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Saikat Chowdhury

Assistant Professor Chowdhury
Department of Biochemistry and Cell Biology

144 Center for Molecular Medicine
Stony Brook University
Stony Brook, NY 11794-5215

Office Phone: 631-632- 2059 
Lab Phone: 631-632-2060

  • Research Description

    Research Description

    We are interested in understanding the civil and mechanical engineering marvels within cells. Just like rebar and cables, which provide support to buildings and bridges, support structures of cells are made up of filamentous cytoskeletal elements like actin, microtubule and intermediate filaments. These dictate cellular morphology, generate forces for cell migration, and form intracellular tracks for movement of molecular motor proteins. These networks are highly regulated and are dynamic in nature. Different proteins interact with these filaments and regulate their polymerization, dissociation, or mediate connectivity between them. Dysregulation or anomaly of the cytoskeletal network are associated with wide range of diseases like developmental disorders, neurodegeneration, delayed wound healing, and cancer metastasis.

    Our lab’s research focuses towards understanding how different cytoskeletal elements work in unison inside the cell, investigate the molecular basis of regulation of these networks, and how these participate in important cellular functions. We use cutting edge Cryo-electron microscopy (EM), novel image processing methodologies along with biochemical and biophysical techniques to decode these cellular engineering feats.

  • Publications



    Rollins MF *, Chowdhury S *, Carter J, Golden SM, Miettinen HM, et al. Structure Reveals a Mechanism of CRISPR-RNAGuided Nuclease Recruitment and Anti-CRISPR Viral Mimicry. Mol Cell . 2019 Mar 1; PubMed PMID: 30872121. ( *Co-equal contribution)


    Otomo T, Chowdhury S, Lander GC. The rod-shaped ATG2A-WIPI4 complex tethers membranes in vitro. Contact (Thousand Oaks). 2018 Dec 21; 1:1-4. PubMed PMID: 30766969; PubMed Central PMCID: PMC6372110. 

    Chowdhury S *, Otomo C *, Leitner A, Ohashi K, Aebersold R, et al. Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proc Natl Acad Sci U S A . 2018 Oct 16; 115(42):E9792-E9801. PubMed PMID: 30185561; PubMed Central PMCID: PMC6196511. ( *Co-equal contribution

    Grotjahn DA *, Chowdhury S *, Xu Y, McKenney RJ, Schroer TA, et al. Cryo-electron tomography reveals that dynactin recruits a team of dyneins for processive motility. Nat Struct Mol Biol . 2018 Mar;25(3):203-207. PubMed PMID: 29416113; NIHMSID: NIHMS931369; PubMed Central PMCID: PMC5969528. ( *Co-equal contribution

    Gardner BM, Castanzo DT, Chowdhury S, Stjepanovic G, Stefely MS, et al. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nat Commun . 2018 Jan 10;9(1):135. PubMed PMID: 29321502; PubMed Central PMCID: PMC5762779. 


    Chen KC, Qu S, Chowdhury S, Noxon IC, Schonhoft JD, et al. The endoplasmic reticulum HSP40 co-chaperone ERdj3/DNAJB11 assembles and functions as a tetramer. EMBO J . 2017 Aug 1;36(15):2296-2309. PubMed PMID:28655754; PubMed Central PMCID: PMC5538767. 

    Rollins MF, Chowdhury S, Carter J, Golden SM, Wilkinson RA, et al. Cas1 and the Csy complex are opposing regulators of Cas2/3 nuclease activity. Proc Natl Acad Sci U S A . 2017 Jun 27;114(26):E5113-E5121. PubMed PMID: 28438998; PubMed Central PMCID: PMC5495223. 

    Chowdhury S *, Carter J *, Rollins MF, Golden SM, Jackson RN, et al. Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. Cell . 2017 Mar 23;169(1):47-57.e11. PubMed PMID: 28340349; NIHMSID: NIHMS859056; PubMed Central PMCID: PMC5478280. ( *Co-equal contribution


    Chowdhury S, Ketcham SA, Schroer TA, Lander GC. Structural organization of the dynein-dynactin complex bound to microtubules. Nat Struct Mol Biol . 2015 Apr;22(4):345-7. PubMed PMID: 25751425; NIHMSID: NIHMS669033; PubMed Central PMCID: PMC4385409.

    Gardner BM, Chowdhury S, Lander GC, Martin A. The Pex1/Pex6 complex is a heterohexameric AAA+ motor with alternating and highly coordinated subunits. J Mol Biol . 2015 Mar 27;427(6 Pt B):1375-1388. PubMed PMID:25659908; NIHMSID: NIHMS661659; PubMed Central PMCID: PMC4355278.


    Sysoeva TA, Chowdhury S, Nixon BT. Breaking symmetry in multimeric ATPase motors. Cell Cycle . 2014;13(10):1509-10. PubMed PMID: 24755939; PubMed Central PMCID: PMC4050149.



    Sysoeva TA *, Chowdhury S *, Guo L, Nixon BT. Nucleotide-induced asymmetry within ATPase activator ring drives σ54-RNAP interaction and ATP hydrolysis. Genes Dev . 2013 Nov 15;27(22):2500-11. PubMed PMID: 24240239; PubMed Central PMCID: PMC3841738. ( *Co-equal contribution)



    Chakraborty A, Wang D, Ebright YW, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R, Nixon BT, Knight J, Weiss S, Ebright RH. Opening and closing of the bacterial RNA polymerase clamp. Science . 2012 Aug 3;337(6094):591-5. PubMed PMID: 22859489; NIHMSID: NIHMS422904; PubMed Central PMCID: PMC3626110.



    Chen B, Sysoeva TA, Chowdhury S, Guo L, De Carlo S, et al. Engagement of arginine finger to ATP triggers large conformational changes in NtrC1 AAA+ ATPase for remodeling bacterial RNA polymerase. Structure . 2010 Nov 10;18(11):1420-30. PubMed PMID: 21070941; NIHMSID: NIHMS251619; PubMed Central PMCID: PMC3001195.



    Chen B, Sysoeva TA, Chowdhury S, Guo L, Nixon BT. ADPase activity of recombinantly expressed thermotolerant ATPases may be caused by copurification of adenylate kinase of Escherichia coli. FEBS J . 2009 Feb;276(3):807-15. PubMed PMID: 19143839; NIHMSID: NIHMS106060; PubMed Central PMCID: PMC2673103.




    Chen B, Sysoeva TA, Chowdhury S, Nixon BT. Regulation and action of the bacterial enhancer-binding protein AAA+ domains. Biochem Soc Trans . 2008 Feb;36(Pt 1):89-93. PubMed PMID: 18208392; NIHMSID: NIHMS106057; PubMed Central PMCID: PMC2692754.

  • Lab members


    Mohammed H. Ali

    Graduate Student

    (Fulbright Fellow)






    Liqun Wang

    Research Technician





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