Do collective atomic fluctuations account for cooperative effects? Molecular dynamics studies of the U1A-RNA complex

Abstract

A complete understanding of gene expression relies on a comprehensive understanding of the protein-RNA recognition process. However, the study of protein-RNA recognition is complicated by many factors that contribute to both binding affinity and specificity, including structure, energetics, dynamical motions, and cooperative interactions. Several recent studies have suggested that energetic coupling between residues contributes to formation of the complex between the U1A protein and stem loop 2 of U1 snRNA as a consequence of a cooperative network of interactions. We have performed molecular dynamics simulations on the U1A-RNA complex, including explicit water and counterions, and analyzed the results based on the calculated positional cross-correlations of atomic fluctuations. The results indicate that cross-correlations calculated on a per residue basis agree well with the observed inter-residue cooperativity and predict that the networks identified to date may also be coupled into an extensive hyper-network that reflects the intrinsic rigidity of the RNA recognition motif. In addition, we report a comparison of the MD calculated correlations with the results of a positional covariance analysis based on the sequences of 330 RNA recognition motifs, including U1A. The calculated inter-residue cross-correlations agree very well with the results of the sites exhibiting positional covariance. Collectively, these results strongly support the hypothesis that collective fluctuations contribute to cooperativity and the corresponding observed thermodynamic coupling. Predictions of additional sites in U1A that may be involved in cooperative networks are advanced.

Figure 1

MD calculated collective atomic fluctuations for the U1A-RNA complex reduced to a residue by residue basis. Magnitudes of calculated correlations are indicated via a grey scale with black, slate gray and light gray regions corresponding to strong (C_ij, = ± 0.75–1.00), moderate (C_ij, = ± 0.50–0.75), and weak (C_ij = ± 0.25–0.50) cross-correlations, respectively. Upper triangle: positive correlations. Lower triangle: negative correlations. Magenta boxes indicate regions of the grid corresponding to residues and nucleotides implicated by biophysical studies as being involved in cooperative networks.– Yellow boxes indicate positions of residues revealed to exhibit high covariance from the Crowder et al. study of 330 RRMs.

Figure 2

Cooperative interactions related to the U1A-RNA binding interface predicted from both MD calculated fluctuations and statistical covariance analysis for U1A. Residues directly in contact with RNA are indicated by an asterisk *. The magnitude of fluctuational covariance between residues corresponds to the line coloring: Purple: C_ij = ± 0.75–1.00; Blue: C_ij, = ±0.50–0.75; Green: C_ij = ± 0.25–0.50.