100 ns molecular dynamics simulations to study intramolecular conformational changes in bax

Abstract

Bax is a pro-apoptotic member of the widely studied Bcl-2 family of apoptotic proteins. Its function is regulated by anti-apoptotic members of the same family. Bcl-xL is one such member, which plays a key role in inhibiting the function of Bax. Recent experimental evidences suggest that intra-molecular conformational changes in the all-helical fold of Bax are necessary for it to be amenable to regulation by Bcl-xL, principal among these being proposed interactions between the N-terminus and α5, α6 (transmembrane TM1.1 and TM1.2) of Bax. The present study is a detailed molecular dynamics investigation of Bax in an aqueous environment, in order to better understand the nature of intra-molecular conformational changes it undergoes before it translocates and inserts into the mitochondrial membrane. A distinct movement of the N-terminal end is observed in a 100ns production run of Bax. Fluctuations across domains are compared for simulations in full-length and deletion mutants of Bax. A series of hydrogen bonding patterns across N-terminal region and α7,8 (BH2 domain) is observed during the simulations. BH2 domain, in turn, acquires new hydrogen bond interactions with TM1 helices. The analysis further revealed other hydrogen bond interactions, across crucial domains in Bax, which are mediated by water molecules across the length of simulation. The structural alliance between N-terminal region and BH2 domain suggests a structural transition cascade leading to the dislocation of TM helices away from hydrophobic interactions that normally prevail with the BH3 domain in the cytosolic form of Bax.