Structure of the Sm binding site from human U4 snRNA derived from a 3 ns PME molecular dynamics simulation

A molecular dynamics simulation of the Sm binding site from human U4 snRNA was undertaken to determine the conformational flexibility of this region a nd to identify RNA conformations that were important for binding of the Sm proteins. The RNA was fully-solvated (>9,000 water molecules) and charge ne utralized by inclusion of potassium ions. A three nanosecond MD simulation was conducted using AMBER with long-range electrostatic forces considered u sing the particle mesh Ewald summation method. The initial model of the Sm binding site region had the central and 3' stem-loops that flanked the Sm s ite co-axial with one another, and with the single-stranded Sm binding site region ([I] conformation). During the course of the trajectory, the axes o f the 3' stem-loop, and later the central stem-loop, became roughly orthogo nal from their original anti-parallel orientation. As these conformational changes occurred, the snRNA adopted first an [L] conformation, and finally a [U] conformation. The [U] conformation was more stable than either the [I ] or [L] conformations, and persisted for the final 1 ns of the trajectory. Analysis of the structure resulting from the MD simulations revealed the b ulged nucleotide, U-114, and the mismatched A(91)-G(110) base pair provided distinctive structural features that may enhance Sm protein binding. Based on the results of the MD simulation and the available experimental data, w e proposed a mechanism for the binding of the Sm protein sub-complexes to t he snRNA. In this model, the D-1/D-2 and E/F/G Sm protein sub-complexes fir st bind the snRNA in the [U] conformation, followed by conformational re-ar rangement to the [I] conformation and binding of the D-3/B Sm protein sub-c omplex.