Mechanism of RNA recognition by a Musashi RNA-binding protein

Abstract

The Musashi RNA-binding proteins (RBPs) regulate translation of target mRNAs and maintenance of cell stemness and tumorigenesis. Musashi-1 (MSI1), long considered as an intestinal and neural stem cell marker, has been more recently found to be over expressed in many cancers. It has served as an important drug target for treating acute myeloid leukemia and solid tumors such as ovarian, colorectal and bladder cancer. One of the reported binding targets of MSI1 is Numb, a negative regulator of the Notch signaling. However, the dynamic mechanism of Numb RNA binding to MSI1 remains unknown, largely hindering effective drug design targeting this critical interaction. Here, we have performed extensive all-atom microsecond-timescale simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which successfully captured multiple times of spontaneous and highly accurate binding of the Numb RNA from bulk solvent to the MSI1 protein target site. GaMD simulations revealed that Numb RNA binding to MSI1 involved largely induced fit in both the RNA and protein. The simulations also identified important low-energy intermediate conformational states during RNA binding, in which Numb interacted mainly with the β2-β3 loop and C terminus of MSI1. The mechanistic understanding of RNA binding obtained from our GaMD simulations is expected to facilitate rational structure-based drug design targeting MSI1 and other RBPs.

Binding Analysis Using Accelerated Molecular Dynamics Simulations and Future Perspectives

“…GaMD can be implemented to a broad range of biological systems. In particular, recent GaMD simulations have revealed important binding mechanisms of small-molecule ligands, 71 , 84 peptides, 116 , 117 proteins 78 and nucleic acids 85 , 86 to the target receptors. 300 ns of GaMD simulations has successfully captured complete folding of chignolin (10 residues) into its native conformation 61 with a minimum RMSD of 0.2 Å relative to the NMR native conformation (PDB: 1UAO).…”

“…We performed all-atom GaMD simulations to study the binding mechanism between Numb RNA and MSI1. 86 For system setup, the Numb RNA was placed ~30 Å away from the MSI1. The AMBER force fields were used with ff14SBonlysc for protein, RNA.LJbb [110][111][112] for RNA and TIP3P model for water molecules.…”

“…Creative Commons license and disclaimer available from: http://creativecommons.org/licenses/by/4.0/legalcode . 86 …”

“… 74 , 81 Here, we will review recent method developments of GaMD, Ligand GaMD (LiGaMD) 82 and Peptide GaMD (Pep-GaMD), 83 which have greatly expanded our capabilities to simulate biomolecular binding processes. More recently, spontaneous binding of various biomolecules to their receptors such as drug binding to membrane proteins like chemokine GPCRs, 71 human angiotensin-converting enzyme 2 (ACE2), 84 and RNA-protein binding 85 , 86 has been demonstrated by GaMD simulations. Furthermore, microsecond LiGaMD and Pep-GaMD simulations were able to simulate repetitive binding and dissociation of small-molecule ligands 82 and highly flexible peptides, 83 and thus enabled ligand/peptide binding thermodynamics and kinetics calculations.…”

Musashi1 and its short C-terminal variants regulate pluripotency states in embryonic stem cells

“…Recent evidence suggests that the C-terminal domain of MSI1 may also interact with RNAs(Chen & Huang, 2020; Chiou et al , 2017; Wang et al , 2020a), but the biological functions, if any, of the potential binding, has not been adequately investigated.…”