A Molecular Dynamics Study into Annexin A1 Induced Membrane Binding and Aggregation

Abstract

Annexins constitute a family of proteins that bind to anionic membranes in a reversible and calcium dependent manner through the unique architecture of their calcium binding sites. In addition, annexins with relatively large N-terminal domains have been identified to cause membrane aggregation and fusion. There is a contradiction between x-ray crystallography and cryo-EM studies as to the proposed mechanism of annexin-induced membrane aggregation. Molecular dynamics simulations were performed in an effort to study the calcium dependent binding of annexin I to a phospholipid bilayer and to investigate the N-terminus as a possible second membrane binding site. Site specific mutations were created on the N-terminus to study the effects phosphorylation has on the tertiary structure of the protein. Simulation trajectories were analyzed in terms of non-bonded interaction energies of protein residues, root mean square deviations of the protein backbone, root mean square fluctuations of residues and nuclear distances between calcium ions and their oxygen ligands. Calcium coordination with lipid headgroups was observed in repeat IV of the core domain. Two lysine residues located in the N-terminus and speculated to be crucial to membrane aggregation displayed significant electrostatic attractions to the phospholipid layer based on MM-PBSA calculations. This thesis will present a model for the mechanism of interaction between annexin A1 and membranes.