Unraveling the behaviour of Intrinsically Disordered Protein c-Myc: A study utilizing Gaussian-Accelerated Molecular Dynamics
The protein c-Myc is a transcription factor that remains largely intrinsically disordered and is known to be involved in various biological processes and is over-expressed in various cancers, making it an attractive drug target. However, intrinsically disordered proteins such as c-Myc do not show funnel-like basins in their free energy landscapes; this makes their druggability a challenge. For the first time, we are proposing a heterodimer model of c-Myc/Max in full length in this work. We used Gaussian-accelerated molecular dynamics (GaMD) simulations to explore the behaviour of c-Myc and its various regions, including the transactivation domain (TAD) and the basic helix-loop-helix-leucine-zipper (bHLH-Zipper) motif, in three different conformational states: (a) monomeric c-Myc (b) c-Myc when bound to its partner protein, Max and (c) when Max was removed after binding. We analyzed the GaMD trajectories using Root Mean Square Deviation (RMSD), Radius of Gyration, Root Mean Square Fluctuation and free energy landscape (FEL) calculations to elaborate the behaviours of these regions. The results showed that the monomeric c-Myc structure showed a higher RMSD fluctuation as compared to the c-Myc/Max heterodimer in the bHLH-Zipper motif. This indicated that the bHLH-Zipper motif of c-Myc is more stable when bound to Max. The TAD region in both monomeric and Max-bound states showed similar plasticity in-terms of RMSD. We also conducted residue decomposition calculations and showed the c-Myc and Max interaction could be driven mainly by electrostatic interactions and the residues Arg299, Ile403 and Leu420 seemed to play important roles in the interaction. Our work provides insights into the behaviour of c-Myc and its regions that could support in the development of drugs that target c-Myc and other intrinsically disordered proteins.