; 27:695-708. [PMID: 28667402 DOI: 10.1007/s00572-017-0786-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
Abstract
In the arbuscular mycorrhizal (AM) symbiosis, plants satisfy part of their nitrogen (N) requirement through the AM pathway. In sorghum, the ammonium transporters (AMT) AMT3;1, and to a lesser extent AMT4, are induced in cells containing developing arbuscules. Here, we have characterized orthologs of AMT3;1 and AMT4 in four other grasses in addition to sorghum. AMT3;1 and AMT4 orthologous genes are induced in AM roots, suggesting that in the common ancestor of these five plant species, both AMT3;1 and AMT4 were already present and upregulated upon AM colonization. An artificial microRNA approach was successfully used to downregulate either AMT3;1 or AMT4 in rice. Mycorrhizal root colonization and hyphal length density of knockdown plants were not affected at that time, indicating that the manipulation did not modify the establishment of the AM symbiosis and the interaction between both partners. However, expression of the fungal phosphate transporter FmPT was significantly reduced in knockdown plants, indicating a reduction of the nutrient fluxes from the AM fungus to the plant. The AMT3;1 knockdown plants (but not the AMT4 knockdown plants) were significantly less stimulated in growth by AM fungal colonization, and uptake of both 15N and 33P from the AM fungal network was reduced. This confirms that N and phosphorus nutrition through the mycorrhizal pathway are closely linked. But most importantly, it indicates that AMT3;1 is the prime plant transporter involved in the mycorrhizal ammonium transfer and that its function during uptake of N cannot be performed by AMT4.
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Affiliation(s)
- Sally Koegel
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
| | | | - Sefer Baday
- SIB Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
- Applied Informatics Department, Informatics Institute, Istanbul Technical University, 34469, Istanbul, Turkey
| | - Odile Chatagnier
- Agroécologie, AgroSupDijon, CNRS, INRA, Université de Bourgogne Franche-Comté, 21000, Dijon, France
| | - Moritz F Lehmann
- Department of Environmental Sciences, Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, Switzerland
| | - Andres Wiemken
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
| | - Thomas Boller
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland
| | - Daniel Wipf
- Agroécologie, AgroSupDijon, CNRS, INRA, Université de Bourgogne Franche-Comté, 21000, Dijon, France
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | | | - Pierre-Emmanuel Courty
- Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056, Basel, Switzerland.
- Agroécologie, AgroSupDijon, CNRS, INRA, Université de Bourgogne Franche-Comté, 21000, Dijon, France.
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24
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Ebert MCCJC, Guzman Espinola J, Lamoureux G, Pelletier JN. Substrate-Specific Screening for Mutational Hotspots Using Biased Molecular Dynamics Simulations. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02634] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maximilian C. C. J. C. Ebert
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Joaquin Guzman Espinola
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
| | - Guillaume Lamoureux
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Department
of Chemistry and Biochemistry and Centre for Research in Molecular
Modeling (CERMM), Concordia University, Montréal, QC H4B 1R6, Canada
| | - Joelle N. Pelletier
- Département
de Biochimie and Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC H3T 1J4, Canada
- PROTEO, The Québec
Network for Research on Protein Function, Engineering and Applications, Québec, QC G1V 0A6, Canada
- Département
de Chimie, Université de Montréal, Montréal, QC H3T 1J4, Canada
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25
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Abstract
To respond to the changing environment, cells must be able to sense external conditions. This is important for many processes including growth, mating, the expression of virulence factors, and several other regulatory effects. Nutrient sensing at the plasma membrane is mediated by different classes of membrane proteins that activate downstream signaling pathways: nontransporting receptors, transceptors, classical and nonclassical G-protein-coupled receptors, and the newly defined extracellular mucin receptors. Nontransporting receptors have the same structure as transport proteins, but have lost the capacity to transport while gaining a receptor function. Transceptors are transporters that also function as a receptor, because they can rapidly activate downstream signaling pathways. In this review, we focus on these four types of fungal membrane proteins. We mainly discuss the sensing mechanisms relating to sugars, ammonium, and amino acids. Mechanisms for other nutrients, such as phosphate and sulfate, are discussed briefly. Because the model yeast Saccharomyces cerevisiae has been the most studied, especially regarding these nutrient-sensing systems, each subsection will commence with what is known in this species.
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26
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Abstract
Acid-base homeostasis is critical to maintenance of normal health. Renal ammonia excretion is the quantitatively predominant component of renal net acid excretion, both under basal conditions and in response to acid-base disturbances. Although titratable acid excretion also contributes to renal net acid excretion, the quantitative contribution of titratable acid excretion is less than that of ammonia under basal conditions and is only a minor component of the adaptive response to acid-base disturbances. In contrast to other urinary solutes, ammonia is produced in the kidney and then is selectively transported either into the urine or the renal vein. The proportion of ammonia that the kidney produces that is excreted in the urine varies dramatically in response to physiological stimuli, and only urinary ammonia excretion contributes to acid-base homeostasis. As a result, selective and regulated renal ammonia transport by renal epithelial cells is central to acid-base homeostasis. Both molecular forms of ammonia, NH3 and NH4+, are transported by specific proteins, and regulation of these transport processes determines the eventual fate of the ammonia produced. In this review, we discuss these issues, and then discuss in detail the specific proteins involved in renal epithelial cell ammonia transport.
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Affiliation(s)
- I David Weiner
- Division of Nephrology, Hypertension and Renal Transplantation, University of Florida College of Medicine, Gainesville, Florida; and Nephrology and Hypertension Section, North Florida/South Georgia Veterans Health System, Gainesville, Florida
| | - Jill W Verlander
- Division of Nephrology, Hypertension and Renal Transplantation, University of Florida College of Medicine, Gainesville, Florida; and Nephrology and Hypertension Section, North Florida/South Georgia Veterans Health System, Gainesville, Florida
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27
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Abdulnour-Nakhoul S, Le T, Rabon E, Hamm LL, Nakhoul NL. Structural determinants of NH3 and NH4+ transport by mouse Rhbg, a renal Rh glycoprotein. Am J Physiol Renal Physiol 2016; 311:F1280-F1293. [PMID: 27681563 PMCID: PMC5210199 DOI: 10.1152/ajprenal.00556.2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 09/21/2016] [Indexed: 11/22/2022] Open
Abstract
Renal Rhbg is localized to the basolateral membrane of intercalated cells and is involved in NH3/NH4+ transport. The structure of Rhbg is not yet resolved; however, a high-resolution crystal structure of AmtB, a bacterial homolog of Rh, has been determined. We aligned the sequence of Rhbg to that of AmtB and identified important sites of Rhbg that may affect transport. Our analysis positioned three conserved amino acids, histidine 183 (H183), histidine 342 (H342), and tryptophan 230 (W230), within the hydrophobic pore where they presumably serve to control NH3 transport. A fourth residue, phenylalanine 128 (F128) was positioned at the upper vestibule, presumably contributing to recruitment of NH4+ We generated three mutations each of H183, H342, W230, and F128 and expressed them in frog oocytes. Immunolabeling showed that W230 and F128 mutants were localized to the cell membrane, whereas H183 and H342 staining was diffuse and mostly intracellular. To determine function, we compared measurements of NH3/NH4+ and methyl amine (MA)/methyl ammonium (MA+)-induced currents, intracellular pH, and surface pH (pHs) among oocytes expressing the mutants, Rhbg, or injected with H2O. In H183 and W230 mutants, NH4+-induced current and intracellular acidification were inhibited compared with that of Rhbg, and MA-induced intracellular alkalinization was completely absent. Expression of H183A or W230A mutants inhibited NH3/NH4+- and MA/MA+-induced decrease in pHs to the level observed in H2O-injected oocytes. Mutations of F128 did not significantly affect transport of NH3 or NH4+ These data demonstrated that mutating H183 or W230 caused loss of function but not F128. H183 and H342 may affect membrane expression of the transporter.
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Affiliation(s)
- Solange Abdulnour-Nakhoul
- Southeast Louisiana Veterans Health Care Network and Department of Medicine, Section of Nephrology, Department of Physiology, Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Louisiana
| | - Trang Le
- Southeast Louisiana Veterans Health Care Network and Department of Medicine, Section of Nephrology, Department of Physiology, Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Louisiana
| | - Edd Rabon
- Southeast Louisiana Veterans Health Care Network and Department of Medicine, Section of Nephrology, Department of Physiology, Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Louisiana
| | - L Lee Hamm
- Southeast Louisiana Veterans Health Care Network and Department of Medicine, Section of Nephrology, Department of Physiology, Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Louisiana
| | - Nazih L Nakhoul
- Southeast Louisiana Veterans Health Care Network and Department of Medicine, Section of Nephrology, Department of Physiology, Tulane Hypertension and Renal Center of Excellence, Tulane University School of Medicine, New Orleans, Louisiana
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28
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Karmakar T, Balasubramanian S. Molecular Dynamics and Free Energy Simulations of Phenylacetate and CO 2 Release from AMDase and Its G74C/C188S Mutant: A Possible Rationale for the Reduced Activity of the Latter. J Phys Chem B 2016; 120:11644-11653. [PMID: 27775347 DOI: 10.1021/acs.jpcb.6b07034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Arylmalonate decarboxylase (AMDase) catalyzes the decarboxylation of α-aryl-α-methyl malonates to produce optically pure α-arylpropionates of industrial and medicinal importance. Herein, atomistic molecular dynamics simulations have been carried out to delineate the mechanism of the release of product molecules phenylacetate (PAC) and carbon dioxide (CO2), from the wild-type (WT) and its G74C/C188S mutant enzymes. Both of the product molecules follow a crystallographically characterized solvent-accessible channel to come out of the protein interior. A higher free energy barrier for the release of PAC from G74C/C188S compared to that in the WT is consistent with the experimentally observed compromised efficiency of the mutant. The release of CO2 precedes that of PAC; free energy barriers for CO2 and PAC release in the WT enzyme are calculated to be ∼1-2 and ∼23 kcal/mol, respectively. Postdecarboxylation, CO2 moves toward a hydrophobic pocket formed by Pro 14, Leu 38, Leu 40, Leu 77, and the side chain of Tyr 48 which serves as its temporary "reservoir". CO2 releases following a channel mainly decorated by apolar residues, unlike in the case of oxalate decarboxylase where polar residues mediate its transport.
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Affiliation(s)
- Tarak Karmakar
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Bangalore 560 064, India
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29
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Orabi EA, English AM. Sulfur-Aromatic Interactions: Modeling Cysteine and Methionine Binding to Tyrosinate and Histidinium Ions to Assess Their Influence on Protein Electron Transfer. Isr J Chem 2016. [DOI: 10.1002/ijch.201600047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
- On leave from Department of Chemistry, Faculty of Science; Assiut University; Assiut 71516 Egypt
| | - Ann M. English
- Department of Chemistry and Biochemistry; Concordia University; 7141 Sherbrooke Street West Montréal Québec H4B 1R6 Canada
- Center for Research in Molecular Modeling (CERMM)Quebec; Network for Research on Protein Function, Engineering, and Applications (PROTEO)
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30
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van den Berg B, Chembath A, Jefferies D, Basle A, Khalid S, Rutherford JC. Structural basis for Mep2 ammonium transceptor activation by phosphorylation. Nat Commun 2016; 7:11337. [PMID: 27088325 PMCID: PMC4852598 DOI: 10.1038/ncomms11337] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 03/14/2016] [Indexed: 11/18/2022] Open
Abstract
Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development. Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear. Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations. Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif. The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR. The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.
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Affiliation(s)
- Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Anupama Chembath
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Damien Jefferies
- School of Chemistry, University of Southampton,
Highfield Campus, Southampton
SO17 1BJ, UK
| | - Arnaud Basle
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton,
Highfield Campus, Southampton
SO17 1BJ, UK
| | - Julian C. Rutherford
- Institute for Cell and Molecular Biosciences, The Medical
School, Newcastle University, Newcastle upon Tyne
NE2 4HH, UK
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31
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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32
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Wang S, MacKay L, Lamoureux G. Development of Semiempirical Models for Proton Transfer Reactions in Water. J Chem Theory Comput 2015; 10:2881-90. [PMID: 26588263 DOI: 10.1021/ct500164h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This letter presents a method for the parametrization of semiempirical models for proton transfer reactions in water clusters. Two new models are developed: AM1-W, which is a reparameterization of the classic AM1 model, and AM1PG-W, which is a modified AM1-like model including a pairwise correction to the core repulsion function. Both models show good performance on hydrogen-bonding energies and on proton transfer energy profiles, which are of great importance for proton transfer reactions in large water clusters and in proteins. The parametrization method introduced is general and can be used to develop any other system-specific semiempirical models.
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Affiliation(s)
- Shihao Wang
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
| | - Laurent MacKay
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM) and ‡Department of Physics, Concordia University , Montréal, Canada
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33
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Neuhäuser B, Dynowski M, Ludewig U. Switching substrate specificity of AMT/MEP/ Rh proteins. Channels (Austin) 2015; 8:496-502. [PMID: 25483282 DOI: 10.4161/19336950.2014.967618] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In organisms from all kingdoms of life, ammonia and its conjugated ion ammonium are transported across membranes by proteins of the AMT/Rh family. Efficient and successful growth often depends on sufficient ammonium nutrition. The proteins mediating this transport, the so called Ammonium Transporter (AMT) or Rhesus like (Rh) proteins, share a very similar trimeric overall structure and a high sequence similarity even throughout the kingdoms. Even though structural components of the transport mechanism, like an external substrate recruitment site, an essential twin histidine pore motif, a phenylalanine gate and the hydrophobic pore are strongly conserved and have been analyzed in detail by molecular dynamic simulations and mutational studies, the substrate(s), which pass the central pores of the AMT/Rh subunits, NH4(+), NH3 + H(+), NH4(+) + H(+) or NH3, are still a matter of debate for most proteins, including the best characterized AmtB protein from Escherichia coli. The lack of a robust expression system for functional analysis has hampered proof of structural and mutational studies, although the NH3 transport function for Rh-like proteins is rarely disputed. In plant transporters belonging to the subfamily AMT1, transport is associated with electrical currents, while some plant transporters, notably of the AMT2 type, were suggested to transport NH3 across the membrane, without associated ionic currents. Here we summarize data in favor of each substrate for the distinct AMT/Rh classes, discuss mutants and how they differ in structure and functionality. A common mechanism with deprotonation and subsequent NH3 transport through the central subunit pore is suggested.
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Affiliation(s)
- Benjamin Neuhäuser
- a Institute of Crop Science; Nutritional Crop Physiology ; University of Hohenheim ; Stuttgart , Germany
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34
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Mechanism of NH 4 + Recruitment and NH 3 Transport in Rh Proteins. Structure 2015; 23:1550-1557. [DOI: 10.1016/j.str.2015.06.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/27/2015] [Accepted: 06/08/2015] [Indexed: 01/19/2023]
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35
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Riahi S, Rowley CN. The CHARMM-TURBOMOLE interface for efficient and accurate QM/MM molecular dynamics, free energies, and excited state properties. J Comput Chem 2014; 35:2076-86. [PMID: 25178266 DOI: 10.1002/jcc.23716] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 01/05/2023]
Abstract
The quantum mechanical (QM)/molecular mechanical (MM) interface between Chemistry at HARvard Molecular Mechanics (CHARMM) and TURBOMOLE is described. CHARMM provides an extensive set of simulation algorithms, like molecular dynamics (MD) and free energy perturbation, and support for mature nonpolarizable and Drude polarizable force fields. TURBOMOLE provides fast QM calculations using density functional theory or wave function methods and excited state properties. CHARMM-TURBOMOLE is well-suited for extended QM/MM MD simulations using first principles methods with large (triple-ζ) basis sets. We demonstrate these capabilities with a QM/MM simulation of Mg(2+) (aq), where the MM outer sphere water molecules are represented using the SWM4-NDP Drude polarizable force field and the ion and inner coordination sphere are represented using QM PBE, PBE0, and MP2 methods. The relative solvation free energies of Mg(2+) and Zn(2+) were calculated using thermodynamic integration. We also demonstrate the features for excited state properties. We calculate the time-averaged solution absorption spectrum of indole, the emission spectrum of the indole 1La excited state, and the electronic circular dichroism spectrum of an oxacepham.
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Affiliation(s)
- Saleh Riahi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3X7, Canada
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36
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Offre P, Kerou M, Spang A, Schleper C. Variability of the transporter gene complement in ammonia-oxidizing archaea. Trends Microbiol 2014; 22:665-75. [PMID: 25169021 DOI: 10.1016/j.tim.2014.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/17/2014] [Accepted: 07/30/2014] [Indexed: 12/19/2022]
Abstract
Ammonia-oxidizing archaea (AOA) are a widespread and abundant component of microbial communities in many different ecosystems. The extent of physiological differences between individual AOA is, however, unknown. Here, we compare the transporter gene complements of six AOA, from four different environments and two major clades, to assess their potential for substrate uptake and efflux. Each of the corresponding AOA genomes encode a unique set of transporters and although the composition of AOA transporter complements follows a phylogenetic pattern, few transporter families are conserved in all investigated genomes. A comparison of ammonia transporters encoded by archaeal and bacterial ammonia oxidizers highlights the variance among AOA lineages as well as their distinction from the ammonia-oxidizing bacteria, and suggests differential ecological adaptations.
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Affiliation(s)
- Pierre Offre
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria.
| | - Melina Kerou
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria
| | - Anja Spang
- Uppsala University, Department of Cell and Molecular Biology, Science for Life Laboratory, Box 596, SE-75123, Uppsala, Sweden
| | - Christa Schleper
- University of Vienna, Department of Ecogenomics and Systems Biology, Archaea Biology and Ecogenomics Division, Althanstrasse 14, A-1090 Wien, Austria.
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37
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Orabi EA, Lamoureux G. Simulation of Liquid and Supercritical Hydrogen Sulfide and of Alkali Ions in the Pure and Aqueous Liquid. J Chem Theory Comput 2014; 10:3221-35. [DOI: 10.1021/ct5002335] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry
and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry
and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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38
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Weiner ID, Verlander JW. Ammonia transport in the kidney by Rhesus glycoproteins. Am J Physiol Renal Physiol 2014; 306:F1107-20. [PMID: 24647713 PMCID: PMC4024734 DOI: 10.1152/ajprenal.00013.2014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/14/2014] [Indexed: 12/26/2022] Open
Abstract
Renal ammonia metabolism is a fundamental element of acid-base homeostasis, comprising a major component of both basal and physiologically altered renal net acid excretion. Over the past several years, a fundamental change in our understanding of the mechanisms of renal epithelial cell ammonia transport has occurred, replacing the previous model which was based upon diffusion equilibrium for NH3 and trapping of NH4(+) with a new model in which specific and regulated transport of both NH3 and NH4(+) across renal epithelial cell membranes via specific membrane proteins is required for normal ammonia metabolism. A major advance has been the recognition that members of a recently recognized transporter family, the Rhesus glycoprotein family, mediate critical roles in renal and extrarenal ammonia transport. The erythroid-specific Rhesus glycoprotein, Rh A Glycoprotein (Rhag), was the first Rhesus glycoprotein recognized as an ammonia-specific transporter. Subsequently, the nonerythroid Rh glycoproteins, Rh B Glycoprotein (Rhbg) and Rh C Glycoprotein (Rhcg), were cloned and identified as ammonia transporters. They are expressed in specific cell populations and membrane domains in distal renal epithelial cells, where they facilitate ammonia secretion. In this review, we discuss the distribution of Rhbg and Rhcg in the kidney, the regulation of their expression and activity in physiological disturbances, the effects of genetic deletion on renal ammonia metabolism, and the molecular mechanisms of Rh glycoprotein-mediated ammonia transport.
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Affiliation(s)
- I David Weiner
- Nephrology and Hypertension Section, North Florida/South Georgia Veterans Health System, Gainesville Florida; and Division of Nephrology, Hypertension, and Transplantation, University of Florida College of Medicine, Gainesville, Florida
| | - Jill W Verlander
- Nephrology and Hypertension Section, North Florida/South Georgia Veterans Health System, Gainesville Florida; and
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39
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K(+) and Na(+) conduction in selective and nonselective ion channels via molecular dynamics simulations. Biophys J 2014; 105:1737-45. [PMID: 24138849 DOI: 10.1016/j.bpj.2013.08.049] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 08/24/2013] [Accepted: 08/30/2013] [Indexed: 12/23/2022] Open
Abstract
Generations of scientists have been captivated by ion channels and how they control the workings of the cell by admitting ions from one side of the cell membrane to the other. Elucidating the molecular determinants of ion conduction and selectivity are two of the most fundamental issues in the field of biophysics. Combined with ongoing progress in structural studies, modeling and simulation have been an integral part of the development of the field. As of this writing, the relentless growth in computational power, the development of new algorithms to tackle the so-called rare events, improved force-field parameters, and the concomitant increasing availability of membrane protein structures, allow simulations to contribute even further, providing more-complete models of ion conduction and selectivity in ion channels. In this report, we give an overview of the recent progress made by simulation studies on the understanding of ion permeation in selective and nonselective ion channels.
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40
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Neuhäuser B, Ludewig U. Uncoupling of ionic currents from substrate transport in the plant ammonium transporter AtAMT1;2. J Biol Chem 2014; 289:11650-11655. [PMID: 24634212 PMCID: PMC4002075 DOI: 10.1074/jbc.c114.552802] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 03/13/2014] [Indexed: 12/20/2022] Open
Abstract
The ammonium flux across prokaryotic, plant, and animal membranes is regulated by structurally related ammonium transporters (AMT) and/or related Rhesus (Rh) glycoproteins. Several plant AMT homologs, such as AtAMT1;2 from Arabidopsis, elicit ionic, ammonium-dependent currents when expressed in oocytes. By contrast, functional evidence for the transport of NH3 and the lack of coupled ionic currents has been provided for many Rh proteins. Furthermore, despite high resolution structures the transported substrate in many bacterial homologs, such as AmtB from Escherichia coli, is still unclear. In a heterologous genetic screen in yeast, AtAMT1;2 mutants with reduced transport activity were identified based on the resistance of yeast to the toxic transport analog methylamine. When expressed in oocytes, the reduced transport capacity was confirmed for either of the mutants Q67K, M72I,and W145S. Structural alignments suggest that these mutations were dispersed at subunit contact sites of trimeric AMTs, without direct contact to the pore lumen. Surprisingly, and in contrast to the wild type AtAMT1;2 transporter, ionic currents were not associated with the substrate transport in these mutants. Whether these data suggest that the wild type AtAMT1;2 functions as H(+)/NH3 co-transporter, as well as how the strict substrate coupling with protons is lost by the mutations, is discussed.
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Affiliation(s)
- Benjamin Neuhäuser
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany.
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
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41
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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42
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van Heeswijk WC, Westerhoff HV, Boogerd FC. Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective. Microbiol Mol Biol Rev 2013; 77:628-95. [PMID: 24296575 PMCID: PMC3973380 DOI: 10.1128/mmbr.00025-13] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present a comprehensive overview of the hierarchical network of intracellular processes revolving around central nitrogen metabolism in Escherichia coli. The hierarchy intertwines transport, metabolism, signaling leading to posttranslational modification, and transcription. The protein components of the network include an ammonium transporter (AmtB), a glutamine transporter (GlnHPQ), two ammonium assimilation pathways (glutamine synthetase [GS]-glutamate synthase [glutamine 2-oxoglutarate amidotransferase {GOGAT}] and glutamate dehydrogenase [GDH]), the two bifunctional enzymes adenylyl transferase/adenylyl-removing enzyme (ATase) and uridylyl transferase/uridylyl-removing enzyme (UTase), the two trimeric signal transduction proteins (GlnB and GlnK), the two-component regulatory system composed of the histidine protein kinase nitrogen regulator II (NRII) and the response nitrogen regulator I (NRI), three global transcriptional regulators called nitrogen assimilation control (Nac) protein, leucine-responsive regulatory protein (Lrp), and cyclic AMP (cAMP) receptor protein (Crp), the glutaminases, and the nitrogen-phosphotransferase system. First, the structural and molecular knowledge on these proteins is reviewed. Thereafter, the activities of the components as they engage together in transport, metabolism, signal transduction, and transcription and their regulation are discussed. Next, old and new molecular data and physiological data are put into a common perspective on integral cellular functioning, especially with the aim of resolving counterintuitive or paradoxical processes featured in nitrogen assimilation. Finally, we articulate what still remains to be discovered and what general lessons can be learned from the vast amounts of data that are available now.
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Dance I. A molecular pathway for the egress of ammonia produced by nitrogenase. Sci Rep 2013; 3:3237. [PMID: 24241241 PMCID: PMC3831235 DOI: 10.1038/srep03237] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/01/2013] [Indexed: 01/19/2023] Open
Abstract
Nitrogenase converts N2 to NH3, at one face of an Fe-Mo-S cluster (FeMo-co) buried in the protein. Through exploration of cavities in the structures of nitrogenase proteins, a pathway for the egress of ammonia from its generation site to the external medium is proposed. This pathway is conserved in the three species Azotobacter vinelandii, Klebsiella pneumoniae and Clostridium pasteurianum. A molecular mechanism for the translocation of NH3 by skipping through a sequence of hydrogen bonds involving eleven water molecules and surrounding aminoacids has been developed. The putative mechanism requires movement aside of some water molecules by up to ~ 1Å. Consistent with this, the surrounding protein is comprised of different chains and has little secondary structure: protein fluctuations are part of the mechanism. This NH3 pathway is well separated from the water chain and embedded proton wire that have been proposed for serial supply of protons to FeMo-co. Verification procedures are suggested.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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Lopes PEM, Huang J, Shim J, Luo Y, Li H, Roux B, Mackerell AD. Force Field for Peptides and Proteins based on the Classical Drude Oscillator. J Chem Theory Comput 2013; 9:5430-5449. [PMID: 24459460 DOI: 10.1021/ct400781b] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion.
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Affiliation(s)
- Pedro E M Lopes
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Jing Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Jihyun Shim
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
| | - Yun Luo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA ; Argonne Leadership Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Building 240, Argonne, Illinois 60439, USA
| | - Hui Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander D Mackerell
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
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45
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Ellerbeck M, Schüßler A, Brucker D, Dafinger C, Loos F, Brachmann A. Characterization of three ammonium transporters of the glomeromycotan fungus Geosiphon pyriformis. EUKARYOTIC CELL 2013; 12:1554-62. [PMID: 24058172 PMCID: PMC3837933 DOI: 10.1128/ec.00139-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 09/15/2013] [Indexed: 11/20/2022]
Abstract
Members of the Glomeromycota form the arbuscular mycorrhiza (AM) symbiosis. They supply plants with inorganic nutrients, including nitrogen, from the soil. To gain insight into transporters potentially facilitating nitrogen transport processes, ammonium transporters (AMTs) of Geosiphon pyriformis, a glomeromycotan fungus forming a symbiosis with cyanobacteria, were studied. Three AMT genes were identified, and all three were expressed in the symbiotic stage. The localization and functional characterization of the proteins in a heterologous yeast system revealed distinct characteristics for each of them. AMT1 of G. pyriformis (GpAMT1) and GpAMT2 were both plasma membrane localized, but only GpAMT1 transported ammonium. Neither protein transported the ammonium analogue methylammonium. Unexpectedly, GpAMT3 was localized in the vacuolar membrane, and it has as-yet-unknown transport characteristics. An unusual cysteine residue in the AMT signature of GpAMT2 and GpAMT3 was identified, and the corresponding residue was demonstrated to play an important role in ammonium transport. Surprisingly, each of the three AMTs of G. pyriformis had very distinct features. The localization of an AMT in the yeast vacuolar membrane is novel, as is the described amino acid residue that clearly influences ammonium transport. The AMT characteristics might reflect adaptations to the lifestyle of glomeromycotan fungi.
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Baday S, Wang S, Lamoureux G, Bernèche S. Different hydration patterns in the pores of AmtB and RhCG could determine their transport mechanisms. Biochemistry 2013; 52:7091-8. [PMID: 24021113 DOI: 10.1021/bi400015f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The ammonium transporters of the Amt/Rh family facilitate the diffusion of ammonium across cellular membranes. Functional data suggest that Amt proteins, notably found in plants, transport the ammonium ion (NH4(+)), whereas human Rhesus (Rh) proteins transport ammonia (NH3). Comparison between the X-ray structures of the prokaryotic AmtB, assumed to be representative of Amt proteins, and the human RhCG reveals important differences at the level of their pore. Despite these important functional and structural differences between Amt and Rh proteins, studies of the AmtB transporter have led to the suggestion that proteins of both subfamilies work according to the same mechanism and transport ammonia. We performed molecular dynamics simulations of the AmtB and RhCG proteins under different water and ammonia occupancy states of their pore. Free energy calculations suggest that the probability of finding NH3 molecules in the pore of AmtB is negligible in comparison to finding water. The presence of water in the pore of AmtB could support the transport of proton. The pore lumen of RhCG is found to be more hydrophobic due to the presence of a phenylalanine conserved among Rh proteins. Simulations of RhCG also reveal that the signature histidine dyad is occasionally exposed to the extracellular bulk, which is never observed in AmtB. These different hydration patterns are consistent with the idea that Amt and Rh proteins are not functionally equivalent and that permeation takes place according to two distinct mechanisms.
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Affiliation(s)
- Sefer Baday
- Swiss Institute of Bioinformatics and Biozentrum University of Basel , Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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Wang J, Fulford T, Shao Q, Javelle A, Yang H, Zhu W, Merrick M. Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. PLoS One 2013; 8:e62745. [PMID: 23667517 PMCID: PMC3647058 DOI: 10.1371/journal.pone.0062745] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/25/2013] [Indexed: 01/02/2023] Open
Abstract
Two conserved histidine residues are located near the mid-point of the conduction channel of ammonium transport proteins. The role of these histidines in ammonia and methylamine transport was evaluated by using a combination of in vivo studies, molecular dynamics (MD) simulation, and potential of mean force (PMF) calculations. Our in vivo results showed that a single change of either of the conserved histidines to alanine leads to the failure to transport methylamine but still facilitates good growth on ammonia, whereas double histidine variants completely lose their ability to transport both methylamine and ammonia. Molecular dynamics simulations indicated the molecular basis of the in vivo observations. They clearly showed that a single histidine variant (H168A or H318A) of AmtB confines the rather hydrophobic methylamine more strongly than ammonia around the mutated sites, resulting in dysfunction in conducting the former but not the latter molecule. PMF calculations further revealed that the single histidine variants form a potential energy well of up to 6 kcal/mol for methylamine, impairing conduction of this substrate. Unlike the single histidine variants, the double histidine variant, H168A/H318A, of AmtB was found to lose its unidirectional property of transporting both ammonia and methylamine. This could be attributed to a greatly increased frequency of opening of the entrance gate formed by F215 and F107, in this variant compared to wild-type, with a resultant lowering of the energy barrier for substrate to return to the periplasm.
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Affiliation(s)
- Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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Orabi EA, Lamoureux G. Molecular Dynamics Investigation of Alkali Metal Ions in Liquid and Aqueous Ammonia. J Chem Theory Comput 2013; 9:2324-38. [DOI: 10.1021/ct4001069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
| | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
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49
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Hall JA, Yan D. The molecular basis of K+ exclusion by the Escherichia coli ammonium channel AmtB. J Biol Chem 2013; 288:14080-14086. [PMID: 23546877 DOI: 10.1074/jbc.m113.457952] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Members of the Amt family of channels mediate the transport of ammonium. The form of ammonium, NH3 or NH4(+), carried by these proteins remains controversial, and the mechanism by which they select against K(+) ions is unclear. We describe here a set of Escherichia coli AmtB proteins carrying mutations at the conserved twin-histidine site within the conduction pore that have altered substrate specificity and now transport K(+). Subsequent work established that AmtB-mediated K(+) uptake occurred against a concentration gradient and was membrane potential-dependent. These findings indicate that the twin-histidine element serves as a filter to prevent K(+) conduction and strongly support the notion that Amt proteins transport cations (NH4(+) or, in mutant proteins, K(+)) rather than NH3 gas molecules through their conduction pores.
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Affiliation(s)
- Jason A Hall
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093-0374.
| | - Dalai Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202-5120
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50
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Orabi EA, Lamoureux G. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J Chem Theory Comput 2013; 9:2035-51. [DOI: 10.1021/ct301123j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
| | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
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