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PLoS Comput Biol. 2017 Jun 15;13(6):e1005603. doi: 10.1371/journal.pcbi.1005603. eCollection 2017 Jun.

Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE.

Ke M1,2,3, Yuan Y2,3,4, Jiang X2,3,4, Yan N2,3,4, Gong H1,3.

Author information

1
MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
2
State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing, China.
3
Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
4
Tsinghua-Peking Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.

Abstract

GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE. Using molecular dynamics simulations, we evaluated the free energy profiles of the transition between inward- and outward-facing conformations for the apo proteins. Our results revealed the correlation between the protonation state and conformational preference in XylE, which is supported by the crystal structures. In addition, our simulations suggested a thermodynamic difference between XylE and GLUT1 that cannot be explained by the single residue variation at the protonation site. To understand the molecular basis, we applied Bayesian network models to analyze the alteration in the architecture of the hydrogen bond networks during conformational transition. The models and subsequent experimental validation suggest that multiple residue substitutions are required to produce the thermodynamic and functional distinction between XylE and GLUT1. Despite the lack of simulation studies with substrates, these computational and biochemical characterizations provide unprecedented insight into the mechanistic difference between proton symporters and uniporters.

PMID:
28617850
PMCID:
PMC5491310
DOI:
10.1371/journal.pcbi.1005603
[Indexed for MEDLINE]
Free PMC Article

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