RUNNING TITLE: Docking/MD of MBP with Fyn-SH3 in aqueous and membrane environments.KEYWORDS: amphipathic α-helix, poly-proline type II (PPII), Fyn-SH3, intrinsicallydisordered protein (IDP); myelin basic protein (MBP); molecular dynamics (MD) simulations; molecular recognition fragment (MoRF); GROMACS;
HIGHLIGHTS:• Myelin basic protein (18.5-kDa MBP) has 3 membrane-associated amphipathic α-helices • Proline-rich region (P93-P98) participates in MBP/Fyn-SH3 interaction over 50-ns MD • Energetically-favorable MBP/Fyn-SH3 interaction in aqueous and membrane contexts • Docking complemented by MD led to a more comprehensive interaction model 2
ABSTRACTThe molecular details of the association between the human Fyn-SH3 domain, and the fragment of 18.5-kDa myelin basic protein (MBP) spanning residues S38-S107 (denoted as xα2-peptide, murine sequence numbering), were studied in silico via docking and molecular dynamics over 50-ns trajectories. The results show that interaction between the two proteins is energetically favorable and heavily-dependent on the MBP proline-rich region (P93-P98) in both aqueous and membrane environments. In aqueous conditions, the xα2-peptide/Fyn-SH3 complex adopts a "sandwich"-like structure. In the membrane context, the xα2-peptide interacts with the Fyn-SH3 domain via the proline-rich region and the β-sheets of Fyn-SH3, with the latter wrapping around the proline-rich region in a form of a clip. These results provide a moredetailed glimpse into the context-dependent interaction dynamics and importance of the β-sheets in Fyn-SH3 and proline-rich region of MBP.3