A method for construction and optimization of lipid nanodisks for molecular dynamics simulationsIvanuš, Bor (Avtor) Rems, Lea (Mentor) Tarek, Mounir (Komentor) nanodisksmimetic peptidesmolecular dynamics simulationsall atomcoarse-grainlipid bilayerLipid-protein interactionsapolipoproteinsLipid nanodisks are lipid bilayer structures stabilized by a belt of alipoproteins. They play a critical role in studying membrane proteins and developing drug delivery systems. Mimetic peptides offer a simplified yet effective alternative to full-length apolipoproteins in stabilizing these nanodisks, providing a platform for understanding lipid-protein interactions and exploring therapeutic applications. The objective of this thesis was to develop, implement, and test a computational protocol for constructing and simulating nanodisks composed of lipid bilayers and stabilized by mimetic peptides, using molecular dynamics all-atom simula tions with the charmm36m forcefield. Five all-atom simulations were conducted to study the structural dynamics of nanodisks formed by 14A peptide dimers and DMPClipids. Anadditional simulation was done by replacing DMPC with POPC and cholesterol, to study the effect of different lipids on nanodisk properties. The presence of cholesterol in the POPC system led to slower stabilization and less shrinkage, likely due to increased membrane rigidity. Coarse-grained simulations using the Martini 3 forcefield were explored for their potential to accelerate sim ulation times. Construction was successful, but the coarse-grain models failed to maintain structural integrity during production runs, indicating that current coarse-grain models may not accurately represent interactions between peptide dimers. While coarse-grain simulations offer the potential for significant accelera tion of the simulation speed, further refinement of the forcefield and stabilization strategies are necessary for reliable nanodisk modeling.20242024-11-12 11:10:13Magistrsko delo/naloga164786VisID: 62754COBISS_ID: 218522371sl