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Transport Mechanism in the Escherichia coli Ammonia Channel AmtB: A Computational Study

  • Yirong MoEmail author
  • Zexing Cao
  • Yuchun Lin
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 12)

Abstract

Computational approaches at various levels have been used to elucidate the mechanism of the ammonium/ammonia transport process through the Escherichia coli AmtB membrane protein. Molecular dynamics (MD) simulations at the classical molecular mechanical (MM) level confirmed that only NH3 can transport through the highly hydrophobic AmtB channel. Thus, NH4 +, which is predominant in solution, must deprotonate before crossing the channel. Significantly, conformational analyses revealed that in the end of the recruitment vestibule, there is a hydrogen bond wire between NH4 + and the carboxylate group of Asp160 via two water molecules. Thus, Asp160 is most likely the proton acceptor from NH4 +. This explains the high conservation of Asp160 in Amt proteins and why the D160A mutant would completely quench the activity of AmtB. The proposed deprotonation mechanism was further examined by the combined QM/MM methods. Computations at both QM(DFT)/MM and QM(PM3)/MM levels concur that the proton transfer starts from a lose of a proton from a nearby water to Asp160 to form a hydroxide anion in the intermediate state, followed by a proton transfer from NH4 + to the hydroxide ion through a water molecule.

Keywords

Molecular dynamics simulation Combined QM/MM Ammonium transport protein Deprotonation mechanism 

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© Springer Netherlands 2010

Authors and Affiliations

  1. 1.Department of Chemistry, The State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical ChemistryXiamen UniversityXiamenP.R. China
  2. 2.Department of ChemistryWestern Michigan UniversityKalamazooUSA

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