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Uptake dynamics in the Lactose permease (LacY) membrane protein transporter
Umeå University, Faculty of Science and Technology, Department of Chemistry.
2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 14324Article in journal (Refereed) Published
Abstract [en]

The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 ± 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog β-D-galactopyranosyl-1-thio-β-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018. Vol. 8, article id 14324
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URN: urn:nbn:se:umu:diva-152181DOI: 10.1038/s41598-018-32624-7ISI: 000445570700017PubMedID: 30254312OAI: oai:DiVA.org:umu-152181DiVA, id: diva2:1252159
Funder
Swedish Research Council, 2013-5901Swedish Research Council, 2016-03610Magnus Bergvall Foundation, 2016-01593Stiftelsen Olle Engkvist Byggmästare, 2015/768NIH (National Institute of Health), R01GM116961Available from: 2018-10-01 Created: 2018-10-01 Last updated: 2018-11-09Bibliographically approved

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Andersson, M.

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