Molecular dynamics simulation studies on Ca2+-induced conformational changes of annexin I

Abstract

Cryo-electron microscopy (EM) and X-ray studies proposed different mechanisms for annexin-induced membrane aggregation. In this work, molecular dynamics (MD) simulation technique was utilized to gain an insight into the calcium-induced conformational changes on annexin I and their implication in membrane aggregation mechanism. MD simulations were performed on the Ca2+ -free annexin I with the N-terminal domain buried inside the core (System 1), the Ca2+ -bound annexin I without N-terminal domain (System 2) and the Ca2+ -bound annexin I with the N-terminal domain exposed (System 3). Our results indicated that calcium binding increases the flexibility of annexin I core domain residues including the calcium coordinating residues. As a result, annexin I was activated to interact with the negatively charged membrane. The exposed N-terminal domain was very flexible and gradually lost the secondary structure during MD simulation, suggesting that the N-terminal may adopt a favorable conformation to bind a second membrane and also explaining the failure of attempts to crystallize the full-length annexin I in the presence of calcium ions. The measured dimensions of the averaged simulation structure of the Ca2+ -bound annexin I with the N-terminal exposed (System 3) support the proposed membrane aggregation mechanism based on X-ray studies.