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Updated: Jun 23, 2025
08:11
Quantitative Methods to Study Protein Arginine Methyltransferase 1-9 Activity in Cells
Published on: August 7, 2021
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How arginine inhibits substrate-binding domain 2 elucidated using molecular dynamics simulations
Maximilian Kienlein1, Martin Zacharias1
1Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.
Protein Science : a Publication of the Protein Society
|June 18, 2024
Summary
Arginine (ARG) binds to the glutamine (GLN) transporter's substrate-binding domain 2 but inhibits GLN transport by preventing the necessary conformational change. A Lys373Ala mutation may overcome this inhibition.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- The substrate-binding domain 2 (SBD2) of bacterial glutamine (GLN) transporters is crucial for GLN uptake.
- SBD2 exists in open and closed conformations, with GLN binding inducing closure for transport.
- Arginine (ARG) binds to SBD2 but inhibits GLN transport without inducing closure.
Purpose of the Study:
- To investigate the molecular mechanism of ARG inhibition of GLN transport by SBD2.
- To understand why ARG binding does not induce the conformational changes necessary for transport.
- To identify potential strategies to overcome ARG-mediated inhibition.
Main Methods:
- Atomistic molecular dynamics (MD) simulations in explicit solvent were employed.
- Absolute binding free energy calculations were performed for ARG and GLN.
- Free energy simulations were used to assess the conformational changes upon ligand binding.
Main Results:
- ARG reversibly binds to the GLN binding site on SBD2 without inducing closure.
- ARG exhibits significant binding affinity, comparable to GLN.
- ARG binding incurs a substantial free energy penalty for SBD2 closure, unlike GLN binding.
- A Lys373Ala mutation was identified that significantly reduces the closing penalty.
Conclusions:
- ARG competitively inhibits GLN binding and transport by preventing the conformational transition of SBD2 to a closed state.
- The Lys373Ala mutation offers a potential method to investigate the role of conformational mismatch in ARG transport inhibition.
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