J. Mondal

Harnessing Transformers to Generate Protein Sequences Prone to Liquid Liquid Phase Separation

This paper uses GPT-based models to generate protein sequences prone to liquid-liquid phase separation and validates their ability to form phase-separated states.

Protein Translation Can Fluidize Bacterial Cytoplasm

This study shows that protein synthesis, particularly ribosome dynamics, enhances fluidity in bacterial cytoplasm by counteracting its glassy nature through metabolic activity.

An Integrated Machine Learning Approach Delineates an Entropic Expansion Mechanism for the Binding of a Small Molecule to α-synuclein

This study uses machine learning to show that fasudil modulates α-synuclein's conformational states through entropic expansion, offering insights into small molecule interactions with IDPs.

Elucidating ATP's Role as Solubilizer of Biomolecular Aggregate

This study shows ATP prevents protein aggregation and dissolves pre-formed aggregates, suggesting it could be a therapeutic agent for protein-aggregation diseases.

Machine Learning Unravels Inherent Structural Patterns in Escherichia Coli Hi-C Matrices and Predicts DNA Dynamics

This paper uses machine learning to analyze Hi-C data from E. Coli, revealing structural patterns and predicting DNA dynamics, showing that a subset of contact pairs suffices for accurate predictions.

Modulation of α-Synuclein Aggregation Amid Diverse Environmental Perturbation

This study computationally simulates α-Synuclein aggregation under various environmental conditions, revealing how different factors influence its phase separation and structural behavior.

A host AAA-ATPase exhibits bacteriolytic activity for clearance of microbial infection

The paper shows that the host AAA-ATPase VCP/p97 has bacteriolytic activity by mechanically extracting ubiquitinated proteins from bacterial membranes, leading to microbial clearance in a mouse sepsis model.

Identifying Selectivity Filters in Protein Biosensor for Ligand Screening

The paper identifies selectivity filters in MopR, a bacterial phenol biosensor, that screen ligands based on chemical features and size, revealing conserved mechanisms for ligand selection.

On the Spatial Positioning of Ribosomes around chromosome in E. coli Cytoplasm

This study shows ribosomes in E. coli are not entirely excluded from the nucleoid, with some located in a central void, suggesting dynamic localization for efficient translation.

Discovery of a Novel 3site State as the Multi-Substrate Bound State of P450cam

This paper discovers a novel 3site state in P450cam where three substrates bind at distinct sites, including the heme active site, and shows how these binding modes synergistically regulate catalysis.

Development of a Data-driven Integrative Model of Bacterial Chromosome

The paper develops a data-driven integrative model of E. coli chromosome that simulates its conformation and predicts higher-resolution contact maps and segregation behavior.

Small molecule modulates α-Synuclein conformation and its oligomerization via Entropy Expansion

This study shows how a small molecule modulates α-synuclein's conformation and oligomerization through an entropy expansion mechanism, potentially offering therapeutic strategies for neurodegenerative diseases.

Phenol Sensing in Nature Modulated via a Conformational Switch Governed by Dynamic Allostery

The paper shows that MopR, an NtrC protein, uses dynamic allostery to sense phenol, altering its conformation and ATPase activity, with implications for evolutionary conservation.

Impact of Inert Crowders on Host-Guest Recognition Process

This study quantifies how inert crowders affect host-guest recognition using molecular dynamics simulations, showing that crowders lower the binding free energy barrier and enhance complex stabilization under certain conditions.

Conformational Ensemble of Monomeric α-Synuclein in Aqueous and Crowded Environments as revealed by Markov State Model

This paper uses Markov state models to characterize metastable conformations of monomeric α-synuclein in aqueous and crowded environments, revealing aggregation-prone and aggregation-resistant states.

DNA-functionalized Gold Nanorods for Targeted Triple-modal Optical Imaging and Photothermal Therapy of Triple-negative Breast Cancer

This paper develops DNA-functionalized gold nanorods for triple-modal optical imaging and photothermal therapy of triple-negative breast cancer, showing preferential tumor accumulation and effective thermal ablation.

Resolving Protein Conformational Plasticity and Substrate Binding Through the Lens of Machine-Learning

This paper uses machine learning to analyze molecular dynamics simulations of protein-ligand binding, identifying conformational states and allosteric sites involved in substrate recognition.

Computational and experimental studies of the breathing motion of a protein loop: implications in PfAMA1-PfRON2 late-stage binding event

This study combines computational simulations and experimental assays to investigate how the domain II loop of PfAMA1 influences the binding kinetics of PfRON2, identifying key residues critical for the interaction.

Hi-C Contacts Encode Heterogeneity in Sub-diffusive Motion of E. coli Chromosomal Loci

The paper uses Hi-C data to show that E. coli chromosome loci exhibit coordinate-dependent sub-diffusive motion, driven by Hi-C-guided long-range interactions.

Molecular Determinants of Ligand Residence in Galectin

This study uses molecular dynamics simulations to investigate the binding dynamics of galectin-3 with its ligand and a synthetic derivative, identifying key residues that enhance ligand residence time.

Mechanistic Insights on ATP's role as Hydrotrope

This study uses simulations to investigate ATP's role as a hydrotrope, showing it can unfold hydrophobic macromolecules and disrupt aggregation, with charge reinforcement and self-aggregation contributing to its effectiveness.

Spontaneous Transmembrane Pore Formation by Short-chain Synthetic Peptide

This paper investigates how a short synthetic β-peptide forms transmembrane pores in lipid bilayers through molecular dynamics simulations, showing sequence-dependent pore formation and membrane disruption.

Mechanistic underpinning of nonuniform collective motions in swarming bacteria

This study uses simulations to show that bacterial swarming speed and vorticity depend non-monotonically on cell aspect ratio due to size-dependent motility forces and mechanical interactions.

Nucleoid associated proteins and their effect on E. coli chromosome

The paper uses Hi-C simulations to study how nucleoid associated proteins affect E. coli chromosome organization, revealing scale-dependent structural changes.

Conformational Reorganisation of Apolipoprotein E Triggered by Phospholipid Assembly

This paper uses molecular dynamics simulations to show that phospholipid binding induces conformational changes in apoE3, leading to an open structure that may facilitate receptor recognition.

Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model

The paper develops a Hi-C-integrated model to map the multiscale organization of E. coli chromosome, revealing a helical structure with macrodomains and chromosomal interaction domains.

Reconciling Conformational Heterogeneity and Substrate Recognition in Cytochrome P450

This paper quantifies conformational heterogeneity in substrate-free cytochrome P450cam using simulations and identifies a dynamic equilibrium between closed and open conformations, suggesting an induced-fit mechanism for substrate recognition.

Unifying the Ambivalent Mechanisms of Protein-Stabilising Osmolytes

This study investigates the mechanisms of protein stabilization by glycine and TMAO using free energy simulations, revealing that glycine follows an osmophobic model while TMAO exhibits ambivalent binding behavior.

Capturing Protein-Ligand Recognition Pathways in Coarse-grained Simulation

This paper demonstrates that coarse-grained simulations can efficiently capture protein-ligand binding pathways, offering a computationally cheaper alternative to all-atom MD simulations.

Non-affine displacements encode collective conformational fluctuations in proteins

The paper identifies non-affine displacements as key to resolving the free energy landscape of macromolecules using time-structured independent component analysis and Markov state models.