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Molecular modeling of cation–π interactions and ammonium permeation in AmtB

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Molecular modeling of cation–π interactions and ammonium permeation in AmtB

Orabi, Esam Abd El-Malek Abd-Allah (2011) Molecular modeling of cation–π interactions and ammonium permeation in AmtB. Masters thesis, Concordia University.

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Abstract

Cation–π interactions are noncovalent interactions known to play various important roles in chemical and biological systems. In proteins, such interactions usually involve Phe, Tyr or Trp in contact with inorganic cations or positively charged amino acids (Arg and Lys). AmtB is a transmembrane protein that has a high affinity for ammonium and facilitates its transport across the membrane which provides a source of nitrogen for amino acid synthesis in bacteria. The amino acid residues that line the pore of the crystallographically-identified outer binding site, S1, of AmtB (Trp148, Phe107, and Phe103) are known to stabilize NH4+ through cation–π interactions. However, the nature of the transported species, NH3 or NH4+, and the permeation mechanism are not yet known. In this study, ab initio quantum mechanical calculations at the MP2/6-311++G(d,p) level of theory are performed on the interaction of Li+, Na+, K+ and NH4+ with benzene monomer, dimer, and trimer in order to measure the strength of cation–π interactions in these systems and to parameterize a polarizable force field for these interactions. The resulting force field is used to investigate cation–π interactions and their effect on π–π interactions in water. Polarizable potential models for NH3, Na+, K+, and NH4+ interacting with H2O and with model compounds of the amino acids found along the AmtB permeation pathway are also developed based on ab initio calculations on these interactions at the same level of theory. The resulting models are used to investigate the binding selectivity of S1 toward NH4+ and the biologically abundant monovalent ions Na+ and K+. The nature of the permeable species and possible permeation mechanisms are also investigated based on molecular dynamics free energy calculations.

Divisions:Concordia University > Faculty of Arts and Science > Chemistry and Biochemistry
Item Type:Thesis (Masters)
Authors:Orabi, Esam Abd El-Malek Abd-Allah
Institution:Concordia University
Degree Name:M. Sc.
Program:Chemistry
Date:12 April 2011
Thesis Supervisor(s):Lamoureux, Guillaume
ID Code:7274
Deposited By:ESAM ABD EL-MAL ORABI
Deposited On:13 Jun 2011 09:11
Last Modified:13 Apr 2013 01:38
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