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

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Kinetics and Dynamics

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 12))

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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.

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  1. Yuchun Lin

    Present address: Department of Chemical Engineering, University of California, Berkeley, Berkeley, California, 94720, USA

Authors and Affiliations

  1. 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 & Zexing Cao

  2. Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008, USA

    Yirong Mo & Yuchun Lin

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  2. Zexing Cao
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Correspondence to Yirong Mo .

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Editors and Affiliations

  1. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Piotr Paneth

  2. Inst. Applied Radiation Chemistry, Dept. Chemistry, Technical University of Lodz, Zeromskiego 116, Lodz, 90-924, Poland

    Agnieszka Dybala-Defratyka

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Mo, Y., Cao, Z., Lin, Y. (2010). Transport Mechanism in the Escherichia coli Ammonia Channel AmtB: A Computational Study. In: Paneth, P., Dybala-Defratyka, A. (eds) Kinetics and Dynamics. Challenges and Advances in Computational Chemistry and Physics, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3034-4_15

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