Course work


1. Electron microscopy and 3D image processing for Life sciences. (MB 212 JAN 2:0)
2. Softwares used for single particle cryo-EM analysis - EMAN/SPARX (http://spider.wadsworth.org/spider_doc/spider/docs/spider.html) RELION (http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page) XMIPP (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/MadridJan2014EM) FREALIGN (http://grigoriefflab.janelia.org/frealign) SIMPLE (https://simplecryoem.com) CRYOSPARC (https://cryosparc.com)

Instruments

Talos Arctica 200 kV cryo-TEM
Vitrobot
120 kV Biotwin TEM
Carbon Coater and Glow Discharger
Highly sophisticated data processing server and work workstations Protein purification lab

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Research interest

Pore-forming toxins-

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Pore-forming toxins (PFTs) are the most common bacterial cytotoxic proteins that cause lysis of eukaryotic cells by destroying selective permeability of the plasma membrane bilayer. PFTs are mostly water-soluble toxin and the toxin monomer self-assembles on the target cell surface to the more stable oligomer, which inserts into the membrane bilayer to form a diffusion channel. Extensive research effort has been devoted to understanding the molecular pore formation mechanisms and the functions of certain model PFTs. Cryo-EM has been recently revolutionized by the employment of direct electron detector (DED). This can facilitate the calculation of 3D structure of PFTs at close to atomic resolution, which might shed light on the molecular mechanisms and the functions of PFTs. Bacterial secretion system- Bacteria use a broad variety of membrane transport systems to deliver effectors to other cells and outer media. Generally, Bacterial secretion systems are protein complexes, present on the cell membranes of bacteria for secretion of substances. Specifically, they are the cellular devices used by pathogenic bacteria to secrete their virulence factors to invade the host cells. These multiprotein systems can be classified into different types based on their specific structure, composition and activity. Till now, nine different secretion pathways have been described – Type I to Type IX secretion systems (T1SS-T9SS). Most of the secretion systems have evolved from or co-evolved with different machineries such as motility, drug efflux or pilli assembly. In recent years, cryo-EM studies have a great role to understand these multiprotein complexes.

Metabolic pathways of Mycobacterium tuberculosis -

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Mycobacterium tuberculosis (Mtb) is the causative agent of one of the deadliest infectious diseases known to man, tuberculosis. Mtb has a remarkable ability to persist inside the oxidatively hostile environment of human phagocytes encountering Reactive Oxygen Species, Reactive Nitrogen Species, low pH and nutrient starvation etc. This remarkable ability of Mtb made it a successful human pathogen. There are certain products generated from different metabolic pathways of Mtb helps it to combat hostile environment inside human. We are interested to know the mechanism as well as the structural details of proteins present in these kinds of metabolic pathway.

Work

Polyketide synthase -

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The iterative type I polyketide synthases (PKS) are multimodular mega-enzyme assembly lines responsible for the biosynthesis of many natural products (NP), which are used as the core structure of many pharmacologically diverse compounds like antibacterial, antifungal, anticancer and immunosuppressive compounds. Many of these NPs are either polyketide or nonribosomal peptide or hybrid backbone. Their biosynthetic pathways include one or more multifunctional PKS modules for the initiation, extension and modification steps leading to compounds such as leinamycin, erythromycin, tylosin and rapamycin. Bioengineering efforts to generate novel natural products, which in turn, can be used as valuable drugs, is a research topic of paramount importance for the past few decades. However, earlier efforts including domain modification and/or swapping to increase the productivity of natural products has failed due to lack of structural knowledge about the PKSs. Therefore, we can apply cryo-electron microscopy technique to study and understand the domain organization and interaction of PKS or NRPS-PKS ,which will also help us to apply new strategies to modify the domain organization to increase chemical diversity of these macromolecules.

Other projects –

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We are also working on different bacterial cytosolic proteins, helical proteins etc. Developing new methods on cryo-electron microscopy is also our interest.

Skills

if any other info

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Publications

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Client Testimonials

  • LAB NEWS:
     •Nayanika won second prize for oral presentation in MBU symposium, 2019
    • Anil won first prize for poster presentation in EMSI, 2019
    • Haaris Ahsan Safdari and Ishika Pramanick, PhD student of our lab won the second and consolation prize respectively in the International Conference on Microscope and XXXIX Annual Meeting of Electron Microscope Society of India, Bhubaneshwar, India (2018)

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  • LAB NEWS:
    Early Career research Award of DST, 2017
    • DBT Advanced Centre for Cryo-electron microscopy (Cryo-EM), 2017
    • Somnath Dutta received Ramanujan Fellowship, 2016

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Past Fellows
1. Alakta Das (May - June 2017), UG student of IISc – Summer training>
2. Navyashree V (July-Sep 2017), Bangalore University – Summer training
3. Anuradha Choudhary (Project Fellow) May 2016-May 2018. (Now Ph.D. student at International Institute of Molecular and Cell Biology,Warsaw, Poland)
4. Abirlal Mukherjee (Project Fellow) 2018-2019. (Now Ph.D. student at Indian Institute of Technology, Roorkee)
5. Manish Sarkar (Project Fellow) 2016-2017 (Now Ph.D. Student at Bose Institute, Kolkata)
6. Suresh Kumar (Project Fellow)
7. Akansha Patel (M.Tech Final Year Project Student) 2016-2017
8. Preeti (Postdoc May 2017-May 2018)
9. Ayushi Shukla (Project Fellow)
10. Puja – Summer training
11. Haaris Ahsan Safdari (MS student 2017-2019)
12. Gyana Prakash Mahapatra (Project Assistant)

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