Explanipedia

Conserved interfaces mediate multiple protein–protein interactions in a prokaryotic metabolon Open

Sanchari Bhattacharyya, Srivastav Ranganathan, Sourav Chowdhury, Bharat V. Adkar, Mark Khrapko , et al. · 2025

Entropy-driven denaturation enables sustainable protein regeneration through rapid gel-solid transition Open

Yichong Wang, Junlang Liu, Michael M. Peters, Ryoma Ishii, D. I. C. Wang , et al. · 2025

Navigating the Fitness Landscapes of Plasmodium falciparum Dihydrofolate Reductase: Evolutionary Insights into Antifolate Resistance Open

Danny Muzata, Dwipanjan Sanyal, Arti Shivram, Dev Mani Pandey, Soumyananda Chakraborti , et al. · 2024

The rapid emergence of drug resistance in malaria parasites poses a significant challenge to the efficacy of antifolate treatments. Traditional drug development approaches, which often rely on empirical screening with limited mechanistic i…

Mapping DHPS Evolvability: Identification of Novel Evolutionarily Critical Sub-Structure through Evolutionary and Structural Analyses of DHPS Open

Dwipanjan Sanyal, Arti Shivram, Suharto Banerjee, Vladimir N. Uversky, Aneesh Sreevallabh Chivukula , et al. · 2024

Protein evolution shapes pathogen adaptation-landscape, particularly in developing drug resistance. The rapid evolution of target proteins under antibiotic pressure leads to escape mutations leading to the problem of antibiotic resistance.…

Entropy Changes in Water Networks Promote Protein Denaturation Open

Yichong Wang, Junlang Liu, Michael M. Peters, Ryoma Ishii, D. I. C. Wang , et al. · 2024

For over a century, an explanation for how concentrated ions denature proteins has proven elusive. Here, we report a novel mechanism of protein denaturation driven by entropy changes in water networks. Experiments and simulations show that…

Studying ECG signals using nonlinear oscillators and Genetic Algorithm Open

Sourav Chowdhury, Apratim Ghosal, Suparna Roychowhury, Indranath Chaudhuri · 2024

Cardiovascular diseases are the leading cause of death and disability in the world and thus their detection is extremely important as early as possible so that it can be prognosed and managed appropriately. Hence, electrophysiological mode…

Conserved interfaces mediate multiple protein-protein interactions in a prokaryotic metabolon Open

Sanchari Bhattacharyya, Srivastav Ranganathan, Sourav Chowdhury, Bharat V. Adkar, Mark Khrapko , et al. · 2024

Enzymes in a pathway often form metabolons through weak protein-protein interactions (PPI) that localize and protect labile metabolites. Due to their transient nature, the structural architecture of these enzyme assemblies has largely rema…

Pilot-pressure-controlled flow valve and fluid system containing same Open

Sourav Chowdhury, D. Rupp, Mark Zima, Brian Cripps, Kevin Curtin · 2023

In a thermal fluid system, a control valve includes a flow valve and a solenoid pilot valve. The flow valve has an inlet and an outlet; a control chamber for receiving a pilot pressure; and a valve member operable by the pilot pressure to …

Simulating the spread of COVID-19 with cellular automata: A new approach Open

Sourav Chowdhury, Suparna Roychowdhury, Indranath Chaudhuri · 2023

Between the years 2020 to 2022, the world was hit by the pandemic of COVID-19 giving rise to an extremely grave situation. The global economy was badly hurt due to the consequences of various intervention strategies (like social distancing…

Empowering drug off-target discovery with metabolic and structural analysis Open

Sourav Chowdhury, Daniel C. Zielinski, Christopher Dalldorf, João V. Rodrigues, Bernhard Ø. Palsson , et al. · 2023

Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchi…

Publisher Correction: The NK cell receptor NKp46 recognizes ecto-calreticulin on ER-stressed cells Open

Sumit Sen Santara, Dian-Jang Lee, Ângela C. Crespo, Jun Hu, Caitlin Walker , et al. · 2023

The NK cell receptor NKp46 recognizes ecto-calreticulin on ER-stressed cells Open

Sumit Sen Santara, Dian-Jang Lee, Ângela C. Crespo, Jun Hu, Caitlin Walker , et al. · 2023

Empowering drug off-target discovery with metabolic and structural analysis Open

Sourav Chowdhury, Daniel Zielenski, Christopher Dalldorf, João V. Rodrigues, Bernhard Ø. Palsson , et al. · 2023

Source Data for all relevant plots have been provided

An integrated understanding of the evolutionary and structural features of the SARS-CoV-2 spike receptor binding domain (RBD) Open

Dwipanjan Sanyal, Suharto Banerjee, Aritra Bej, Vaidehi Roy Chowdhury, Vladimir N. Uversky , et al. · 2022

A native chemical chaperone in the human eye lens Open

Eugene Serebryany, Sourav Chowdhury, Christopher N. Woods, David C. Thorn, Nicki Watson , et al. · 2022

Cataract is one of the most prevalent protein aggregation disorders and still the most common cause of vision loss worldwide. The metabolically quiescent core region of the human lens lacks cellular or protein turnover; it has therefore ev…

Author response: A native chemical chaperone in the human eye lens Open

Eugene Serebryany, Sourav Chowdhury, Christopher N. Woods, David C. Thorn, Nicki Watson , et al. · 2022

Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Cataract is one of the…

The NK receptor NKp46 recognizes ecto-calreticulin on ER-stressed cells Open

Sumit Sen Santara, Ângela C. Crespo, Dian-Jang Lee, Jun Hu, Ying Zhang , et al. · 2021

Natural killer cells (NK) are a first line of immune defense to eliminate infected, transformed and stressed cells by releasing cytotoxic granules 1 . NK activation is controlled by the balance of signals transmitted by activating and inhi…

Development of antibacterial compounds that constrain evolutionary pathways to resistance Open

Yanmin Zhang, Sourav Chowdhury, João V. Rodrigues, Eugene I. Shakhnovich · 2021

Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here, we applied an integrated computational and experiment…

Author response: Development of antibacterial compounds that constrain evolutionary pathways to resistance Open

Yanmin Zhang, Sourav Chowdhury, João V. Rodrigues, Eugene I. Shakhnovich · 2021

Empowering systems-guided drug target discovery with metabolic and structural analysis Open

Sourav Chowdhury, Daniel C. Zielinski, Christopher Dalldorf, João V. Rodrigues, Bernhard Ø. Palsson , et al. · 2021

Elucidating intracellular drug targets has been a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we developed a s…

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model Open

Achinta Sannigrahi, Sourav Chowdhury, Bidisha Das, Amrita Banerjee, Animesh Halder , et al. · 2021

Aggregation of Cu–Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, amyotrophic lateral sclerosis (ALS). Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in me…

Author response: The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS model Open

Achinta Sannigrahi, Sourav Chowdhury, Bidisha Das, Amrita Banerjee, Animesh Halder , et al. · 2021

Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Aggregation of Cu–Zn superoxi…

A native chemical chaperone in the human eye lens Open

Eugene Serebryany, Sourav Chowdhury, Nicki Watson, Arthur McClelland, Eugene I. Shakhnovich · 2020

Cataract is one of the most prevalent protein aggregation disorders and still the biggest cause of vision loss worldwide. The human lens, in its core region, lacks turnover of any cells or cellular components; it has therefore evolved rema…

A native chemical chaperone in the human eye lens Open

Eugene Serebryany, Sourav Chowdhury, Christopher N. Woods, David C. Thorn, Nicki Watson , et al. · 2020

Cataract is one of the most prevalent protein aggregation disorders and still the most common cause of vision loss worldwide. The metabolically quiescent core region of the human lens lacks cellular or protein turnover; it has therefore ev…

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an<i>in vitro</i>ALS Model Open

Achinta Sannigrahi, Sourav Chowdhury, Bidisha Das, Amrita Banerjee, Animesh Halder , et al. · 2020

Aggregation of Cu-Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, ALS. Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not corre…

Evolutionary Analyses of Sequence and Structure Space Unravel the Structural Facets of SOD1 Open

Sourav Chowdhury, Dwipanjan Sanyal, Sagnik Sen, Vladimir N. Uversky, Ujjwal Maulik , et al. · 2019

Superoxide dismutase (SOD) is the primary enzyme of the cellular antioxidant defense cascade. Misfolding, concomitant oligomerization, and higher order aggregation of human cytosolic SOD are linked to amyotrophic lateral sclerosis (ALS). A…

Unitary Thermal Energy Management for Propulsion Range Augmentation (UTEMPRA) Open

Sourav Chowdhury, Mark Zima · 2019

Battery Electric Vehicles (BEVs) encounter weather-dependent driving range. A major drain on the vehicle battery is the HVAC system which, when typically using resistive heating only, can result in a reduction of up to 50% of the driving r…

Network mapping of the conformational heterogeneity of SOD1 by deploying statistical cluster analysis of FTIR spectra Open

Sourav Chowdhury, Sagnik Sen, Amrita Banerjee, Vladimir N. Uversky, Ujjwal Maulik , et al. · 2019

Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis Open

Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik, Krishnananda Chattopadhyay · 2019

Additional file 7 of Understanding the evolutionary trend of intrinsically structural disorders in cancer relevant proteins as probed by Shannon entropy scoring and structure network analysis Open

Sagnik Sen, Ashmita Dey, Sourav Chowdhury, Ujjwal Maulik, Krishnananda Chattopadhyay · 2019

Shannon entropy score of proteins under Calpain-type cysteine protease DEK1 protein family responsible for acute lymphoblastic leukemia. (XLSX 15 kb)

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