ArticlePLoS computational biology2007
Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
- Prokaryotic ammonium transporters: what has three decades of research revealed?Microbiology (Reading, England) · 2023Article
- Exaggerated trans-membrane charge of ammonium transporters in nutrient-poor marine environments.Open biology · 2022Article
- A pore-occluding phenylalanine gate prevents ion slippage through plant ammonium transporters.Scientific reports · 2019Article
- Different transport behaviors of NH4 (+) and NH3 in transmembrane cyclic peptide nanotubes.Journal of molecular modeling · 2016Article
- Uncoupling of ionic currents from substrate transport in the plant ammonium transporter AtAMT1;2.The Journal of biological chemistry · 2014Article
- Switching substrate specificity of AMT/MEP/ Rh proteins.Channels (Austin, Tex.) · 2014Review
- Nitrogen assimilation in Escherichia coli: putting molecular data into a systems perspective.Microbiology and molecular biology reviews : MMBR · 2013Review
- A molecular pathway for the egress of ammonia produced by nitrogenase.Scientific reports · 2013Article
- The molecular basis of K+ exclusion by the Escherichia coli ammonium channel AmtB.The Journal of biological chemistry · 2013Article
- Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB.The journal of physical chemistry. B · 2009Article
- Bubbles, gating, and anesthetics in ion channels.Biophysical journal · 2008Article
- Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Ammonia-induced formation of an AmtB-GlnK complex is not sufficient for nitrogenase regulation in the photosynthetic bacterium Rhodobacter capsulatus.Journal of bacteriology · 2008Article
- The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel.Biophysical journal · 2007Article
- A stable water chain in the hydrophobic pore of the AmtB ammonium transporter.Biophysical journal · 2007Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The AmtB channel passively allows the transport of NH4(+) across the membranes of bacteria via a "gas" NH3 intermediate and is related by homology (sequentially, structurally, and functionally) to many forms of Rh protein (both erythroid and nonerythroid) found in animals and humans. New structural information on this channel has inspired computational studies aimed at clarifying various aspects of NH4(+) recruitment and binding in the periplasm, as well as its deprotonation. However, precise mechanisms for these events are still unknown, and, so far, explanations for subsequent NH3 translocation and reprotonation at the cytoplasmic end of the channel have not been rigorously addressed. We employ molecular dynamics simulations and free energy methods on a full AmtB trimer system in membrane and bathed in electrolyte. Combining the potential of mean force for NH4(+)/NH3 translocation with data from thermodynamic integration calculations allows us to find the apparent pKa of NH4(+) as a function of the transport axis. Our calculations reveal the specific sites at which its deprotonation (at the periplasmic end) and reprotonation (at the cytoplasmic end) occurs. Contrary to most hypotheses, which ascribe a proton-accepting role to various periplasmic or luminal residues of the channel, our results suggest that the most plausible proton donor/acceptor at either of these sites is water. Free-energetic analysis not only verifies crystallographically determined binding sites for NH4(+) and NH3 along the transport axis, but also reveals a previously undetermined binding site for NH4(+) at the cytoplasmic end of the channel. Analysis of dynamics and the free energies of all possible loading states for NH3 inside the channel also reveal that hydrophobic pressure and the free-energetic profile provided by the pore lumen drives this species toward the cytoplasm for protonation just before reaching the newly discovered site.
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