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Download fileFree Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter
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posted on 2018-08-28, 20:17 authored by Balaji Selvam, Shriyaa Mittal, Diwakar ShuklaPepTSo is a proton-coupled bacterial symporter, from
the major facilitator superfamily (MFS), which transports di-/tripeptide
molecules. The recently obtained crystal structure of PepTSo provides an unprecedented opportunity to gain an understanding of
functional insights of the substrate transport mechanism. Binding
of the proton and peptide molecule induces conformational changes
into occluded (OC) and outward-facing (OF) states, which we are able
to characterize using molecular dynamics (MD) simulations. The structural
knowledge of the OC and OF state is important to fully understand
the major energy barrier associated with the transport cycle. In order
to gain functional insight into the interstate dynamics, we performed
extensive all atom MD simulations. The Markov state model was constructed
to identify the free energy barriers between the states, and kinetic
information on intermediate pathways was obtained using the transition
pathway theory (TPT). TPT shows that the OF state is obtained by the
movement of TM1 and TM7 at the extracellular side approximately 12–16
Å away from each other, and the inward movement of TM4 and TM10
at the intracellular halves to 3–4 Å characterizes the
OC state. Helix distance distributions obtained from MD simulations
were compared with experimental double electron–electron resonance
spectroscopy and were found to be in excellent agreement with previous
studies. We also predicted the optimal positions for placement of
methane thiosulfonate spin label probes to capture the slowest protein
dynamics. Our finding sheds light on the conformational cycle of this
key membrane transporter and the functional relationships between
the multiple intermediate states.
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TPTintracellular halveshelix distance distributionsFree Energy LandscapeMFSmembrane transporterfacilitator superfamilypeptide moleculeMarkov state modeltransport cycleTransporter PepTprotein dynamicsmethane thiosulfonateTM 4TM 7TM 1substrate transport mechanismTM 10transition pathway theoryMD simulationslabel probesenergy barriercrystal structureenergy barriersOC stateatom MD simulationsComplete Transport Cycleextracellular side