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Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse‐grained simulations
Author(s) -
Jewel Yead,
Dutta Prashanta,
Liu Jin
Publication year - 2017
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25340
Subject(s) - lactose permease , symporter , periplasmic space , chemistry , crystallography , molecular dynamics , protonation , biophysics , biochemistry , computational chemistry , escherichia coli , biology , transporter , organic chemistry , gene , ion
Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H + symport process. Lactose/H + symport is a highly complex process that involves sugar translocation, H + transfer, and large‐scale protein conformational changes. The complete picture of lactose/H + symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse‐grained force field that couples the united‐atom protein models with the coarse‐grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β ‐ d ‐galactopyranosyl‐1‐thio‐ β ‐ d ‐galactopyranoside (TDG) molecule to a wild‐type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X‐ray experiment. Transitions from inward‐facing to outward‐facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron–electron resonance and thiol cross‐linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H‐bonds breaking at the periplasmic side, interdomain salt‐bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition.