D. Sarkar

Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

This study enhances the thermostability of the photorespiratory enzyme glycerate 3-kinase using structure-based recombination guided by molecular dynamics simulations.

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

The paper compares pore structure and dynamics in bacterial microcompartment shell proteins under different geometries using molecular modeling and simulations.

Context-dependent acetylation of the virulence regulator PhoP accounts for carbon-source specific mycobacterial growth inhibition under acidic conditions

The paper shows that PhoP acetylation, influenced by acidic conditions and carbon sources, affects mycobacterial growth and virulence.

3-epicaryoptin induces G2/M phase cell cycle arrest and apoptosis in human breast cancer cells by disrupting the microtubule network, an in vitro and in silico investigation

This study investigates 3-epicaryoptin's anti-cancer effects on MCF-7 cells, showing it induces G2/M arrest and apoptosis by disrupting microtubules.

Structural Remodeling of Fungal Cell Wall Promotes Resistance to Echinocandins

The paper investigates how fungal cell wall remodeling in response to echinocandins leads to drug resistance by altering carbohydrate polymer assembly and physical properties.

Dual functioning by the PhoR sensor is a key determinant to Mycobacterium tuberculosis virulence

This study identifies PhoR as a dual-function sensor kinase/phosphatase in M. tuberculosis, revealing its role in virulence through pH and salt sensing and regulation of the PhoP regulon.

Protein semisynthesis underscores role of a conserved lysine in activation and desensitization of acid-sensing ion channels

This study uses semisynthesis to investigate the role of a conserved lysine in ASIC1a function, showing its importance in activation and desensitization.

Glycyrrhizin, an inhibitor of HMGB1 induces autolysosomal degradation function and inhibits H. pylori infection

This study shows glycyrrhizin, an HMGB1 inhibitor, restores lysosomal function and reduces H. pylori infection in gastric cells and mice.

Convergence of two global regulators to coordinate expression of essential virulence determinants of Mycobacterium tuberculosis

The paper identifies a regulatory mechanism where CRP and PhoP co-activate virulence genes in M. tuberculosis through protein-protein interactions and promoter recruitment.

Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level

The paper identifies PhoP's role in regulating cAMP levels in M. tuberculosis by repressing the PDE Rv0805, affecting stress response and intracellular survival.

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

This paper introduces an adaptive ensemble refinement method for protein structures using MDFF and RADICAL-Cybertools, improving correlation with cryo-EM density maps by 40%.

Molecular connectivity between extra-cytoplasmic sigma factors and PhoP accounts for integrated mycobacterial stress response

This study investigates how PhoP interacts with sigma factors to regulate mycobacterial stress responses under different conditions, revealing distinct roles in pH and redox homeostasis.

Design, Fabrication, and Theoretical Investigation of a Cost-Effective Laser Printing Based Colorimetric Paper Sensor for Non-Invasive Glucose and Ketone Detection

This paper presents a laser-printing based colorimetric paper sensor for non-invasive glucose and ketone detection in urine, validated by a dynamic model and a web/desktop app for accurate quantification.

P2X2 receptor subunit interfaces are missense variant hotspots where mutations tend to increase apparent ATP affinity

This study maps missense variants in P2X2 receptor inter-subunit interfaces and shows mutations often increase apparent ATP affinity and show energetic coupling.

Data-guided Multi-Map variables for ensemble refinement of molecular movies

This paper introduces a method to refine molecular simulations using data-guided collective variables, showing improved free-energy estimates and structural accuracy compared to existing models.

"Tracking the Rain Bird": Modeling the monthly distribution of Pied cuckoo in India

This study models the monthly distribution of Pied cuckoos in India using bioclimatic variables and citizen science data, showing seasonal shifts and environmental influences.

Assessing tiger corridor functionality with landscape genetics and modelling across Terai-Arc Landscape, India

The paper assesses tiger corridor functionality in the Terai-Arc Landscape using landscape genetics and GIS modelling, identifying critical corridors and subpopulations for conservation.

Expansion Revealing: Decrowding Proteins to Unmask Invisible Brain Nanostructures

Expansion Revealing decrowds proteins to reveal previously invisible nanostructures in brain tissue, including presynaptic calcium channel alignment and amyloid nanoclusters in Alzheimer's models.

Specific OCRL1 patient mutations differentially impact Lowe Syndrome cellular phenotypes

This study shows how different OCRL1 mutations affect Lowe Syndrome cellular phenotypes and introduces a conformational disease mechanism.

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

CryoFold determines protein structures from electron density maps using molecular dynamics and physical knowledge, producing ensembles of low-energy conformations validated experimentally.

Mind reading of the proteins: Deep-learning to forecast molecular dynamics

This paper uses deep learning to predict molecular dynamics from simulation data, finding that non-equilibrium MD is easier to train and performance improves with atom independence assumptions.

Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

The paper uses a photothermal model to predict flowering times of lentil genotypes across environments and identifies groups with different temperature and photoperiod sensitivity.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

The paper evaluates cryo-EM model quality using benchmark maps, showing high accuracy and reproducibility across 13 teams and recommending multiple metrics for model assessment.

Metabolic switching of Mycobacterium tuberculosis during hypoxia is controlled by the virulence regulator PhoP

This study shows that PhoP integrates hypoxia with nitrogen metabolism in Mtb, controlling metabolic switching during hypoxia and affecting bacterial growth.