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Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with
Chandramouli Natarajan1, Anand Srivastava1
1Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India.
Abstract:
Accurately sampling the membrane-bound conformations of peripheral membrane proteins (PMP) using classical all-atom molecular dynamics simulations (AAMD) is a formidable enterprise due to the wide rugged free energy landscape of the protein-membrane system. In general, AAMD-based extraction of binding geometry requires simulations of multiple systems with different initial user-defined binding poses that may not be exhaustive. As an alternative, advanced sampling methods are also applied to elucidate the membrane-binding mechanism of PMPs. But these techniques are generally computationally expensive and often depend on the choice of the collective variables (CV). In this work, we showcase the utility of CV-free replica exchange with the hybrid tempering (REHT) method in capturing the membrane-bound conformations of PMPs by testing it on the Osh4 amphipathic lipid-packing sensor (ALPS) motif, a 27 amino-acid membrane-binding peptide. We show that REHT samples all the membrane-bound conformations of the Osh4 ALPS peptide observed in AAMD simulations and does it in a highly efficient manner. We clearly show that, out of the two significant conformations, the peptide prefers horizontal conformations over vertical ones. In both the conformations, REHT captures all the vital residue-wise membrane contacts. The transition between the two configurations is not uncommon as our calculations reveal a ~1 kT free energy difference between the two conformations. Interestingly, from our simulations, we also find that the transition from vertical to horizontal conformation involves limited unfolding of the main helix's last turn. From our findings, we conclude that REHT samples the membrane-bound conformations of Osh4 ALPS peptide very efficiently and also provides additional insights and information that are often not available with regular piece-wise AAMD simulations. The method can be used as an efficient tool to explore the membrane-binding mechanisms of PMPs.
Insights
This study introduces a new computational method, CV-free replica exchange with hybrid tempering (REHT), for efficiently sampling membrane-bound protein conformations. REHT accurately captures diverse binding poses of peripheral membrane proteins, offering insights beyond traditional simulations.
Area of Science:
- Biophysics
- Computational Biology
- Molecular Dynamics
Background:
- Peripheral membrane proteins (PMPs) play crucial roles in cellular processes.
- Simulating PMP membrane-bound conformations with all-atom molecular dynamics (AAMD) is challenging due to complex free energy landscapes.
- Existing methods often require extensive simulations or depend on predefined collective variables.
Purpose of the Study:
- To evaluate the efficiency and accuracy of the CV-free replica exchange with hybrid tempering (REHT) method.
- To capture diverse membrane-bound conformations of peripheral membrane proteins.
- To investigate the binding mechanism of the Osh4 amphipathic lipid-packing sensor (ALPS) motif.
Main Methods:
- Utilized CV-free replica exchange with hybrid tempering (REHT) simulations.
- Tested the method on the Osh4 ALPS peptide, a known membrane-binding motif.
- Compared REHT results with traditional all-atom molecular dynamics (AAMD) simulations.
Main Results:
- REHT efficiently sampled all membrane-bound conformations of the Osh4 ALPS peptide observed in AAMD.
- The peptide showed a preference for horizontal over vertical membrane-bound conformations.
- Calculations revealed a small free energy difference (~1 kT) between conformations and identified helix unfolding during transitions.
Conclusions:
- CV-free REHT is a highly efficient method for sampling PMP membrane-bound states.
- REHT provides valuable insights into PMP-membrane interactions, complementing traditional AAMD simulations.
- This method can be a powerful tool for exploring PMP binding mechanisms.
