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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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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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Hussain MA, Mahadevi AS, Sastry GN. Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation. Phys Chem Chem Phys 2015; 17:1763-75. [DOI: 10.1039/c4cp03434a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of increasing methyl substitution on onium ions in their complexes with CO2 and aromatic systems has been analyzed using DFT calculations.
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Affiliation(s)
- M. Althaf Hussain
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - A. Subha Mahadevi
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - G. Narahari Sastry
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
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Direct observation of electrogenic NH4(+) transport in ammonium transport (Amt) proteins. Proc Natl Acad Sci U S A 2014; 111:9995-10000. [PMID: 24958855 DOI: 10.1073/pnas.1406409111] [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] [Indexed: 01/07/2023] Open
Abstract
Ammonium transport (Amt) proteins form a ubiquitous family of integral membrane proteins that specifically shuttle ammonium across membranes. In prokaryotes, archaea, and plants, Amts are used as environmental NH4(+) scavengers for uptake and assimilation of nitrogen. In the eukaryotic homologs, the Rhesus proteins, NH4(+)/NH3 transport is used instead in acid-base and pH homeostasis in kidney or NH4(+)/NH3 (and eventually CO2) detoxification in erythrocytes. Crystal structures and variant proteins are available, but the inherent challenges associated with the unambiguous identification of substrate and monitoring of transport events severely inhibit further progress in the field. Here we report a reliable in vitro assay that allows us to quantify the electrogenic capacity of Amt proteins. Using solid-supported membrane (SSM)-based electrophysiology, we have investigated the three Amt orthologs from the euryarchaeon Archaeoglobus fulgidus. Af-Amt1 and Af-Amt3 are electrogenic and transport the ammonium and methylammonium cation with high specificity. Transport is pH-dependent, with a steep decline at pH values of ∼5.0. Despite significant sequence homologies, functional differences between the three proteins became apparent. SSM electrophysiology provides a long-sought-after functional assay for the ubiquitous ammonium transporters.
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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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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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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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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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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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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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Tripathi R, Nair NN. Thermodynamic and Kinetic Stabilities of Active Site Protonation States of Class C β-Lactamase. J Phys Chem B 2012; 116:4741-53. [DOI: 10.1021/jp212186q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology, Kanpur, 208016 Kanpur,
India
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