Abhishek Mazumder, Ph.D.

DBT/Wellcome Trust India Alliance Intermediate Fellow
Structural Biology & Bioinformatics
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Research Focus

I am a biochemist using single-molecule fluorescence microscopy to answer fundamental questions in biology. My current work aims to elucidate the mechanism of gene regulation in bacteria by observing structural transitions in individual macromolecular assemblies in real-time. I plan to use the knowledge gained from such fundamental mechanistic studies to develop therapeutic agents and diagnostic methods against the emerging threat of antibiotic-resistant bacteria. We are particularly interested in: 1. The mechanism of transcription-translation coupling in bacteria. 2. Development of new tools to study protein conformational dynamics in live cells. 3. Liquid-liquid phase separation in biology.

Credentials

  • Postdoctoral Research Associate, 2017-2022, University of Oxford, UK.
  • Postdoctoral Research Associate, 2013-2017, Rutgers University, USA.
  • PhD in Biotechnology, 2012, CSIR-Indian Institute of Chemical Biology, India.

Honours & Awards

  • 2022    DBT/Wellcome Trust India Alliance Intermediate Fellowship. 
  • 2020    Ramalingaswami Re-entry Fellowship, DBT, India.
  • 2013    Charles and Johanna Busch Postdoctoral Award, Rutgers University, USA. 
  • 2003    Satish Sinha Memorial Award, University of Calcutta, India. 

Grants & Supports

  • 2023-2027   DBT/Wellcome Trust India Alliance Intermediate Fellowship.

Patents & Publications

Publications:

  1. Mazumder, A , Ebright, R.H., Kapanidis, A.N.  Transcription initiation at a consensus bacterial promoter proceeds via a “bind-unwind-load-and-lock” mechanism. (2021) Oct 7, Elife;   Corresponding author. Significance of the work: This work solves a long-standing puzzle in transcription initiation and shows that unwinding of double-stranded DNA occurs outside the RNA polymerase (RNAP) active site cleft and that the RNAP clamp locks and holds the loaded single-stranded DNA in the active site cleft.
  2. Mazumder, A , Wang, A., Uhm, H., Ebright, R.H., Kapanidis, A.N.  (2021) RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations and non-specific binding. Nucleic Acids Res; Mar 21, 49,2790–2802;   Corresponding author. Significance of the work: This work elucidates variations in RNAP clamp conformational dynamics in response to different conditions and discusses possible implications of such variations in mechanism of promoter search and transcription initiation.
  3. Mazumder, A., Lin, M., Kapanidis, A., Ebright, R.H. (2020). Closing and opening of the RNA polymerase trigger loop. Proc. Natl. Acad. Sci, USA, 2020 Jul 7;117(27):15642-15649. Significance of the work: This work directly shows for the first time that a small structural module called the trigger loop, which lies near the active site of RNAP, closes and opens during each nucleotide addition cycle – and essentially functions as the beating heart of this important enzyme. This work was cited as an article of special significance by Faculty Opinions (previously F1000).
  4. Gilboa, B., Jing, B., Cui, T., Sow, M., Plochowietz, A., Mazumder, A., and Kapanidis, A. N. (2019). Confinement-free wide-field ratiometric tracking of single fluorescent molecules. Biophysical Journal, 117(11):2141-2153.
  5. Duchi, D.*, Mazumder, A.*, Malinen, A.M., Ebright, R.H. and Kapanidis, A.N. (2018) The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. * co-first author; Nucleic Acids Res; 46, 7284-7295. Significance of the work: This work shows for the first time using real-time smFRET that the RNAP clamp is mobile in solution in the millisecond to second timescale and elucidates clamp conformational status in presence of inhibitors and also at different stages of transcription.
  6. Mazumder, A.  and Kapanidis, A. N.  (2019). Recent advances in 70 dependent transcription initiation.   Corresponding author; Journal of Molecular Biology; 431(20):3947-3959. 
  7. Lin, W., Das, K., Degen, D., Mazumder, A., Duchi, D., Wang, D., Ebright, Y.W., Ebright, R.Y., Sineva, E., Gigliotti, M. et al. (2018) Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular Cell, 70, 60-71 e15. Significance of the work: This work establishes the mechanism by which the antibiotic Lipiarmycin functions—by locking the RNAP clamp in an open conformation using high resolution structural data and smFRET measurements.
  8. Roy, K., Mazumder, A., Ghosh, P., Naiya, G., Ghosh, B. and Roy, S. (2018) A peptide-based synthetic transcription factor selectively activates transcription in a mammalian cell. Chem. Commun. (Camb), 54, 1611-1614. Significance of the work: This work demonstrates engineering of a synthetic transcription activator which functions with high specificity in-vivo.
  9. Mazumder, A., Batabyal, S., Mondal, M., Mondol, T., Choudhury, S., Ghosh, R., Chatterjee, T., Bhattacharyya, D., Pal, S.K. and Roy, S. (2017) Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys, 19, 14781-14792. Significance of the work: This work reports the intriguing observation that small variations in the DNA sequence could result in altered dynamic properties at a distal site of a DNA binding protein. Interestingly such different dynamical properties were shown to directly impact functional outcomes.
  10. Chakraborty, A., Mazumder, A., Lin, M., Hasemeyer, A., Xu, Q., Wang, D., Ebright, Y.W. and Ebright, R.H. (2015) Site-specific incorporation of probes into RNA polymerase by unnatural-amino-acid mutagenesis and Staudinger-Bertozzi ligation. Methods Mol Biol, 1276, 101-131. Significance of the work: This work outlines a general strategy and detailed procedures for site-specific but non-disruptive introduction of fluorophores into a large multi subunit protein -- the bacterial RNA polymerase -- using unnatural amino acids and bio-orthogonal reactions.
  11. Batabyal, S., Mondol, T., Choudhury, S., Mazumder, A. and Pal, S.K. (2013) Ultrafast interfacial solvation dynamics in specific protein DNA recognition. Biochimie, 95, 2168-2176.
  12. Roy, S, Ghosh, P., Roy, N.S., Mazumder, A., Roy, K., Manna, A.K., Mallick, S., Ahmed, I. (2013) Peptide based molecules as protein-protein interaction inhibitors: tools for chemical genetics and therapy. Current Chemical Biology Volume 6, 145-163.
  13. Mazumder, A., Bandyopadhyay, S., Dhar, A., Lewis, D.E., Deb, S., Dey, S., Chakrabarti, P. and Roy, S. (2012) A genetic network that balances two outcomes utilizes asymmetric recognition of operator sites. Biophys J, 102, 1580-1589. Significance of the work: This work shows how asymmetry in a bacterial transcription factor influences functioning of a classical genetic circuit.
  14. Mazumder, A.*, Maiti, A.*, Roy, K. and Roy, S. (2012) A synthetic peptide mimic of lambda-Cro shows sequence-specific binding in vitro and in vivo. * co-first author ACS Chem Biol, 7, 1084-1094. Significance of the work: This work reports engineering of a synthetic transcription repressor which was shown to function with specificity in-vitro and in-vivo.
  15. Mondol, T., Batabyal, S., Mazumder, A., Roy, S. and Pal, S.K. (2012) Recognition of different DNA sequences by a DNA-binding protein alters protein dynamics differentially. FEBS Lett, 586, 258-262.

 

MANUSCRIPTS SUBMITTED TO BIORXIV

  1. Kümmerlin, M., Mazumder, A. , Kapanidis, A.N.  (2022) Bleaching-resistant single-molecule fluorescence and FRET monitoring based on fluorophore exchange via transient DNA binding. (BioRxiv).   Corresponding author. Significance of the work: In this work we develop a general method to circumvent photobleaching of fluorescent probes by replenishing fluorescent probes throughout the experiment using transient binding of fluorescently labelled single-stranded DNAs to complementary target DNA strands which are attached to a target molecule.
  2. Andrews, R., Steuer, H., El-Sagheer, A.H., Mazumder, A., El Sayyed, H., Shivalingam, A., Brown, T., Kapanidis, A.N. (2022) Transient DNA binding to gapped DNA substrates links DNA sequence to the single-molecule kinetics of protein-DNA interactions. (BioRxiv). Significance of the work: In this work we introduce a single-molecule imaging method that reads short DNA sequences via transient binding of fluorescent DNA imagers to a single DNA molecule. The assay would help connect kinetics of protein-DNA interactions with DNA sequence at the single molecule level and enable high-throughput functional interrogation of large DNA libraries. 
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