A. Ramanathan

Senescent cells inhibit muscle differentiation via the SASP-lipid 15d-PGJ2 mediated modification and control of HRas

This study identifies 15d-PGJ2, a lipid from senescent cells, as a mediator of muscle differentiation inhibition via HRas modification and MAPK-Erk activation.

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

This paper adapts a deep learning-driven sampling technique for RNA stem-loop folding, showing it can efficiently explore phase space with lower computational cost than traditional methods.

C-terminal cysteines of HRas control Erk signaling and 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) mediated inhibition of myoblast differentiation.

This study shows that mutations in HRas C-terminal cysteines affect its subcellular localization and signaling, and that 15d-PGJ2 from senescent cells inhibits myoblast differentiation via HRas Cys184.

PROTEOMICS OF HYPOTHERMIC ADAPTATION REVEALS THAT RBM3 ENHANCES MITOCHONDRIAL METABOLISM AND MUSCLE STEM-CELL DIFFERENTIATION

This study identifies RBM3 as a key mediator of hypothermic adaptation in skeletal muscle myoblasts, showing it enhances mitochondrial metabolism and muscle stem-cell differentiation.

Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action

This study develops an AI-driven multi-resolution simulation workflow to study SARS-CoV-2 RTC dynamics, combining cryo-EM with mesoscale simulations and AI methods.

Structural dynamics of the β-coronavirus Mpro protease ligand binding sites

The paper compares ligand-binding sites of Mpro proteases from SARS-CoV2, SARS-CoV, and MERS-CoV using deep learning and Markov state models to assess structural dynamics and conservation.

High Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Non-Covalent Inhibitor

This paper identifies a novel non-covalent inhibitor of SARS-CoV-2 main protease through high throughput virtual screening, validated by biochemical assays, X-ray crystallography, and molecular dynamics simulations.

ARYL HYDROCARBON RECEPTOR BLOCKS AGING-INDUCED SENESCENCE IN THE LIVER AND FIBROBLAST CELLS

This study shows that the aryl hydrocarbon receptor (AhR) restricts aging-induced senescence in liver and fibroblast cells, reducing senescence markers and tumor burden.

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

The paper introduces a method to integrate neutron reflectometry data into molecular dynamics simulations to improve structural accuracy and conformational exploration of membrane-associated proteins.

Biochemical and structural analysis reveals the Neurofibromin (NF1) protein forms a high-affinity dimer

This study shows Neurofibromin forms a high-affinity dimer through biochemical and structural analysis, with implications for its function in RAS-MAPK signaling.

Cardiolipin-dependent Properties of Model Mitochondrial Membranes from Molecular Dynamics Simulations

This study uses molecular dynamics simulations to examine how cardiolipin concentration affects biophysical properties in ternary mitochondrial lipid mixtures, finding minor structural changes but significant impacts on lipid diffusion and curvature.

Deep clustering of protein folding simulations

This paper uses a convolutional variational autoencoder to cluster protein folding simulations and identify conformational substates, achieving 89% contact prediction accuracy.