Quantifying Membrane Curvature Sensing of Peripheral Proteins by Simulated Buckling and Umbrella Sampling

Abstract

Membrane curvature plays an essential role in the organization and trafficking of membrane associated proteins. Comparison or prediction of the experimentally resolved protein concentrations adopted at different membrane curvatures requires direct quantification of the relative partitioning free energy. Here, we present a highly efficient and simple to implement a free-energy calculation method which is able to directly resolve the relative partitioning free energy of proteins as a direct function of membrane curvature, i.e., a curvature sensing profile, within (coarse-grained) molecular dynamics simulations. We demonstrate its utility by resolving these profiles for two known curvature sensing peptides, namely ALPS and α-synuclein, for a membrane curvature ranging from −1/6.5 to +1/6.5 nm–1. We illustrate that the difference in relative partitioning (binding) free energy between these two extrema is only about 13 k B T for both peptides, illustrating that the driving force of curvature sensing is subtle. Furthermore, we illustrate that ALPS and α-synuclein sense curvature via a contrasting mechanism, which is differentially affected by membrane composition. In addition, we demonstrate that the intrinsic spontaneous curvature of both of these peptides lies beyond the range of membrane curvature accessible in micropipette aspiration experiments, being about 1/7 nm –1. Our approach offers an efficient and simple to implement in silico tool for exploring and screening the membrane curvature sensing mechanisms of proteins.

Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36

“… 32 − 35 Since its discovery, ALPS has served as an important model peptide in many computational studies on curvature/lipid packing sensing, 36 − 38 also in our own group. 12 , 13 Second, we will include an amphipathic helix (AH) that was derived from the NS5A protein of hepatitis C virus (HCV) and discovered to sense and rupture vesicles in a size-dependent manner: small vesicles (including HCV particles themselves) were more readily ruptured than bigger ones, and this size range overlaps with the diameter of many enveloped viruses (50–160 nm). 39 , 40 Indeed, the antiviral activity of HCV AH was later found for several unrelated viruses, including Zika, Dengue, and West Nile viruses.…”

“…We recently illustrated how relative binding free energies due to differences in membrane curvature 12 and lipid packing defects 13 can be quantified in CG molecular simulations via umbrella sampling. With these studies, we also showed that curvature and lipid packing defect sensing are in fact equivalent phenomena, implying that a protein’s ability to sense positive membrane curvature can be alternatively inferred from its ability to sense packing defects.…”

Membrane interactions of mitochondrial lipid transfer proteins

“…With this activity proteins can be guided to predominantly bind to membrane regions of a certain curvature (Antonny, 2011). To analyze whether Ups1 displays a membrane curvature sensing activity we first used an in silico approach to directly resolve the relative partitioning free energy of proteins as a direct function of membrane curvature, i.e., a curvature sensing profile, within (coarse-grained) molecular dynamics simulations (Stroh and Risselada, 2021). For a membrane curvature ranging from −0.188 nm −1 (K min ) to +0.188 nm −1 (K max ) we obtained a change in the binding (partitioning) free energy of ΔF = 9.2 kbT ± 1.5 kbT (95 % confidence interval), with Ups1 preferring partitioning to regions of positive membrane curvature (Figure 2C & D).…”

Efficient quantification of lipid packing defect sensing by amphipathic peptides; comparing Martini 2 & 3 with CHARMM36

“…5A-B), as described previously. 12 The poorly binding HCV NH and M2 NH peptides were not considered here, since surface adhesion is a prerequisite in this approach. From this experiment, we obtained sensing free energy profiles as a function of membrane curvature (Fig.…”

“…[31][32][33][34] Since its discovery, ALPS has served as an important model peptide in many computational studies on curvature/lipid packing sensing, [35][36][37] also in our own group. 12,13 Second, we will include an amphipathic helix (AH) that was derived from the NS5A protein of hepatitis C virus (HCV) and discovered to sense and rupture vesicles in a size-dependent manner: small vesicles (including HCV particles themselves) were more readily ruptured than bigger ones and this size range overlaps with the diameter of many enveloped viruses (50-160 nm). 38,39 And, indeed, antiviral activity of HCV AH was later found for several unrelated viruses, including Zika, Dengue and West Nile virus.…”