Systems analysis of ribosomal CAR-site dynamics

Abstract

Developing approaches to link structure and function is an ongoing challenge in computational and structural biology. Using a systems-level framework, we present here an analysis pipeline in a Python package, mdsa-tools, that constructs network representations of structures in a time series of trajectory frames from molecular dynamics (MD) simulations. Here, we demonstrate its use on a ribosomal subsystem. The subsystem is centered on the CAR interaction surface, a "brake pad" adjacent to the aminoacyl (A-site) decoding center that tunes protein translation rates. We leverage unsupervised learning algorithms to explore the conformational landscape of behaviors visited by two versions of the subsystem (brake-on and brake-off) that differ at the codon 3 adjacent to the A-site codon. Our network representations of MD frames embody H-bond interactions between all pairwise combinations of residues in the system. By utilizing per-frame vector representations of network edges, we can apply standard clustering and dimensionality reduction methods to explore behavioral differences between the brake-on and brake-off versions of the system. K-means clustering of frame vectors revealed a striking separation of the two system versions, consistent with principal components analysis (PCA) embeddings and Uniform Manifold Approximation and Projection (UMAP) embeddings. Dissection of K-means centroids and PCA loadings highlighted H-bond interactions between residue pairs in the ribosomes peptidyl site (P site), suggesting potential allosteric signaling across the subsystem. Author summaryWith the impressive development of computational algorithms to successfully simulate the dynamics of biological molecules over time, the exploration and incorporation of systems modes of analysis is a natural next step to begin to understand the molecular dynamics behaviors that emerge from these experiments. Following the approaches of classical molecular genetics, we used a "computational genetics" paradigm where we introduced changes (mutations) in potentially important residues, changing their identities or modifying their chemical properties, and asked how the dynamic system responded to these changes, viewing the simulations as a series of movie frames of the dynamic structure over time. Starting with network representations of each frames structure, where the nodes are residues, and the edges denote H-bond interactions between the residues, we used several unsupervised machine learning algorithms to uncover behavioral changes in the different mutated versions of the system. Applied to our ribosome neighborhood, this revealed unexpected changes in behavior at the ribosome peptidyl site (P site) in response to mutating mRNA residues on the other side of the aminoacyl site (A site) codon, suggesting long-range allosteric interactions across the neighborhood.