Computational protocol: Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

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Protocol publication

[…] We provide an analysis of a human beta-amyloid protein D42 (dimer of DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA) as well as some comparisons with the beta-amyloid D40 (same sequence less the 2 terminal amino acids IA) . The initial protein structures of D42 and D40 were derived from published NMR experiments, i.e., PDB structures 2BEG and 1BA4 . We investigate structure formation and evolution and binding kinetics on a symmetric 1-palmitoyl-2-oleoyl-phosphatidylcholine (PC) single bilayer system and an asymmetric 1-palmitoyl-2-oleoyl-phosphatidylcholine/1-palmitoyl-2-oleoyl-phosphatidylserine (PC/PS) double bilayer system (, , , , , , ). We also provide residue contact-maps of the dimer on the symmetric and asymmetric bilayer systems (, , ).Further, we sort the lipids into annular and non-annual regions (). Finally, we plot the lipid-number mismatch and surface area per lipid mismatch of several asymmetric lipid membrane systems (). The design of the initial structures () of the dimer protein and lipid bilayer systems is provided in Materials and Methods of the research article . The data was created using in-house scripts (surround for annular and non-annular region identification, and a python script for sorting of DSSP output) , , g-tools (a suite of analysis programs available through the GROMACs MD engine ) for secondary structure analysis, binding kinetics, and residue contact maps, and VMD for visualization of structures. […]

Pipeline specifications

Software tools GROMACS, VMD
Application Protein structure analysis