AK

Abhinav Koyamangalath Vadakkepat

Birkbeck, University of London, Indian Institute of Science Bangalore, Maulana Abul Kalam Azad University of Technology, West Bengal, University of Kerala

ORCID iD 0000-0001-8202-7757
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About

I studied Biochemical Engineering at University of Kerala, India and after finishing M. Tech in Biotechnology from Kolkata, moved to MBU, IISc to do PhD with Prof. M. Vijayan in X-ray crystallography and a postdoc with Professor Gabriel Waksman at Birkbeck College, London on cryo-EM.

Prior to my admission for PhD, I worked briefly on studying the extreme pH stress tolerance of Vibrio cholerae in human intestine and design of novel inhibitors for HIV-1 protease as part of my M. Tech and B. Tech project dissertations respectively.

PhD Research (2010-2017):
My PhD research work involved structural and biophysical characterization of lectins which are important in host-pathogen interactions and plant defence. One part involved resolving two specific nuances pertaining to carbohydrate binding to jacalin, a plant lectin using X-ray crystallographic and in-solution experiments. Initial objective was to probe monosaccharide anomeric selectivity, an observation with important implications in HIV therapeutics. This study led to the establishment of sugar distortion as a novel strategy for modulating affinity. This hypothesis was also tested subsequently with higher oligosaccharides leading to a paradigm shift in the field as it challenged the prevailing belief of enthalpic factors predominantly driving protein-carbohydrate affinity. The second unexplored issue was to establish a relationship between nature of the glycosidic linkage and spatial preferences of reducing/non-reducing ends of a disaccharide during lectin binding. This work led to an interesting structural rationale for this preference and a probable mode of binding for complex O-type mucins. The section part of my PhD research involved carrying out exploratory biochemical and structural studies on putative lectins identified using in-sillico scanning from mycobacterial and archeal genomes. These lectins were discovered for the first time in this work and some of these proteins were purified and biophysically characterised. Crystal structure of the first lectin from archeal domain of life, i.e. β-prism I lectin from Methanoccoccus voltae was determined at 2.6 Å. Structural and biochemical characterization of microbial lectins opened up a completely new frontier in glycobiology and subsequent work from the lab have led to multiple publications biochemically validating the in-sillico predictions. I have also contributed to 2 unrelated collaborative projects: 1. Studying ligand-complexes of panthothenate-kinase (PanK) from M. tuberculosis, an important anti-TB drug target and 2. Studying native and ligand bound structures of polyketide synthase (pks3) from Aegle marmelos, implicated in biosynthesis of clinically important polyketide antibiotics, to establish a basis for its wide substrate specificity.

My postdoctoral work involved understanding the architecture of Type-4 secretion systems (T4SSs) implicated in mediating DNA transfer during bacterial conjugation, a process central to dissemination of antibiotic resistance within bacteria. In addition to characterizing E. coli R388 T4SS using single-particle cryo-EM and biophysical methods, I also contributed to understanding T4SS energetics by biochemically characterizing VirB4 ATPase, the largest T4SS protein and purifying a complex of VirB4 with another ATPase VirB11 implicated in pilus biogenesis. The structure of VirB4 ATPase was eventually determined as a trimer of dimers at 3.4 Å by cryo-EM and was shown to contain a novel fold. Coevolution-based strategies used to predict the interface between VirB4 and VirB11 validated by double-pulldown experiments enabled me to model the VirB4 and VirB11 complex. This is the first known example of any hexameric ATPase bound to another hexameric ATPase undertaking substrate translocation. Most importantly, structure of VirB4 allowed us to resolve the correct symmetry of the R388 T4SS, a long-standing issue in the field, eventually leading to the first near-atomic resolution structure of a fully-assembled T4SS from any system. The structure of this 2.8 MegaDalton double membrane spanning macromolecular machine not only elucidates only how various proteins assemble into a T4SS but also illustrates an entirely novel mechanism of pilus biogenesis. I have also recently solved high-resolution structure of a detergent free T4SS from E. coli pKM101 plasmid featuring additional elements which allows us to visualize the pilus biogenesis mechanism in action. Furthermore, I have also purified and solved the high-resolution structure of the E. coli R388 conjugative pilus using helical reconstruction cryo-EM. Structures of T4SSs (R3888 and pKM101) along with the pilus provides a strong framework to design phenotypes which inhibit DNA transfer and trap T4SS intermediates enabling us to address important mechanistic questions pertaining to pilus biogenesis and DNA transfer.

Employment

  • Birkbeck, University of London Postdoctoral Research Assistant
    2017 - 2025

Education

  • Indian Institute of Science Bangalore PhD in Biophysics and Structural Biology (X-ray crystallography)
    2010 - 2017
  • Maulana Abul Kalam Azad University of Technology, West Bengal M. Tech Biotechnology
    2008 - 2010
  • University of Kerala B. Tech Biochemical Engineering
    2004 - 2008

Projects & Funding

Projects & funding information is unavailable.

Publications (12)