Membrane Anisotropy Reshapes Scale-Free Correlations and Directional Mechanical Susceptibility in Transmembrane Proteins

Quantifying the Energetics of Protein-Mediated Stabilization of Membrane Deformation.

Membrane curvature plays a central role in a wide range of biological processes, yet a quantitative and transferable description of its underlying energetics remains challenging. In this work, we develop a "reaction coordinate" within the Umbrella-Sampling framework to compute the free-energy cost associated with local membrane bending in both coarse-grained and atomistic simulations. The methodology is systematically validated across diverse lipid environments, including pure bilayers with varying tail unsaturation, tail length, and headgroup chemistry, where it reproduces established trends in membrane-mechanical rigidity. Extension to mixed lipid systems further captures composition-dependent modulation of bending energetics, including cholesterol-induced responses. Finally, we apply the framework to membrane-active proteins with distinct curvature-generation mechanisms and demonstrate that the method successfully captures the protein modulation of the free-energy cost of local membrane deformation. Furthermore, the method is transferable to atomistic membrane systems while maintaining reasonable computational efficiency, providing a unified approach for quantifying membrane bending energetics across lipids, proteins, and simulation scales.

Can interfacial relaxation encode three-dimensional membrane remodelling?

MEM-CALVADOS: A Residue-Level Model for Flexible Proteins at Membrane Interfaces

The model provides a computationally efficient framework for studying conformational ensembles and assembly of proteins at bilayer–water interfaces and is validated against Wimley–White free energies of transfer of hydrophobic peptides and against an experimentally refined conformational ensemble of a flexible membrane receptor.

Bilayer Elastic Properties Modulate Interface Energetics of Transmembrane β-Barrels.

Assembly energetics of transmembrane proteins occurs through the orchestrated molecular interplay of the protein's membrane partitioning free energy and the mechanical and physicochemical properties of the bilayer. While amphipathic residues help accommodate diametrically opposite forces and the steep energy gradient at the membrane-water interface, the magnitude to which the intrinsic curvature and elastic energy of the bilayer regulates protein thermodynamics at the interface remains poorly understood. Here, using PagP as a model β-barrel, we compare the per-residue energetics of an interface site across membranes with(out) distinct curvature stress, lipid packing, and headgroup chemistry. In vesicles, the measured interface energetics correlates well with known free energy scales. Interestingly, unlike vesicles, we show that planar bicelles impose fundamentally distinct membrane-protein coupling regimes: (i) PagP experiences altered folding with a stabilized membrane-associated intermediate and (ii) side chain transfer free energies are restructured in a residue-specific manner. Additionally, the energetics are unaffected by the presence of nonlamellar lipids. Our results reveal an unexpected dependence of partitioning energetics on both bilayer elastic energy and lipid packing defects, demonstrating how subtle changes in membrane physical properties could redirect protein folding pathways and thermodynamics. Our findings underscore the need for caution when extrapolating side chain transfer free energies from simplified model membranes to crowded, compositionally complex in vivo environments.

Structure, Diffusion, and Relaxation in a Charge-Neutral ProTalpha-Histone H1 Condensate

Condensates formed by oppositely charged intrinsically disordered proteins provide model systems for understanding how transient electrostatic interactions govern structure and dynamics in biomolecular assemblies. Here we investigate a nearly charge-neutral condensate composed of 50 Prothymosin alpha (ProTalpha) and 40 Histone H1 molecules using a single-bead-per-residue coarse-grained model combining the HPS hydropathy model for disordered regions with a Go model for the globular domain of Histone H1 under NPT conditions at pressures from 2 to 12 bar. We find that chain dimensions, including the radius of gyration (Rg), end-to-end distance (Ree), and their ratio R, are insensitive to pressure, indicating that chain conformations remain largely unchanged over the pressure range studied. Histone H1 exhibits systematically larger values of R than ProTalpha because of its globular-core plus disordered-tail architecture. Translational diffusion coefficients decrease monotonically with pressure, from approximately 0.22 to 0.06 nm^2/ns, with substantial chain-to-chain heterogeneity comparable to the mean diffusion coefficient. Chain relaxation follows a stretched exponential with beta less than 1 that decreases with pressure. ProTalpha relaxation times of approximately 12 to 40 ns obey Rouse scaling, whereas Histone H1 deviates because of the internal constraint imposed by its globular domain. ProTalpha-Histone H1 contact lifetimes of approximately 0.43 to 0.56 ns are much shorter than the Rouse relaxation time, placing the system firmly in the fast-exchange regime where transient electrostatic contacts renormalize chain friction rather than acting as permanent cross-links, consistent with the moderate stretching exponent beta of approximately 0.55 to 0.70 observed across all pressures.

Observation of Mechanical and Kinetic Distinctions between Individual Isoleucine and Arginine Residues in a Peptide Dissociating from a Model Lipid Bilayer

The data reveal that both the mechanics and kinetics of peptide detachment are sensitive to the identity and sequence position of individual residues, highlighting the power of integrating CG MD and single-molecule force spectroscopy to unravel residue-specific, sequence-dependent factors underlying peptide–lipid interactions.