Project
Investigation of the SecYEG-YidC protein complex
Membrane protein insertion by the SecYEG–YidC complex is a fundamental cellular process that underlies the biogenesis of many essential transmembrane proteins, yet its molecular mechanism remains incompletely understood. In particular, how the presence of a substrate modulates the structural and energetic coupling between SecYEG, YidC, the surrounding lipid bilayer, and water is still unclear. Addressing these questions requires simulations that capture both atomic-level interactions and large-scale conformational rearrangements, as well as sufficient sampling to resolve free-energy landscapes. We therefore employed large-scale all-atom and coarse-grained molecular dynamics simulations, complemented by non-equilibrium pulling and umbrella sampling calculations, to investigate substrate-dependent effects on structure, dynamics, and energetics. The results reveal conserved interaction motifs at the SecYEG–YidC interface alongside pronounced resolution-dependent differences in substrate mobility and free-energy profiles. These findings demonstrate the necessity of high-performance computing resources to enable multi-resolution modeling and extensive sampling across biologically relevant length and time scales.
Project Details
Project term
April 15, 2025–November 30, 2025
Affiliations
Forschungszentrum Jülich
Institute
Institute of Biological Information processing
Principal Investigator
Methods
Molecular dynamics (MD) simulations were carried out using GROMACS, employing the CHARMM36m force field for all-atom representations and the Martini 3 force field with an elastic network for coarse-grained models. The simulated systems comprised the SecYEG–YidC complex embedded in a mixed lipid bilayer and were investigated both in the presence and absence of the NuoK1 substrate. Following standard energy minimization and equilibration protocols, extended equilibrium simulations were performed to characterize the structural stability and interaction patterns of the complex. In addition, non-equilibrium steered MD simulations were conducted by applying external forces to separate SecYEG and YidC within the membrane plane. Configurations extracted along these pulling trajectories were used to define umbrella sampling windows. For each window, restrained MD simulations were performed to ensure sufficient sampling, and the resulting trajectories were combined using the weighted histogram analysis method (WHAM) to calculate the potential of mean force (PMF) associated with complex dissociation.
Results
Both all-atom and coarse-grained simulations identify stable periplasmic interaction hotspots that maintain the SecYEG–YidC interface largely independently of substrate presence. The NuoK1 substrate interacts primarily with SecY via its C-terminal region and with YidC through a central segment, but the resulting mechanical response differs by resolution: atomistic simulations show overly strong substrate binding and restricted mobility, whereas coarse-grained simulations allow substrate sliding consistent with the proposed insertion mechanism. Lipid analyses reveal a persistent lipid-filled pocket between SecYEG and YidC, enriched in POPG and depleted of POPC upon substrate insertion, while water penetration into the interface is more pronounced in the coarse-grained model. Accordingly, the PMF increases monotonically in the atomistic system but exhibits a plateau in the coarse-grained simulations, highlighting resolution-dependent differences in interaction strength despite agreement on key structural features.
Discussion
The agreement between atomistic and coarse-grained simulations on interaction hotspots and lipid organization suggests that the overall architecture of the SecYEG–YidC complex is robust. However, the pronounced differences in substrate mobility and PMF profiles indicate that atomistic simulations may overestimate specific protein–substrate interactions, potentially limiting their ability to capture insertion dynamics on accessible timescales. Coarse-grained models, while less detailed, appear better suited for describing large-scale mechanical responses of the complex. Future work should combine refined coarse-grained models with targeted atomistic simulations to better balance accuracy and sampling efficiency. Extending simulations to longer timescales, varying lipid compositions, and exploring additional substrates could further clarify the insertion mechanism and help assess the transferability of the observed interaction patterns.
Additional Project Information
DFG classification: 305 Biological Chemistry and Food Chemistry
Software: Gromacs
Cluster: CLAIX