Theory and simulation of biomolecular systems: Protein-mediated membrane remodeling.

摘要

Plasma membrane geometry is very important in many biological processes, such as clathrin mediated endocytosis (CME). Bin/Amphiphysin/Rvs (BAR) domain containing proteins are extensively found in CME processes where they sense and remodel membrane curvatures. In vivo, BAR domains can initiate the process as well as recruit key proteins in the scission and uncoating stages. In vitro, BAR domains selectively bind to membranes with different curvatures. In various concentrations, BAR domains also tubulate and vesiculate membranes.;The underlying mechanism in BAR domain mediated membrane remodeling is not well understood. Experiments suffer from resolution restrictions when probing nanoscale properties. In this thesis, multiscale modeling and molecular dynamics simulations were employed to study these in-depth biophysical questions. Large-scale atomistic simulations investigated multiple endophilin N-BAR protein configurations and predict the most probable membrane bound protein structure. To study the membrane sensing mechanism, the folding free energy profiles of the amphipathic H0 helix of the N-BAR domain were obtained, where the curvature of membrane promotes the peptide folding by several kcal/mol. Together with quantitative analysis on the hydrophobic defects on membrane, a cooperative mechanism of amphipathic helix folding and hydrophobic defect promotion was proposed.;The geometry of the plasma membrane is very important in many biological processes, such as clathrin mediated endocytosis (CME). Bin/Amphiphysin/Rvs (BAR) domain containing proteins are extensively found in CME processes where they sense and remodel membrane curvatures. In vivo, BAR domains can initiate the process as well as recruit key proteins in the scission and uncoating stages. In vitro, BAR domains selectively bind to membranes with different curvatures. In various concentrations, BAR domains also promote membrane tubulation and vesiculation.;The underlying mechanism in BAR domain mediated membrane remodeling is not well understood. Experiments suffer from resolution restrictions when probing nanoscale properties. In this thesis, multiscale modeling and molecular dynamics simulations were employed to study these in-depth biophysical questions. Large-scale atomistic simulations investigated multiple endophilin N-BAR protein configurations and predict the most probable membrane bound protein structure. To study the membrane sensing mechanism, the folding free energy profiles of the amphipathic H0 helix of the N-BAR domain were obtained, where the curvature of membrane promotes the peptide folding by several kcal/mol. Together with quantitative analysis on the hydrophobic defects on membrane, a cooperative mechanism of amphipathic helix folding and hydrophobic defect promotion was proposed.;Coarse-grained models were developed systematically based on atomistic results. These coarse-grained simulations studied N-BAR oligomer structure on coated tubules, as well as formation of protein arrays on membrane liposomes. These results shed light on the larger picture of the membrane remodeling process and provide valuable insights into the structure determination in electron microscopy experiments. Furthermore, a coarse-graining method was developed to reproduce the atomistic potential field near the protein. Promising results on several systems show that the method is especially useful in modeling macromolecules. The method also provides a roadmap of a potential fitting approach for obtaining coarse-grained parameters and can be applied to many situations.