MutSα's Multi-Domain Allosteric Response to Three DNA Damage Types Revealed by Machine Learning

Abstract

MutSα is a key component in the mismatch repair (MMR) pathway. This protein is responsible for initiating the signaling pathways for DNA repair or cell death. Herein we investigate this heterodimer's post-recognition, post-binding response to three types of DNA damage involving cytotoxic, anti-cancer agents-carboplatin, cisplatin, and FdU. Through a combination of supervised and unsupervised machine learning techniques along with more traditional structural and kinetic analysis applied to all-atom molecular dynamics (MD) calculations, we predict that MutSα has a distinct response to each of the three damage types. Via a binary classification tree (a supervised machine learning technique), we identify key hydrogen bond motifs unique to each type of damage and suggest residues for experimental mutation studies. Through a combination of a recently developed clustering (unsupervised learning) algorithm, RMSF calculations, PCA, and correlated motions we predict that each type of damage causes MutSα to explore a specific region of conformation space. Detailed analysis suggests a short range effect for carboplatin-primarily altering the structures and kinetics of residues within 10 angstroms of the damaged DNA-and distinct longer-range effects for cisplatin and FdU. In our simulations, we also observe that a key phenylalanine residue-known to stack with a mismatched or unmatched bases in MMR-stacks with the base complementary to the damaged base in 88.61% of MD frames containing carboplatinated DNA. Similarly, this Phe71 stacks with the base complementary to damage in 91.73% of frames with cisplatinated DNA. This residue, however, stacks with the damaged base itself in 62.18% of trajectory frames with FdU-substituted DNA and has no stacking interaction at all in 30.72% of these frames. Each drug investigated here induces a unique perturbation in the MutSα complex, indicating the possibility of a distinct signaling event and specific repair or death pathway (or set of pathways) for a given type of damage.

Visualizing correlated motion with HDBSCAN clustering

“…Correlated motion between the connector and lever domains of this complex in response to cisplatinated DNA has been previously indicated experimentally and seen in a previous computational study . Some previous computational work has indicated that MutS α 's response to cisplatinated DNA is localized to the ATP‐ase domain, as indicated by Figure d.…”

“…In the other cluster (red), we see residues from the ATP‐ase domain and the clamp domain. As the clamp domain is near damaged DNA, this similarity of dynamics between the clamp and ATP‐ase domain may indicate signaling leading to response by the ATP domain, which has been experimentally demonstrated and discussed at some length in previous computational work . In this example, clustering on a similarity matrix composed of dot products of all correlation vectors (Fig.…”

“…c,d) indicate communication across the two dimers. Such allosteric communication between MSH2 and MSH6 has been a topic of much interest in previous studies …”

Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

“…Then, given a frame of conformation, we constructed a binary feature vector of all possible pairs of residues with hydrogen bonding. This reduced feature set has been recently adopted as inputs for decision tree learning and helped identify allosteric response to three type of DNA damages (Ryan L. Melvin, Thompson, Godwin, Gmeiner, & Salsbury, 2017).…”

Chemistry of Fluorinated Pyrimidines in the Era of Personalized Medicine

“…Specifically, FdU alters the dynamics of the base pair opening in duplex DNA, which could affect how uracil excision repair enzymes recognize and excise 5-FU from DNA [ 9 , 71 , 72 ]. The MMR complex MutSα also differentially binds base pair mismatches that include FdU, which can affect the balance between repair signaling and induction of apoptosis [ 73 ].…”