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"...the more we know, the more we feel our ignorance; the more we feel how much remains unknown....."

- Sir Humphrey Davy -

Major Techniques Used

Cryo electron microscopy:

The journal Nature called it the “research method of the year” in 2015. 

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The CryoEM Facility at CSIR-IICB (CIF- Central Instrumentation Facility):

The Facility hosts a state-of-the-art Tecnai G2 POLARA cryo-electron microscope (300 KV, field emission gun) equipped with an 4k x 4k FEI Eagle camera that allows efficient collection of high-resolution structural data. The facility also includes dedicated freezing instrument (Vitrobot Mark IV) to make cryo-grids, glow discharge (TEDPELLA INC PELCO easiGlow) and carbon coater (Quorum Technologies Ltd Q150TE).

Major Projects

Protein biogenesis on the ribosome:

Ribosome not only serves as a platform for protein synthesis but also ribosomal tunnel exit site acts as a podium for co-translational maturation of the nascent polypeptide chains that include N-terminal enzymatic processing where two proteolytic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP) are involved.  The emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor (TF).  Limited structural studies related to the nascent chain interacting proteins in bacterial systems have been reported.  We want to explore the interplay among the proteins and ribosome.

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J Mol Biol. 2019 Mar 29;431(7):1426-1439. doi: 10.1016/j.jmb.2019.02.002. Epub 2019 Feb 10.

Synthesis of proteins by decoding messenger RNA (mRNA) is a dynamic process and is carried out by the molecular machine ribosome in all living organisms. Bacterial ribosome-related processes are prominent targets of antimicrobial drugs. Interestingly, there is growing evidence that, beyond the canonical translation factors, a plethora of additional non-ribosomal factors (believed to function as regulatory factors) interact with the ribosome particularly under various stress conditions.  However, the understanding of functions and molecular mechanisms of many of these regulatory proteins has remained limited, despite their biological importance.  We aim at characterizing interactions of ribosome-associated, yet-unknown factors with the ribosome using cryo-electron microscopy (cryo-EM).

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Sci Rep. 2016 Jan 29;6:19936. doi: 10.1038/srep19936.

Besides the well-characterized GTPases that have critical roles in the translation cycle, another class of GTPases is now implicated in ribosome function (RA-GTPases).   These proteins interact with either the large or the small subunit of the ribosome, largely in a nucleotide specific manner.  HflX is one such conserved, Obg family GTPases.  Intriguingly, several studies proved that E. coli HflX binds and hydrolyzes both GTP and adenosine triphosphate (ATP).  Recent studies have demonstrated its crucial role during heat stress.  Goal of one of the lab projects is to elucidate mechanisms of action of HflX on 70S ribosome and ribosomal subunits (50S and 30S) during heat stress.

Interaction of heat stress-related protein HflX with the bacterial ribosome:

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J Cell Biol. 2018 Jul 2;217(7):2519-2529. doi: 10.1083/jcb.201711131. Epub 2018 Jun 21.

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Apart from its role in translation, intrinsic role of ribosome in protein folding had been an interesting topic of research for a long time.  Ribosome-mediated protein folding has been studied in prokaryotic system in great detail but in case of eukaryotic system it still needs to be studied to illuminate the process in more details. One of our ribosome-related research interests is to understand eukaryotic ribosome-mediated protein folding aspect from the structural view-point. Our study already revealed the mechanistic insight of reactivation of protein from denatured and molten-globule state by eukaryotic ribosome and subsequent disassembly of the ribosomal subunits. Our focus further extends towards understanding role of possible protein factors in ribosome mediated protein folding.

Ribosome-assisted protein folding:

PLoS One. 2016 Apr 21;11(4):e0153928. doi: 10.1371/journal.pone.0153928. eCollection 2016.

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​Biochem Biophys Res Commun. 2016 Jan 22;469(4):923-9. doi: 10.1016/j.bbrc.2015.12.107. Epub 2015 Dec 24.

Serotonin (5-HT) receptors are one of the major classes of G-protein coupled receptor (GPCR) family which play a crucial role in neuromodulation. Dysfunctional serotonin receptors are implicated in many psychiatric and mental disorders and hence are the primary targets for a large number of antipsychotic drugs. Since, the membrane proteins are highly dynamic in nature; exploration of their structure is highly interesting. However expression and purification of full-length GPCR in its native form is highly challenging. High-resolution structural investigation of ligand bound GPCRs may provide a novel insight into GPCRs signaling pathway which subsequently will lead to drug development against several neurological disorders. Therefore, our lab aim to optimize the expression and purification of serotonin GPCRs for structural studies using Cryo-EM.

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Investigating the structure and dynamics of Serotonin GPCRs:

Biopolymers. 2019 Aug 30:e23329. doi: 10.1002/bip.23329. [Epub ahead of print]

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Development of inhibitors targeting fibrillation involved in neuro-degenerative diseases:

Protein aggregation is associated with various neurodegenerative diseases as Alzheimer’s, characterized by amyloid beta plaque formation in brain. Amyloid beta also forms resistant co-aggregates with fibrinogen which is pertinent with cerebral amyloid angiopathy. The project aims at  identifying small peptide based anti-amyloid therapies.

Unraveling conformational reorganizations of different domains of p300 and p53 upon complex formation:

Disruption of the appropriate regulation pattern of gene expression has a great impact on cellular function and responsible for many diseases. Transcription is considered as one of the most important regulatory cellular processes that directly controls the gene expression.  Previously, pre-initiation and initiation were believed as the most crucial steps of transcription from the regulatory point of view, but growing evidence shows that elongation is also a dynamic and highly regulated step of transcription cycle and capable of coordinating downstream events. Tumor suppressor p53 is a stress-induced transcription factor that can regulate both transcription initiation and elongation at different RNA Pol II-transcribed genes. Interaction of p53 with its coactivator p300 is central to the transactivation activity of p53 and that interaction in turn paves the way for beginning of various important cellular pathways.  Our recent studies show the full-length cryo-EM structure of histone acetyltransferase (HAT) p300 in unbound condition and in complex with the conventional tumor suppressor p53.  Comparison of these two structures elucidates the changes in the domain organizations of p300 upon activation by its nonhistone substrate p53 and also helps to propose a possible mechanism of activation of p300 by means of p53.

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Biochemistry. 2019 Aug 13;58(32):3434-3443. doi: 10.1021/acs.biochem.9b00333. Epub 2019 Jul 31.

Stabilizing bio-active forms of the proteins involved in metabolic diseases:

Structural & functional Studies on Diabetes associated proteins-human insulin and islet amyloid polypeptide(hIAPP). Effect of natural polyphenolic compounds on insulin & hIAPP fibrillation and finding potent non toxic excipient for the long term stability of commercially formulated insulin. Structural analysis of insulin & hIAPP oligomers using Cryo-Electron micrographs.

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