Lactose permease (LacY) transports various sugar molecules across the plasma membrane by proton symport mechanism. Two key aspects of the transport mechanism, namely the sugar binding and the proton translocation, are studied here. LacY binds to a-anomers of sugars with higher affinity compared to �. The alchemical free energy perturbation method is used to calculate binding free energies and understand the anomeric binding phenomenon. Our calculations quantitatively agree with the experimentally observed differential binding and reveal a detailed description of the anomeric binding phenomenon. The exact mechanism of LacY coupling transport of sugar molecules with the translocation of protons is unknown. However, residues important to sugar binding neighbor those that are involved in proton translocation.  QM/MM is used to study the proton translocation mechanism, specifically the SCC-DFTB/MM-GSBP protocol. The QM/MM calculations help understand the key protein residues involved in proton translocation and the translocation pathway.

Study of ligand binding thermodynamics and proton translocation in lactose permease of <i>Escherichia coli</i>

243rd National Meeting (2012)

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Study of ligand binding thermodynamics and proton translocation in lactose permease of Escherichia coli