D. Bhowmik

Hypertrophic cardiomyopathy mutations Y115H and E497D disrupt the folded-back state of human beta-cardiac myosin allosterically

This study investigates how HCM mutations Y115H and E497D disrupt the folded-back state of human beta-cardiac myosin, leading to hypercontractility by destabilizing the OFF-state.

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

The paper characterizes the structural ensemble of an IDP complex using SANS, MD simulations, and a deep learning algorithm, revealing distinct conformational clusters.

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

The paper investigates how gating interactions between loops in the L1 metallo-β-lactamase affect active site conformational changes and identifies key residues critical for enzyme activity.

Gut microbiota modulation in response to combination of Escherichia coli Nissle 1917 and sugars: Lessons from comparative analysis of fecal microbiota of two healthy donors from 2019-2021

The study examines how Escherichia coli Nissle 1917 combined with different sugars affects gut microbiota in two donors over 1.5 years, showing variations in microbial composition based on prebiotics and initial community structure.

Hypertrophic cardiomyopathy mutations in the pliant and light chain-binding regions of the lever arm of human β-cardiac myosin have divergent effects on myosin function

This study examines how mutations in different regions of the β-cardiac myosin lever arm affect motor function and autoinhibition, revealing divergent effects based on mutation location.

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.

Emergence of multiple variants of SARS-CoV-2 with signature structural changes

This study analyzes SARS-CoV-2 genome divergence and identifies structural changes in viral proteins across four distinct genetic groups.

Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets

The paper uses AI and molecular dynamics to analyze SARS-CoV-2 spike protein structure, revealing flexibility in the S2 domain and hinge region that could inform therapeutic targets.

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.

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.