Interpreting the dynamics of binding interactions of snRNA and U1A using a coarse-grained model (Biophysical Journal)

The binding interactions of small nuclear RNAs (snRNA) and the associated protein factors are critical to the function of spliceosomes in alternatively splicing primary RNA transcripts. While molecular dynamics simulations are a powerful tool to interpret the mechanism of biological processes, the atomic-level simulations are, however, too expensive and with limited accuracy for the large-size systems such as snRNA-protein complexes. We extend the coarse-grained Gaussian network model (GNM) which models the RNA-protein complexes as a harmonic chain of C?, P and O4` atoms, to investigating the impact of the snRNA binding interaction on the dynamic stability of the human U1A protein which is a major component of the spliceosomal U1 small nuclear ribonucleoprotein particle.