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. 2016 Apr 7;7(7):1219-24.
doi: 10.1021/acs.jpclett.6b00153. Epub 2016 Mar 17.

Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers

Fiona B Naughton  1 , Antreas C Kalli  1 , Mark S P Sansom  1
Affiliations

Association of Peripheral Membrane Proteins with Membranes: Free Energy of Binding of GRP1 PH Domain with Phosphatidylinositol Phosphate-Containing Model Bilayers

Fiona B Naughton et al. J Phys Chem Lett. .

Abstract

Understanding the energetics of peripheral protein-membrane interactions is important to many areas of biophysical chemistry and cell biology. Estimating free-energy landscapes by molecular dynamics (MD) simulation is challenging for such systems, especially when membrane recognition involves complex lipids, e.g., phosphatidylinositol phosphates (PIPs). We combined coarse-grained MD simulations with umbrella sampling to quantify the binding of the well-explored GRP1 pleckstrin homology (PH) domain to model membranes containing PIP molecules. The experimentally observed preference of GRP1-PH for PIP3 over PIP2 was reproduced. Mutation of a key residue (K273A) within the canonical PIP-binding site significantly reduced the free energy of PIP binding. The presence of a noncanonical PIP-interaction site, observed experimentally in other PH domains but not previously in GRP1-PH, was also revealed. These studies demonstrate how combining coarse-grained simulations and umbrella sampling can unmask the molecular basis of the energetics of interactions between peripheral membrane proteins and complex cellular membranes.

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Figures

Figure 1
Figure 1
Initial structure of the GRP1-PH domain bound to a PIP3 in a lipid bilayer membrane. GRP1-PH is shown in blue in a cartoon representation; PIP3 is shown in red. The lipid bilayer is represented by the headgroup phosphate particles of the POPC and POPS molecules, shown in light and dark brown respectively. The grey arrow indicates direction of pulling used generate the reaction pathway for the subsequent umbrella sampling windows.
Figure 2
Figure 2
PMF profiles for wild-type GRP1-PH bound to PIP3 or PIP2 (main Figure) and GRP1-PH-K273A mutant bound to PIP3 (inset). Protein-lipid separation is measured from the protein centre-of-mass to the lipid 1-phosphate along the membrane normal. Error estimates were obtained from bootstrap analysis.
Figure 3
Figure 3
A. Three-dimensional histogram of the orientation of the GRP1-PH domain relative to the membrane throughout the first 18 umbrella sampling windows (which covers the distance until the PMF profile levels off), for the GRP1-PH/PIP3 system. RZZ is the component of the rotation matrix relative to the initial configuration (which corresponds to RZZ = 1); the 'restrained distance' indicates the protein centre-of-mass to lipid backbone phosphate separation at which each window was restrained. B. Representative structures of GRP1-PH bound to PIP3 in the ‘canonical’ (C) and ‘atypical’ (A) modes. GRP1-PH is shown in cartoon representation in blue; the surface is coloured by average number of lipid contacts in the windows where each mode is dominant. PIP3 is shown in red and phosphate groups of POPC/POPS in grey.
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