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Bizior A, Williamson G, Harris T, Hoskisson PA, Javelle A. Prokaryotic ammonium transporters: what has three decades of research revealed? MICROBIOLOGY (READING, ENGLAND) 2023; 169:001360. [PMID: 37450375 PMCID: PMC10433425 DOI: 10.1099/mic.0.001360] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
The exchange of ammonium across cellular membranes is a fundamental process in all domains of life. In plants, bacteria and fungi, ammonium represents a vital source of nitrogen, which is scavenged from the external environment. In contrast, in animal cells ammonium is a cytotoxic metabolic waste product and must be excreted to prevent cell death. Transport of ammonium is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. In addition to their function as transporters, Amt/Mep/Rh proteins play roles in a diverse array of biological processes and human physiopathology. Despite this clear physiological importance and medical relevance, the molecular mechanism of Amt/Mep/Rh proteins has remained elusive. Crystal structures of bacterial Amt/Rh proteins suggest electroneutral transport, whilst functional evidence supports an electrogenic mechanism. Here, focusing on bacterial members of the family, we summarize the structure of Amt/Rh proteins and what three decades of research tells us concerning the general mechanisms of ammonium translocation, in particular the possibility that the transport mechanism might differ in various members of the Amt/Mep/Rh superfamily.
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Affiliation(s)
- Adriana Bizior
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Gordon Williamson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Thomas Harris
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
| | - Arnaud Javelle
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RE, UK
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2
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Kellom M, Pagliara S, Richards TA, Santoro AE. Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments. Open Biol 2022; 12:220041. [PMID: 35857930 PMCID: PMC9277239 DOI: 10.1098/rsob.220041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Transporter proteins are a vital interface between cells and their environment. In nutrient-limited environments, microbes with transporters that are effective at bringing substrates into their cells will gain a competitive advantage over variants with reduced transport function. Microbial ammonium transporters (Amt) bring ammonium into the cytoplasm from the surrounding periplasm space, but diagnosing Amt adaptations to low nutrient environments solely from sequence data has been elusive. Here, we report altered Amt sequence amino acid distribution from deep marine samples compared to variants sampled from shallow water in two important microbial lineages of the marine water column community-Marine Group I Archaea (Thermoproteota) and the uncultivated gammaproteobacterial lineage SAR86. This pattern indicates an evolutionary pressure towards an increasing dipole in Amt for these clades in deep ocean environments and is predicted to generate stronger electric fields facilitating ammonium acquisition. This pattern of increasing dipole charge with depth was not observed in lineages capable of accessing alternative nitrogen sources, including the abundant alphaproteobacterial clade SAR11. We speculate that competition for ammonium in the deep ocean drives transporter sequence evolution. The low concentration of ammonium in the deep ocean is therefore likely due to rapid uptake by Amts concurrent with decreasing nutrient flux.
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Affiliation(s)
- Matthew Kellom
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Stefano Pagliara
- Living Systems Institute and Biosciences, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - Thomas A. Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Alyson E. Santoro
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA, USA
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3
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A pore-occluding phenylalanine gate prevents ion slippage through plant ammonium transporters. Sci Rep 2019; 9:16765. [PMID: 31727964 PMCID: PMC6856177 DOI: 10.1038/s41598-019-53333-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/31/2019] [Indexed: 01/08/2023] Open
Abstract
Throughout all kingdoms of life, highly conserved transport proteins mediate the passage of ammonium across membranes. These transporters share a high homology and a common pore structure. Whether NH3, NH4+ or NH3 + H+ is the molecularly transported substrate, still remains unclear for distinct proteins. High-resolution protein structures of several ammonium transporters suggested two conserved pore domains, an external NH4+ recruitment site and a pore-occluding twin phenylalanine gate, to take over a crucial role in substrate determination and selectivity. Here, we show that while the external recruitment site seems essential for AtAMT1;2 function, single mutants of the double phenylalanine gate were not reduced in their ammonium transport capacity. Despite an unchanged ammonium transport rate, a single mutant of the inner phenylalanine showed reduced N-isotope selection that was proposed to be associated with ammonium deprotonation during transport. Even though ammonium might pass the mutant AMT pore in the ionic form, the transporter still excluded potassium ions from being transported. Our results, highlight the importance of the twin phenylalanine gate in blocking uncontrolled ammonium ion flux.
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4
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Different transport behaviors of NH4 + and NH3 in transmembrane cyclic peptide nanotubes. J Mol Model 2016; 22:233. [DOI: 10.1007/s00894-016-3081-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
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5
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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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6
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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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7
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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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8
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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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9
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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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10
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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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11
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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12
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Ullmann RT, Andrade SLA, Ullmann GM. Thermodynamics of transport through the ammonium transporter Amt-1 investigated with free energy calculations. J Phys Chem B 2012; 116:9690-703. [PMID: 22804733 DOI: 10.1021/jp305440f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Amt-1 from Archaeoglobus fulgidus (AfAmt-1) belongs to the Amt/Rh family of ammonium/ammonia transporting membrane proteins. The transport mode and the precise microscopic permeation mechanism utilized by these proteins are intensely debated. Open questions concern the identity of the transported substrate (ammonia and/or ammonium) and whether the transport is passive or active. To address these questions, we studied the overall thermodynamics of the different transport modes as a function of the environmental conditions. Then, we investigated the thermodynamics of the underlying microscopic transport mechanisms with free energy calculations within a continuum electrostatics model. The formalism developed for this purpose is of general utility in the calculation of binding free energies for ligands with multiple protonation forms or other binding forms. The results of our calculations are compared to the available experimental and theoretical data on Amt/Rh proteins and discussed in light of the current knowledge on the physiological conditions experienced by microorganisms and plants. We found that microscopic models of electroneutral and electrogenic transport modes are in principle thermodynamically viable. However, only the electrogenic variants have a net thermodynamic driving force under the physiological conditions experienced by microorganisms and plants. Thus, the transport mechanism of AfAmt-1 is most likely electrogenic.
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Affiliation(s)
- R Thomas Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany.
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13
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14
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Wang S, Orabi EA, Baday S, Bernèche S, Lamoureux G. Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate. J Am Chem Soc 2012; 134:10419-27. [DOI: 10.1021/ja300129x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shihao Wang
- Department of Chemistry and
Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University, 7141 Sherbrooke Street West,
Montréal, Québec H4B 1R6, Canada
| | - 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
| | - Sefer Baday
- Swiss Institute of Bioinformatics
and Biozentrum, University of Basel, Klingelbergstrasse
50/70, CH-4056 Basel, Switzerland
| | - Simon Bernèche
- Swiss Institute of Bioinformatics
and Biozentrum, University of Basel, Klingelbergstrasse
50/70, CH-4056 Basel, Switzerland
| | - 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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15
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Gumbart J. Exploring substrate diffusion in channels using biased molecular dynamics simulations. Methods Mol Biol 2012; 914:337-350. [PMID: 22976037 DOI: 10.1007/978-1-62703-023-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Substrate transport and diffusion through membrane-bound channels are processes that can span a range of time scales, with only the fastest ones being amenable to most atomic-scale equilibrium molecular dynamics (MD) simulations. However, the application of forces within a simulation can greatly accelerate diffusion processes, revealing important structural and energetic features of the channel. Here, we demonstrate the use of two methods for applying biases to a substrate in a simulation, using the ammonia/ammonium transporter AmtB as an example. The first method, steered MD, applies a constant force or velocity constraint to the substrate, permitting the exploration of potential substrate pathways and the barriers encountered, although typically far outside of equilibrium. On the other hand, the second method, adaptive biasing forces, is quasi-equilibrium, permitting the derivation of a potential of mean force, which characterizes the free energy of the substrate during transport.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.
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16
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Tahrokh E, Ebrahimi M, Ebrahimi M, Zamansani F, Sarvestani NR, Mohammadi-Dehcheshmeh M, Ghaemi MR, Ebrahimie E. Comparative study of ammonium transporters in different organisms by study of a large number of structural protein features via data mining algorithms. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0057-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily. Proc Natl Acad Sci U S A 2011; 108:3970-5. [PMID: 21368153 DOI: 10.1073/pnas.1007240108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AmtB, a member of the Rh/Amt/MEP superfamily, is responsible for ammonia transport in Escherichia coli. The ammonia pathway in AmtB consists of a narrow hydrophobic lumen in between hydrophilic periplasmic and cytoplasmic vestibules. A series of molecular dynamics simulations (greater than 0.4 μs in total) were performed to determine the mechanism of solute recruitments and selectivity by the periplasmic vestibule. The results show that the periplasmic vestibule plays a crucial role in solute selectivity, and its solute preferences follow the order of NH4(+) > NH3 > CO2. Based on our results, NH4(+) recruitment is initiated by its interaction with either E70 or E225, highly conserved residues located at the entrance of the vestibule. Subsequently, the backbone carbonyl groups at the periplasmic vestibule direct NH4(+) to the conserved aromatic cage at the bottom of the vestibule (known as the Am1 site). The umbrella sampling simulations suggest that the conserved residue D160 is not directly involved in the ammonia conduction; rather its main function is to keep the structure of periplasmic vestibule intact. The MD simulations also revealed that two partially stacked phenyl rings of F107 and F215, separating the periplasmic vestibule from the hydrophobic lumen, flip open and closed simultaneously with a frequency of approximately 10(8) flipping events per second. These results show how the periplasmic vestibule selectively recruits NH4(+) to the Am1 site, and also that the synchronized flipping of two phenyl rings potentially facilitates the solute transition from the periplasmic vestibule to the hydrophobic lumen in the Rh/Amt/MEP superfamily.
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18
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Hub JS, Winkler FK, Merrick M, de Groot BL. Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. J Am Chem Soc 2010; 132:13251-63. [PMID: 20815391 DOI: 10.1021/ja102133x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As a member of the ubiquitous ammonium transporter/methylamine permease/Rhesus (Amt/MEP/Rh) family of membrane protein channels, the 50 kDa Rhesus channel (Rh50) has been implicated in ammonia (NH(3)) and, more recently, also in carbon dioxide (CO(2)) transport. Here we present molecular dynamics simulations of spontaneous full permeation events of ammonia and carbon dioxide across Rh50 from Nitrosomonas europaea. The simulations show that Rh50 is functional in its crystallographic conformation, without the requirement for a major conformational change or the action of a protein partner. To assess the physiological relevance of NH(3) and CO(2) permeation across Rh50, we have computed potentials of mean force (PMFs) and permeabilities for NH(3) and CO(2) flux across Rh50 and compare them to permeation through a wide range of lipid membranes, either composed of pure lipids or composed of lipids plus an increasing cholesterol content. According to the PMFs, Rh50 is expected to enhance NH(3) flux across dense membranes, such as membranes with a substantial cholesterol content. Although cholesterol reduces the intrinsic CO(2) permeability of lipid membranes, the CO(2) permeabilities of all membranes studied here are too high to allow significant Rh50-mediated CO(2) flux. The increased barrier in the PMF for water permeation across Rh50 shows that Rh50 discriminates 40-fold between water and NH(3). Thus, Rh50 channels complement aquaporins, allowing the cell to regulate water and NH(3) flux independently. The PMFs for methylamine and NH(3) are virtually identical, suggesting that methylamine provides an excellent model for NH(3) in functional experiments.
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Affiliation(s)
- Jochen S Hub
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden.
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19
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Wang J, Yang H, Zuo Z, Yan X, Wang Y, Luo X, Jiang H, Chen K, Zhu W. Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB. J Phys Chem B 2010; 114:15172-9. [DOI: 10.1021/jp104508k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jinan Wang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Huaiyu Yang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhili Zuo
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiuhua Yan
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Yong Wang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Kaixian Chen
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China, School of Biomedical Sciences, Curtin University of Technology, Perth WA 6485, Australia, and School of Science, East China University of Science and Technology, Shanghai, 200237, China
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Lamoureux G, Javelle A, Baday S, Wang S, Bernèche S. Transport mechanisms in the ammonium transporter family. Transfus Clin Biol 2010; 17:168-75. [DOI: 10.1016/j.tracli.2010.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 06/14/2010] [Indexed: 02/09/2023]
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21
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Nygaard TP, Alfonso-Prieto M, Peters GH, Jensen MØ, Rovira C. Substrate Recognition in the Escherichia coli Ammonia Channel AmtB: A QM/MM Investigation. J Phys Chem B 2010; 114:11859-65. [DOI: 10.1021/jp102338h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Thomas P. Nygaard
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Günther H. Peters
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Morten Ø. Jensen
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
| | - Carme Rovira
- MEMPHYS—Center for Biomembrane Physics, Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark, Computer Simulation and Modeling Laboratory (CoSMoLab), Parc Científic de Barcelona, 08028 Barcelona, Spain, Institut de Química Teòrica i Computacional (IQTCUB), Department of Life Sciences and Chemistry, Roskilde University, DK-4000 Roskilde, Denmark, and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08019 Barcelona, Spain
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Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate. Proc Natl Acad Sci U S A 2009; 106:21614-8. [PMID: 19966228 DOI: 10.1073/pnas.0907315106] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer membrane protein OprP from Pseudomonas aeruginosa forms a phosphate selective pore. To understand the mechanism of phosphate permeation and selectivity, we used three simulation techniques [equilibrium molecular dynamics simulations, steered molecular dynamics, and calculation of a potential of mean force (PMF)]. The PMF for phosphate reveals a deep free energy well midway along the OprP channel. Two adjacent phosphate-binding sites (W1 and W2), each with a well depth of approximately 8 kT, are identified close to the L3 loop in the most constricted region of the pore. A dissociation constant for phosphate of 6 microM is computed from the PMF, within the range of reported experimental values. The transfer of phosphate between sites W1 and W2 is correlated with changes in conformation of the sidechain of K121, which serves as a "charged brush" to facilitate phosphate passage between the two subsites. OprP also binds chloride, but less strongly than phosphate, as calculated from a Cl(-) PMF. The difference in affinity and hence selectivity is due to the "Lys-cluster" motif, the positive charges of which interact strongly with a partially dehydrated phosphate ion but are shielded from a Cl(-) by the hydration shell of the smaller ion. Our simulations suggest that OprP does not conform to the conventional picture of a channel with relatively flat energy landscape for permeant ions, but rather resembles a membrane-inserted binding protein with a high specificity that allows access to a centrally located binding site from both the extracellular and the periplasmic spaces.
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23
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Ma H, Boogerd FC, Goryanin I. Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. J Biotechnol 2009; 144:175-83. [DOI: 10.1016/j.jbiotec.2009.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 08/28/2009] [Accepted: 09/04/2009] [Indexed: 12/17/2022]
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24
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Zidi-Yahiaoui N, Callebaut I, Genetet S, Le Van Kim C, Cartron JP, Colin Y, Ripoche P, Mouro-Chanteloup I. Functional analysis of human RhCG: comparison with E. coli ammonium transporter reveals similarities in the pore and differences in the vestibule. Am J Physiol Cell Physiol 2009; 297:C537-47. [DOI: 10.1152/ajpcell.00137.2009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Rh glycoproteins are members of the ammonium transporter (Amt)/methylamine permease (Mep)/Rh family facilitating movement of NH3 across plasma membranes. Homology models constructed on the basis of the experimental structures of Escherichia coli AmtB and Nitrosomonas europaea Rh50 indicated a channel structure for human RhA (RhAG), RhB (RhBG), and RhC (RhCG) glycoproteins in which external and internal vestibules are linked by a pore containing two strictly conserved histidines. The pore entry is constricted by two highly conserved phenylalanines, “twin-Phe.” In this study, RhCG function was investigated by stopped-flow spectrofluorometry measuring kinetic pH variations in HEK293E cells in the presence of an ammonium gradient. The apparent unitary NH3 permeability of RhCG was determined and was found to be close to that of AmtB. With a site-directed mutagenesis approach, critical residues involved in Rh NH3 channel activity were highlighted. In the external vestibule, the importance of both the charge and the conformation of the conserved aspartic acid was shown. In contrast to AmtB, individual mutations of each phenylalanine of the twin-Phe impaired the function while the removal of both resulted in recovery of the transport activity. The impact of the mutations suggests that, although having a common function and a similar channel structure, bacterial AmtB and human Rh vary in several aspects of the NH3 transport mechanisms.
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Affiliation(s)
- Nedjma Zidi-Yahiaoui
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Isabelle Callebaut
- Centre National de la Recherche Scientifique, UMR7590, Université Pierre et Marie Curie Paris 6, Paris France
| | - Sandrine Genetet
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Caroline Le Van Kim
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Jean-Pierre Cartron
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Yves Colin
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Pierre Ripoche
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
| | - Isabelle Mouro-Chanteloup
- Institut National de la Santé et de la Recherche Médicale, UMR-S665,
- Institut National de la Transfusion Sanguine,
- Université Paris Diderot-Paris 7, and
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25
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Channel-like NH3flux by ammonium transporter AtAMT2. FEBS Lett 2009; 583:2833-8. [DOI: 10.1016/j.febslet.2009.07.039] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 07/01/2009] [Indexed: 12/16/2022]
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26
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Lin Y, Cao Z, Mo Y. Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB. J Phys Chem B 2009; 113:4922-9. [PMID: 19278252 PMCID: PMC2676109 DOI: 10.1021/jp810651m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular dynamics simulations on the wild-type AmtB protein and its D160A homology model have been performed. Although no significant structural changes due to the mutation of Asp160 were observed, calculations confirmed the critical role of Asp160 for the recognition and binding of NH(4)(+) in AmtB. The carboxyl group of Asp160 is approximately 8 A from NH(4)(+), but their favorable through-space electrostatic interaction is further enhanced by a hydrogen bond chain involving Ala162 (the backbone carbonyl group) and Gly163 (the backbone amide group). This explains the occurrence of the second binding site in AmtB which does not exist in the D160A mutant, as shown in the computed energy profiles. As the initially buried carboxyl group of Asp160 links to the ammonium ion in the periplasmic binding vestibule through a chain of water molecules, a likely deprotonation venue thus is from ammonium to Asp160. Combined QM(PM3)/MM molecular dynamics simulations showed that indeed Asp160 can serve as the proton acceptor and the overall proton transfer process needs to overcome a barrier of merely 7.7 kcal/mol, which is in good agreement with our previous QM(DFT)/MM optimizations. Significantly, the proton transfer adopts an unconventional mechanism by migrating the negative charge from the carboxyl group of Asp160 to NH(4)(+) via two water molecules, which can be illustrated as -CO(2)(-)...H(2)O...H(2)O...NH(4)(+) --> -COOH...H(2)O...OH(-)...NH(4)(+) --> -COOH...H(2)O...H(2)O...NH(3). Apparently, this is also a charge recombination process and thus is exothermic.
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Affiliation(s)
- Yuchun Lin
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Zexing Cao
- Department of Chemistry, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
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27
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Boeckstaens M, André B, Marini AM. Distinct Transport Mechanisms in Yeast Ammonium Transport/Sensor Proteins of the Mep/Amt/Rh Family and Impact on Filamentation. J Biol Chem 2008; 283:21362-70. [DOI: 10.1074/jbc.m801467200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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28
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Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB. Proc Natl Acad Sci U S A 2008; 105:5040-5. [PMID: 18362341 DOI: 10.1073/pnas.0711742105] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The conduction mechanism of Escherichia coli AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic "gate" formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH(4)(+) deprotonation takes place at S1 before NH(3) conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport.
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Abstract
We suggest that bubbles are the bistable hydrophobic gates responsible for the on-off transitions of single channel currents. In this view, many types of channels gate by the same physical mechanism-dewetting by capillary evaporation-but different types of channels use different sensors to modulate hydrophobic properties of the channel wall and thereby trigger and control bubbles and gating. Spontaneous emptying of channels has been seen in many simulations. Because of the physics involved, such phase transitions are inherently sensitive, unstable threshold phenomena that are difficult to simulate reproducibly and thus convincingly. We present a thermodynamic analysis of a bubble gate using morphometric density functional theory of classical (not quantum) mechanics. Thermodynamic analysis of phase transitions is generally more reproducible and less sensitive to details than simulations. Anesthetic actions of inert gases-and their interactions with hydrostatic pressure (e.g., nitrogen narcosis)-can be easily understood by actions on bubbles. A general theory of gas anesthesia may involve bubbles in channels. Only experiments can show whether, or when, or which channels actually use bubbles as hydrophobic gates: direct observation of bubbles in channels is needed. Existing experiments show thin gas layers on hydrophobic surfaces in water and suggest that bubbles nearly exist in bulk water.
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30
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Fan Y, Lund L, Yang L, Raushel FM, Gao YQ. Mechanism for the Transport of Ammonia within Carbamoyl Phosphate Synthetase Determined by Molecular Dynamics Simulations. Biochemistry 2008; 47:2935-44. [DOI: 10.1021/bi701572h] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yubo Fan
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Liliya Lund
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Lijiang Yang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Yi-Qin Gao
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
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31
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Ammonia-induced formation of an AmtB-GlnK complex is not sufficient for nitrogenase regulation in the photosynthetic bacterium Rhodobacter capsulatus. J Bacteriol 2007; 190:1588-94. [PMID: 18156251 DOI: 10.1128/jb.01643-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A series of Rhodobacter capsulatus AmtB variants were created and assessed for effects on ammonia transport, formation of AmtB-GlnK complexes, and regulation of nitrogenase activity and NifH ADP-ribosylation. Confirming previous reports, H193 and H342 were essential for ammonia transport and the replacement of aspartate 185 with glutamate reduced ammonia transport. Several amino acid residues, F131, D334, and D335, predicted to be critical for AmtB activity, are shown here for the first time by mutational analysis to be essential for transport. Alterations of the C-terminal tail reduced methylamine transport, prevented AmtB-GlnK complex formation, and abolished nitrogenase switch-off and NifH ADP-ribosylation. On the other hand, D185E, with a reduced level of transport, was capable of forming an ammonium-induced complex with GlnK and regulating nitrogenase. This reinforces the notions that ammonia transport is not sufficient for nitrogenase regulation and that formation of an AmtB-GlnK complex is necessary for these processes. However, some transport-incompetent AmtB variants, i.e., F131A, H193A, and H342A, form ammonium-induced complexes with GlnK but fail to properly regulate nitrogenase. These results show that formation of an AmtB-GlnK complex is insufficient in itself for nitrogenase regulation and suggest that partial ammonia transport or occupation of the pore by ammonia is essential for this function.
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32
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Lupo D, Li XD, Durand A, Tomizaki T, Cherif-Zahar B, Matassi G, Merrick M, Winkler FK. The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins. Proc Natl Acad Sci U S A 2007; 104:19303-8. [PMID: 18032606 PMCID: PMC2148285 DOI: 10.1073/pnas.0706563104] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Indexed: 12/19/2022] Open
Abstract
The Rhesus (Rh) proteins are a family of integral membrane proteins found throughout the animal kingdom that also occur in a number of lower eukaryotes. The significance of Rh proteins derives from their presence in the human red blood cell membrane, where they constitute the second most important group of antigens used in transfusion medicine after the ABO group. Rh proteins are related to the ammonium transport (Amt) protein family and there is considerable evidence that, like Amt proteins, they function as ammonia channels. We have now solved the structure of a rare bacterial homologue (from Nitrosomonas europaea) of human Rh50 proteins at a resolution of 1.3 A. The protein is a trimer, and analysis of its subunit interface strongly argues that all Rh proteins are likely to be homotrimers and that the human erythrocyte proteins RhAG and RhCE/D are unlikely to form heterooligomers as previously proposed. When compared with structures of bacterial Amt proteins, NeRh50 shows several distinctive features of the substrate conduction pathway that support the concept that Rh proteins have much lower ammonium affinities than Amt proteins and might potentially function bidirectionally.
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Affiliation(s)
- Domenico Lupo
- *Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Xiao-Dan Li
- *Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Anne Durand
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Takashi Tomizaki
- Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Baya Cherif-Zahar
- Université Paris Descartes, Institut National de la Santé et de la Recherche Médicale U845, Faculté de Medecine René Descartes, F-75015 Paris, France; and
| | - Giorgio Matassi
- Institut Jacques Monod Centre National de la Recherche Scientifique-Unite Mixte de Recherche 7592, Université Paris 6 et Université Paris 7, 2 Place Jussieu, 75251 Paris Cedex 05, France
| | - Mike Merrick
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Fritz K. Winkler
- *Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
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33
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Khavrutskii IV, McCammon JA. Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints. J Chem Phys 2007; 127:124901. [PMID: 17902931 DOI: 10.1063/1.2771172] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a generalization of the gradient-augmented harmonic Fourier beads method for finding minimum free-energy transition path ensembles and similarly minimum potential energy paths to allow positional restraints on the centers of mass of selected atoms. The generalized gradient-augmented harmonic Fourier beads (ggaHFB) method further extends the scope of the HFB methodology to studying molecule transport across various mobile phases such as lipid membranes. Furthermore, the new implementation improves the applicability of the HFB method to studies of ligand binding, protein folding, and enzyme catalysis as well as modeling equilibrium pulling experiments. Like its predecessor, the ggaHFB method provides accurate energy profiles along the specified paths and in certain simple cases avoids the need for path optimization. The utility of the ggaHFB method is demonstrated with an application to the water permeation through a single-wall (5,5) carbon nanotube with a diameter of 6.78 A and length of 16.0 A. We provide a simple rationale as to why water enters the hydrophobic nanotube and why it does so in pulses and in wire assembly.
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Affiliation(s)
- Ilja V Khavrutskii
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA.
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34
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Cao Z, Mo Y, Thiel W. Deprotonation Mechanism of NH4+ in theEscherichia coli Ammonium Transporter AmtB: Insight from QM and QM/MM Calculations. Angew Chem Int Ed Engl 2007; 46:6811-5. [PMID: 17668906 DOI: 10.1002/anie.200701348] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
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35
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Cao Z, Mo Y, Thiel W. Deprotonation Mechanism of NH4+ in theEscherichia coli Ammonium Transporter AmtB: Insight from QM and QM/MM Calculations. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200701348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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36
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Ishikita H. Modulation of the protein environment in the hydrophilic pore of the ammonia transporter protein AmtB upon GlnK protein binding. FEBS Lett 2007; 581:4293-7. [PMID: 17707821 DOI: 10.1016/j.febslet.2007.07.085] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 07/30/2007] [Accepted: 07/31/2007] [Indexed: 11/29/2022]
Abstract
The conduction of ammonia/ammonium (NH3/NH4(+)) through the channel protein AmtB is inhibited by the binding of the signal transduction protein GlnK. In the AmtB-GlnK binding interface, there exists an NH3/NH4(+) binding site--Am6. The calculated pK(a) values at the Am6 sites in both the AmtB-GlnK complex and isolated AmtB implies the dominance of an uncharged NH3 state. The GlnK protein binding causes a significant downshift in the Am6 pK(a) value of the AmtB. However, this downshift is perfectly compensated by the reorientation of the protein backbone (carbonyl group of Cys312 from the AmtB part) upon AmtB-GlnK complex formation.
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Affiliation(s)
- Hiroshi Ishikita
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
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37
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Bostick DL, Brooks CL. On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophys J 2007; 92:L103-5. [PMID: 17434945 PMCID: PMC1877791 DOI: 10.1529/biophysj.107.109165] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structural characterization of the bacterial channel, AmtB, provides a glimpse of how members of its family might control the protonated state of permeant ammonium to allow for its selective passage across the membrane. In a recent study, we employed a combination of simulation techniques that suggested ammonium is deprotonated and reprotonated near dehydrative phenylalanine landmarks (F107 and F31, respectively) during its passage from the periplasm to the cytoplasm. At these landmarks, ammonium is forced to maintain a critical number ( approximately 3) of hydrogen bonds, suggesting that the channel controls ammonium (de)protonation by controlling its coordination/hydration. In the work presented here, a free energy-based analysis of ammonium hydration in dilute aqueous solution indicates, explicitly, that at biological pH, the transition from ammonium (NH(4)(+)) to ammonia (NH(3)) occurs when these species are constrained to donate three hydrogen bonds or less. This result demonstrates the viability of the proposal that AmtB indirectly controls ammonium (de)protonation by directly controlling its hydration.
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Affiliation(s)
- David L Bostick
- Department of Molecular Biology and Center for Theoretical Biological Physics, The Scripps Research Institute, La Jolla, California 92037, USA
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38
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Lamoureux G, Klein ML, Bernèche S. A stable water chain in the hydrophobic pore of the AmtB ammonium transporter. Biophys J 2007; 92:L82-4. [PMID: 17351012 PMCID: PMC1852352 DOI: 10.1529/biophysj.106.102756] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The accessibility of water molecules to the pore of the AmtB ammonium transporter is studied using molecular dynamics simulations. Free energy calculations show that the so-called hydrophobic pore can stabilize a chain of water molecules in a well of a few kcal/mol, using a favorable electrostatic binding pocket as an anchoring point. Moreover, the structure of the water chain matches precisely the electronic density maxima observed in x-ray diffraction experiments. This result questions the general assumption that the AmtB pore only contains ammonia (NH(3)) molecules diffusing in a single file fashion. The probable presence of water molecules in the pore would influence the relative stability of NH(3) and NH(4)(+), and thus calls for a reassessment of the overall permeation mechanism in ammonium transporters.
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Affiliation(s)
- Guillaume Lamoureux
- Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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