Biological and Life Sciences

Professor Balaji Prakash studied Physics at the University of Hyderabad and made a transition to Biology at the Indian Institute of Science, Bangalore, where he obtained his PhD. After a successful postdoctoral stint at the Max-Planck Institute for Molecular Physiology in Germany, he joined the Indian Institute of Technology, Kanpur as one of the founding faculty of the department of Biological Sciences in 2002. In 2015, he relocated to CSIR-Central Food Technological Research Institute, Mysore (CFTRI), to head the newly created interdisciplinary department – the Department of Molecular Nutrition. He joined Ahmedabad University in July 2020 as Professor at Biological and Life Sciences, School of Arts and Sciences.

Professor Prakash was awarded the International Senior Research Fellowship of the Wellcome Trust, UK, in 2004, and the National Bioscience Award (DBT) in 2010. He was elected as a Member of the Guha Research Conference in 2011 and a Fellow of India’s National Academy of Sciences in 2013. Thirteen Ph.D. and seventeen M. Tech students graduated  under his supervision. He successfully obtained a large amount of funding for research from National and International agencies.

Professor Prakash is a structural biologist, fascinated by enzymes, and attempts to understand the catalytic mechanisms that enzymes employ, the rules that govern their evolution, and engineer them for specific applications. Using a combination of bioinformatics, biochemistry and biophysics, a major thrust area in his laboratory has been to understand enzyme catalysis and unravel intriguing structure-function relationships in them with the aim of designing new anti-bacterial molecules.

Besides basic science, his interest in interdisciplinary research led to fascinating applications across disciplines, for example the use of bacteria and yeast for the printing and fabrication of electronic circuits, micro lenses for OLEDs and Braille printing on ordinary paper, and designing / re-engineering antibodies for pharmaceutical companies. More recently, at CFTRI, using rational design approaches, his group developed new anti-microbial peptides that can be used for food preservation.

For more information, please see his  CV

Enzymes fascinate me and employing structural biology, biochemistry and bioinformatics approaches, I attempt to understand the catalytic mechanisms they employ, the rules that govern their evolution, and then engineer them for specific applications. We are also interested in the evolution of enzyme mechanisms across homologues (and also across enzyme families) in different bacteria. This helps us understand how such minute species-specific variations among homologues allow tailoring the function of the enzyme to the given bacteria. We wish to use this knowledge for developing new and safer anti-bacterial molecules. In this regard, the primary interest of my lab is to understand key enzymes involved in bacterial diseases (detailed below) to finally identify potential ‘druggable’ sites in these enzymes, such that specific inhibitors against pathogenic bacteria may be designed.

Structure based approaches for the design of new antibiotics that safeguard the gut microbiome.
Most antibiotics used to contain bacterial infections suffer from two main drawbacks: first they are chemicals that have benefits but also several side-effects; and second, they not only act on disease causing pathogenic bacteria but also destroy the gut bacteria. Most naturally occurring proteins and peptides from plants are considered safer than chemical drugs. During my PhD and later on in my career too, I had worked towards understanding plant proteins: I used this understanding at CFTRI, Mysore, to address the first drawback. Starting from peptides naturally present in food sources, and using principles of Rational design, we created new and safer anti-microbial peptides to contain bacteria (see below “My interest in Inter-disciplinary and translational research”).

Antibiotics destroy gut bacteria too. The loss of gut bacteria, which play a beneficial role, do not re-grow to desired levels post-infection and therefore the compromised health of an individual in the long run. Most probiotics revive gut bacteria, but only partially. Destroying the gut microbiome due to the continued use of antibiotics is known to result in obesity, dysregulated immune response, insulin resistance and other related health outcomes. The current attempts in my lab inquire the possibility of designing antibiotics that specifically target pathogenic bacteria while minimally affecting the gut bacteria.

In the last 17 years, using a combination of bioinformatics, biochemistry and biophysics, a major thrust area in my laboratory has been to develop inhibitors against the target enzymes listed below. To employ structure-based approaches for the design of antibiotics, it is important to understand structure-function relationships in these enzymes, the catalytic mechanisms they employ and the mechanisms governing their regulation. An important insight I gained through my work on these enzymes, concerns the evolution of these mechanisms across homologues and enzyme families, in different bacteria. This led us to understand how such species-specific variations among homologues allow tailoring the function of the enzyme to the given bacteria. We also attempt to identify common rules that govern the evolution of mechanisms across homologues and predict how newer mechanisms may evolve. This knowledge allows us to engineer enzymes for specific applications. Extending the concept of species-specific variations, and using principles of structure-based drug design; I believe it is possible to design new anti-bacterial molecules that selectively inhibit the target enzyme from selected pathogenic bacteria but not its homologue from the gut bacteria. This approach should pave way for safer antibiotics that also safeguard the human microbiome. We are aware this is extremely challenging, but our attempts in this direction are underway.

Towards this, the following target enzymes – GTPases involved in ribosome biogenesis, Rel proteins that allow bacteria to survive stress and GlmU, a Sugar Nucleotidyl transferase (SNT) that participates in Mycolic acid biosynthesis – are being investigated.

Species specific variations in GTPases and the evolution of new GTP hydrolysis mechanisms: One of the first questions our group attempted to answer was how GTPases hydrolyze GTP? In this work, supported by a Wellcome trust fellowship, in 2004, we discovered an atypical subgroup of GTPases and termed them HAS-GTPases or ‘Hydrophobic Amino acid Substituted-GTPases’ (Mishra, et.al. Proteins, 2005). HAS-GTPases are atypical and interesting for the following reasons. These hydrolyze GTP efficiently, despite lacking a catalytic glutamine, which is conserved and important to the function of most signaling GTPases like Ras and Ga proteins. A puzzle, however, is that in classical GTPases like Ras, an analogous mutation of a glutamine to a hydrophobic residue renders it oncogenic. We suggested novel catalytic mechanisms for HAS-GTPases (Mishra et.al. Proteins, 2005) and indeed, diverse novel mechanisms discovered later, concurred with our predictions. Subsequently, we showed that a number of HAS-GTPases bind ribosomal subunits (Anand et al, 2006, and 2010 Tomar et al, 2009, and 2011, Jain et al, 2009, and 2013) and likely participate in its biogenesis: Understanding Ribosome binding GTPases led to us to explore their potential as candidates for designing new antibiotics. These efforts continue in our laboratory.

In addition, the catalytic mechanisms adopted by these enzymes continue to fascinate us. We addressed variations in GTP hydrolysis mechanisms and presented a theory that unifies these variations (Anand et al, 2013, Majumdar, et al, 2017). Interestingly, we deciphered how structural plasticity allows distinct GTP hydrolysis mechanisms to operate in the same GTPase depending on the biological context it has to satisfy. We continue to work on the evolution of GTP hydrolysis mechanisms in different GTPases like FeoB, Era and EngA and identify newer hydrolysis mechanisms that seem to be tailored to the biological context they function for. Exploiting this knowledge, we are examining means to inhibit EngA, which exhibits fascinating nucleotide dependent conformational changes and also has a unique domain organization in the homologues from the bifidobacteria. These bring out interesting possibilities for the design of safer antibiotics, while safeguarding the microbiome.

Species specific variations in Sugar Nucleotidyl transferases (SNTs).  We began working on an anti-bacterial target, GlmU - an enzyme responsible for mycolic acid biosynthesis and important for cell wall formation in bacteria. Towards this, and to obtain a mechanistic understanding of its function, we determined the crystal structures of GlmU and established the catalytic mechanisms for the two reactions - acetyltransfer (Jagtap et al, 2012) and uridyltransfer (Jagtap et al, 2013) - that it catalyzes to make the product UDP-GlcNAc. This led us to generalize the understanding of catalytic mechanisms not only to GlmU homologues but also to the entire family of Sugar Nucleotidyl transferases (SNTs) that it belongs to.

Similar to GTPases, in SNTs too, we understood how subtle differences in active site residues bring about mechanistic variations in nucleotidyltransfer reaction. Resolving a long debate in the field, we showed that this reaction is assisted by two Mg2+ ions. For the first time, using X-ray crystallography, we captured structural snapshots that depict how the product of this reaction (pyrophosphate) exits the active site along a tunnel: One of the active site Mg2+ ions remains coordinated to the product pyrophosphate and facilitates its exit (Vithani et al, 2018; Vithani et al, 2020). Molecular dynamics simulations supported these observations, and suggested that ‘product release’ is likely rate limiting in SNTs. These results establish a new role for Mg2+ in catalysis and propose a general mechanism for product release.  Exploiting the species-specific variations identified in GlmU, we wish to design antibiotics specific to pathogenic GlmU.

Species specific variations in Rel Proteins that mediate bacterial stress response: Rel proteins metabolize a hyperphosphorylated guanine nucleotide (p)ppGpp to aid bacteria overcome unfavorable environmental conditions. We deciphered the mechanism for ppGpp synthesis (unpublished data). We also identified unique sequence motifs that provide distinct regulation in different Rel homologues (Sajish et al, 2007; and 2009) and like with the other targets, this information can be exploited for drug design against Rel proteins. We continue to study structure function relationships in Rel proteins and variations presented by several bacterial homologues, including those from the gut bacteria. More recently, we clarified a long-standing debate in the field and proposed a revised catalytic mechanism for (p)ppGpp synthesis in Rel proteins (Patil, et al. 2020).

My interest is in Inter-disciplinary and translational research.

I enjoy interdisciplinary research that solves a problem using diverse approaches. At BSBE, IIT-Kanpur, working with engineers from Material Science division, we showed a novel use of Microbes for printing and fabrication of electronic circuits, micro lenses for organic light emitting diodes and for Braille printing on ordinary paper (Mehta et al, 2015, 2016a, & 2016b). My expertise in protein engineering also provided me an opportunity to work with Cellerant Pharmaceuticals, USA to design/re-engineer antibodies.

Tailoring natural peptides for safer antibiotics and food preservation.

During my PhD I was initiated to plant proteins and their interesting properties. Plant seeds contain a large number of protease inhibitors of animal, fungal, and bacterial origin. One of the well-studied families of these inhibitors is the Bowman-Birk family (BBI), which have an unusual high thermal stability and can with stand a wide range of pH.

More recently, at CSIR-CFTRI – a food technology institute, I was instrumental in  building a young interdisciplinary department called “Molecular Nutrition’ that researches at the cross roads of modern molecular sciences and the traditional food science. We explored several interesting and challenging problems in this area. Using molecular approaches, our research at CFTRI, has led to the design of specific set of plant based peptides that can be safer than chemical drugs, and can additionally be used as a new technology for food preservation.

Microorganisms are the causative agents for food spoilage and foodborne diseases - the latter are of key concern to public health. The food preservatives which are currently in use have disadvantages - compromised activity, applicability, safety and emergence of resistance. Our efforts at CFTRI, are geared towards translating ideas obtained from basic research towards developing molecules to a) develop safer antibiotics and b) to reduce/prevent food spoilage and thereby extend the shelf life of foods. We combined our understanding of BBIs with structure based rational design approaches for this: By exploiting the high stability of pant BBIs, we tailored them using rational design approaches since they are faster, more accurate and reasonably predictive; and allow development of effective molecules in the least number of design iterations. As against synthesizing 1000s of peptides that a conventional high throughput design would entail, with minimal modifications we were able to tailor the peptide BBIs in just 20 cycles. Most importantly, our design did not incorporate any unnatural amino acid – making these safer for use. The final peptides show a broad spectrum of activity against food borne bacteria, are stable under a wide range of temperature and pH, resistant to serine proteases, biocompatible, short and simple - making them promising for use as safer anti-biotics, as food preservatives and other applications. (See Patents listed under publications).

Patents:

1) Title of the Invention: Microbes based printing for fabrication of electronic circuits.

Invention:        IN-843732 (Open); United States Patent USWO2014/184687 A1. 2014.

Inventors:        Deepak Gupta; Sunita Mehta; Saravanan Murugeson; Balaji Prakash.

2) Title of the Invention: ANTIMICROBIAL PEPTIDE AND ITS USE THEREOF. 

            Inventors: Balaji Prakash, Yashwanth L.V. & Abhishek Acharya .

           Indian Patent Application No. 201711027060 dated July 31, 2017

           International: PCT/IN2017/050419.

Research Publications:

Total publications – 46 [in International Journals : 43; in National Journals: 2, Book Chapters: 1.]
From India as Independent PI: Published 38 [as Corresponding author $ – 28].

Publications.
Total publications – 46 [in International Journals : 43; in National Journals: 2, Book Chapters: 1.]
From India as independent PI: Published 38 [as Corresponding author $ – 28]. 

1. Pratik Rajendra Patil, Neha Vithani, Virender Singh, Ashok Kumar and Balaji Prakash$. A revised mechanism for (p)ppGpp synthesis by Rel proteins: The critical role of the 2’-OH of GTP. Journal of Biological Chemistry (2020) (In press). Article chosen as “Editor’s Choice”.  [International Peer reviewed – American Society for Biochemistry and Molecular Biology, IF – 4.01]. https://pubmed.ncbi.nlm.nih.gov/32719004/
2. Neha Vithani, Balaji Prakash$ and Nisanth N. Nair$. Mechanism of Nucleotidyltransfer Reaction and Role of Mg2+ ion in Sugar Nucleotidyltransferases. Biophysical Journal. (2020) 119, 619–627. [International Peer reviewed – Biophysical society and Molecular, IF – 3.66]. https://www.cell.com/biophysj/fulltext/S0006-3495(20)30493-8
3. Vaibhav Bias, Pooja Aggarwal, Prashant Bharadwaj, and Balaji Prakash$. Classification, characterization and structural analysis of sugar nucleotidylyltransferase family of enzymes. Biochem Biophys Res Commun. (2020) 525(3):780-785. [International Peer reviewed – FEBs Press, IF – 2.7]. https://www.sciencedirect.com/science/article/abs/pii/S0006291X2030437X
4. Vaibhav Bias, Sahil Batra, and Balaji Prakash$. Identification of two highly promiscuous thermostable sugar nucleotidylyltransferases for glycorandomization. FEBS. J. (2018) 285, 2840-2855. [International Peer reviewed – FEBs Press, IF – 4.74].  https://www.ncbi.nlm.nih.gov/pubmed/29806742
5. Yashavanth L.V*, Abhishek Acharya*, Balaji Prakash$. Structural basis of non?canonical polyphenol oxidase activity in DLL?II ? a lectin from Dolichos lablab. Biotech and Appl. Biochem. (2018) DOI: 10.1002/bab.1653. [International Peer reviewed – Wiley, IF – 1.5]. https://www.ncbi.nlm.nih.gov/pubmed/29572945
6. Neha Vithani, Pravin Kumar Ankush Jagtap, Sunil Kumar Verma, Ravi Tripathi, Shalini Awasthi, Nisanth N. Nair$ and Balaji Prakash$. Mechanism of Mg2+-accompanied product release in sugar nucleotidyltransferases. Structure (2018). 26, 459-66.e3. [International Peer reviewed – Cell press, IF – 5.0]. https://www.ncbi.nlm.nih.gov/pubmed/29514078
7. Yashavanth L. Vishweshwaraiah, Balaji Prakash and Lalitha R. Gowda$. Expression profiling of the Dolichos lablab lectin during germination and development of the seed. Plant Physiology and Biochemistry. (2018). 124, 10-19. [International Peer reviewed – Elsevier, IF – 3.1]. https://www.ncbi.nlm.nih.gov/pubmed/29324242
8. Soneya Majumdar, Abhishek Acharya and Balaji Prakash$. Structural Plasticity mediates distinct GAP-dependent GTP hydrolysis mechanisms in Rab33 and Rab5. FEBS. J. (2017) 284, 4358-4375. [International Peer reviewed – FEBs Press, IF – 4.74]. https://www.ncbi.nlm.nih.gov/pubmed/29095572
9. Vaibhav Singh Bais, Balaram Mohapatra, Nadim Ahamad, Sanjana Boggaram, Sandeep Verma$ and Balaji Prakash$. Investigating the Inhibitory Potential of 2-Aminopurine Metal Complexes Against Serine/Threonine Protein Kinases from Mycobacterium Tuberculosis. Tuberculosis (2018) 108, 47-55.  [International Peer reviewed – Elsevier, IF – 2.8]. https://www.ncbi.nlm.nih.gov/pubmed/29523327
10. Neha Vithani, Sahil Batra, Balaji Prakash$ and Nisanth Nair$. Elucidating the GTP Hydrolysis Mechanism in FeoB – a Hydrophobic Amino Acid substituted GTPase. ACS Catalysis (2017), 7, 902−906. [International Peer reviewed – American Chemical Society, IF – 12.22]. https://pubs.acs.org/doi/abs/10.1021/acscatal.6b03365
11. Soneya Majumdar, Abhishek Acharya, Sushil Kumar Tomar and Balaji Prakash$. Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions. Biochimica et Biophysica Acta  - (Proteins and Proteomics) (2017) 1865, 289–303. [International Peer reviewed – Elsevier, IF – 2.54]. https://www.ncbi.nlm.nih.gov/pubmed/27979707
12. Sunita Mehta, Saravanan Murugeson, Balaji Prakash, Deepak$. Microbes based printing for fabrication of microlenses for organic light emitting diodes. Organic Electronics (2016) 35: 199-207. [International Peer reviewed – Elsevier, IF – 3.5]. https://www.sciencedirect.com/science/article/pii/S1566119916302191
13. Sunita Mehta, Saravanan Murugeson, Balaji Prakash, Deepak$. Development of process for generating three dimensional microbial patterns amenable for engineering use. RSC Advances (2016), 6: 22586-22593. [International Peer reviewed – Royal Soc. Chemistry, IF – 3.05]. https://pubs.rsc.org/en/content/articlelanding/2016/ra/c5ra26863j#!divAbstract
14. Sunita Mehta, Saravanan Murugeson, Balaji Prakash, Deepak$.  Fabrication of three dimensional patterns of wide dimensional range using microbes and their applications. Scientific Reports. (2015). 5:15416. doi: 10.1038/srep15416. [International Peer reviewed – Nature press, IF – 4.53]. https://www.nature.com/articles/srep15416
15. Vinod Kumar, Saravanan Murugeson, Neha Vithani, Balaji Prakash and Lalitha R Gowda$. A salt-bridge stabilized C-terminal hook is critical for the dimerization of a Bowman Birk inhibitor. Archives of Biochemistry and Biophysics. (2015) 566:15-25. [International Peer reviewed – Elsevier, IF – 3.02]. https://www.ncbi.nlm.nih.gov/pubmed/25527163
16. Neha Vithani, Vaibhav Bais and Balaji Prakash$. GlmU (N-acetylglucosamine-1 phosphate uridyltransferase) bound to three magnesium ions and ATP at the active site. Acta Cryst. F (2014) 70, doi:10.1107/S2053230X14008279. [International Peer reviewed – International Union of Crystallography, IF – 1.19]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051520/
17. Shiv Singh, Vaibhav Bais, Balaji Prakash and Nishith Verma$. Multi-scale carbon micro/nanofibers-based adsorbents for protein-immobilization. Materials Science and Engineering C (2014) 38, 46-54. [International Peer reviewed – Elsevier, IF – 5.08]. https://www.sciencedirect.com/science/article/pii/S0928493114000502
18. Nikhil Jain, Neha Vithani, Abu Rafay and Balaji Prakash$. Identification and characterization of a hitherto unknown nucleotide binding domain and an intricate inter-domain regulation in HflX, a ribosome binding GTPase. Nucleic Acids Research (2013) 41, 9557-69. [International Peer reviewed – Oxford University Press, IF – 11.15]  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814362/
19. Pravin Kumar Ankush Jagtap, Sunil Kumar Verma, Neha Vithani, Vaibhav Bais and Balaji Prakash$. Crystal structures identify an atypical two-metal ion mechanism for uridyl transfer in GlmU: Its significance to sugar nucleotidyltransferases. Journal of Molecular Biology. (2013), 425, 1745 -1759.[International Peer reviewed – Elsevier, IF – 4.9]. https://www.sciencedirect.com/science/article/pii/S0022283613001216
20. Anand Baskaran, Soneya Majumdar and Balaji Prakash$. The Structural Basis Unifying Diverse GTP Hydrolysis Mechanisms. Biochemistry (2013) 52,1122-30. [International Peer reviewed – American Chemical Society, IF – 2.94]. https://pubs.acs.org/doi/abs/10.1021/bi3014054
21. Megha Gulati, Nikhil Jain, Baskaran Anand, Balaji Prakash and Robert Britton. Mutational analysis of the ribosome assembly GTPase RbgA provides insight into ribosome interaction and ribosome stimulated GTPase activation. Nucleic Acids Research (2013), 41, 3217–3227.[International Peer reviewed – Oxford University Press, IF – 11.15]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3597669/
22. Pravin Kumar Ankush Jagtap, Vijay Soni, Neha Vithani, Gagan Deep Jhingan, Vaibhav Singh Bais, Vinay Kumar Nandicoori$, and Balaji Prakash$. Substrate bound crystal structures reveal features unique to Mycobacterium tuberculosis N-acetyl-glucosamine-1-phosphate uridyltransferase and a catalytic mechanism for acetyltransfer. Journal of Biological chemistry (2012) 287, 39524-37. [International Peer reviewed – American Society for Biochemistry and Molecular Biology, IF – 4.01]. http://www.jbc.org/content/early/2012/09/11/jbc.M112.390765.full.pdf
23. Abu Rafay, Soneya Majumdar, and Balaji Prakash$. Exploring potassium-dependent GTP hydrolysis in TEES family GTPases. FEBS Open Bio (2012) 2, 173-177. [International Peer reviewed – Elsevier, IF-2.10]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3642159/
24. Sushil Kumar Tomar, Prashant Kumar, Soneya Majumdar, Varun Bhaskar, Prasun Dutta and Balaji Prakash$.  Extended C-terminus and length of the linker connecting the G-domains arespecies-specific variations in the EngA family of GTPases. FEBS Open Bio  (2012) 2, 191–195. [International Peer reviewed – Elsevier, IF – 2.10]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3642160/
25. Sushil Kumar Tomar, Prashant Kumar, Balaji Prakash$. Deciphering the catalytic machinery in a universally conserved ribosome binding ATPase YchF. Biochem. Biophys. Res. Commun. (2011), 408, 459–464. [International Peer reviewed – Elsevier, IF – 2.56]. https://www.sciencedirect.com/science/article/pii/S0006291X11006371
26. Ashish Arora ,Nagasuma R. Chandra , Amit Das , Balasubramanian Gopal , Shekhar C. Mande, Balaji Prakash, Ravishankar Ramachandran, Rajan Sankaranarayanan, K. Sekar, Kaza Suguna, Anil K. Tyagi, Mamannamana Vijayan. Structural biology of Mycobacterium tuberculosis proteins: The Indian efforts, Tuberculosis (2011), 91, 456-68. [International Peer reviewed – Elsevier, IF – 2.8]. https://www.sciencedirect.com/science/article/abs/pii/S1472979211000606
27. Baskaran Anand, Parag Surana and Balaji Prakash$. Deciphering the Catalytic Machinery in 30S Ribosome Assembly GTPase YqeH. PloS ONE (2010), 5(4): e9944. doi:10.1371/journal.pone.0009944. [International Peer reviewed – Public Library of Science, IF 2.78]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848588/
28. Divya Tiwari, Rajnish Kumar Singh, Kasturi Goswami, Sunil Kumar Verma, Balaji Prakash and Vinay Kumar Nandicoori$. The N-terminal region of protein kinase G from Mycobacterium tuberculosis plays a regulatory role in modulating kinase activity and survival in the host macrophages. Journal of Biological Chemistry (2009) 284, 27467-79.[International Peer reviewed – American Society for Biochemistry and Molecular Biology, IF – 4.01]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785676/
29. Baskaran Anand, Parag Surana, Sagar Bhogaraju, Sushmita Pahari and Balaji Prakash$. Circularly permuted GTPaseYqeH binds 30S ribosomal subunit: Implications for its role in ribosome assembly. Biochem. Biophys. Res. Commun. (2009), 386, 602–606. [International Peer reviewed – Elsevier, IF – 2.56]. https://www.sciencedirect.com/science/article/pii/S0006291X09012194
30. Sunil Kumar Verma, Mamta Jaiswal, Neeraj Kumar, Amit Parikh, Vinay Kumar Nandicoori, Balaji Prakash$. Crystal structure of N-acetylglucosamine-1-phosphate uridyltransferase (GlmU) from Mycobacterium tuberculosis in a cubic space group. Acta Cryst. F. (2009), 65: 435–439. [International Peer reviewed – International Union of Crystallography, IF – 1.19]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675579/
31. Sushil Kumar Tomar, Neha Dhimole, Moon Chatterji and Balaji Prakash$. Distinct GTP/GDP bound states of the tandem G-domains of Escherichia Coli EngA regulate ribosome binding.  Nucleic Acids Research (2009) 37(7):2359-70. [International Peer reviewed – Oxford University Press, IF – 11.15]. https://academic.oup.com/nar/article/37/7/2359/1020977
32. Mathew Sajish, Sissy Kalayil, Sunil Kumar Verma, Vinay Kumar Nandicoori$ and Balaji Prakash$. The Significance of ExDD and RxKD Motifs Conservation in Rel Proteins. Journal of Biological Chemistry (2009), 284, 9115-9123. [International Peer reviewed – American Society for Biochemistry and Molecular Biology, IF – 4.01]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666561/
33. Nikhil Jain, Neha Dhimole, Abu Rafay Khan, Debojyoti De, Sushil Kumar, Tomar, Mathew Sajish, DipakDutta, PradeepParrack and Balaji Prakash$. E.coliHflX interacts with 50S ribosomal subunits in presence of nucleotides. Biochem. Biophys. Res. Commun. (2009), 379, 201-5. [International Peer reviewed – Elsevier, IF – 2.56]. https://www.sciencedirect.com/science/article/pii/S0006291X08024054
34. Amit Parikh*, Sunil Kumar Verma*, Shazia Khan, Balaji Prakash$ & Vinay Kumar Nandicoori$. PknB mediated phosphorylation of a novel substrate, N-acetylglucosamine-1-phosphate uridyltransferase (GlmU), modulates its acetyltransferase activity. Journal of Molecular Biology. (2009), 386, 451-64. [International Peer reviewed – Elsevier, IF – 4.9]. https://www.sciencedirect.com/science/article/pii/S0022283608015337
35. Mathew Sajish, Divya Tiwari, Dimple Rananaware, Vinay Kumar Nandicoori$ and Balaji Prakash$. A Charge Reversal Differentiates (p)ppGpp Synthesis by Monofunctional and BifunctionalRel Proteins. Journal of Biological Chemistry. (2007) 282, 34977-34983. [International Peer reviewed – American Society for Biochemistry and Molecular Biology, IF – 4.01]. http://www.jbc.org/content/282/48/34977.full
36. Baskaran Anand, Sunil Kumar Verma, Balaji Prakash$. Structural stabilization of GTP-binding domains incircularly permuted GTPases: Implications for RNA binding. Nucleic Acids Research. (2006) 34, 2196-2205. [International Peer reviewed – Oxford University Press, IF – 11.15].  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1450330/
37. Rajeev Mishra, Sudheer Kumar Gara, Shambhavi Mishra, Balaji Prakash$. Analysis of GTPases carrying hydrophobic amino acid substitutions in lieu of the catalytic glutamine: Implications for GTP hydrolysis. Proteins: Structure, Function, and Bioinformatics (2005) 59, 332-338. [International Peer reviewed – Wiley, IF – 2.5] https://onlinelibrary.wiley.com/doi/full/10.1002/prot.20413. 

From Post-Doctoral and Doctoral Work: 8

1. Gerrit.J.K.Praefcke, Stephen Kloep, Utz Benscheid, Hanke Lilie, Balaji Prakash and Christian Herrmann. Identification of Residues in the Human Guanylate-binding Protein 1 Critical for Nucleotide Binding and Cooperative GTP Hydrolysis. J. Mol. Biol. (2004) 344, 257-269. [International Peer reviewed – Elsevier, IF – 4.89]. https://www.sciencedirect.com/science/article/pii/S0022283604011684
2. Balaji Prakash*, Holger Rehmann*, Eva Wolf*, Alma Rueppel, Johan de Rooij, Johannes. L. Bos& Alfred Wittinghofer$.  Structure and Regulation of the cAMP binding domains of Epac2. Nature. Struct. Mol. Biol.(2003)10, 26-32. Cover Article (* refers to equal contributors) [International Peer reviewed – Nature press, IF – 12.595]. https://www.nature.com/articles/nsb878
3. Balaji Prakash*, Louis Renault*, Gerrit.J.K.Praefcke, Christian Herrmann$ & Alfred  Wittinghofer$. Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism.  EMBO Journal (2000), 19, 4555-4564. [International Peer reviewed – EMBO press, IF – 9.79 ]. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC302049/
4. Balaji Prakash, Gerrit. J.K.Praefcke, Louis Renault, Alfred Wittinghofer$ & Christian Herrmann$. Structure of human Guanylate-binding protein-1 representing a class of GTP-binding proteins with unique properties.  Nature (2000), 403, 567-571. [International Peer reviewed – Nature press, IF – 41.57]. https://www.nature.com/articles/35000617
5. Balaji Prakash, M.R.N. Murthy, Y. N. Sreerama, D .Rajagopal Rao & Lalitha R Gowda$. Studies on simultaneous inhibition of trypsin and chymotrypsin by horsegram Bowman-Birk  inhibitor.  Journal of Biosciences (1997), 22(5), 545-554. [National Peer reviewed – Indian Academy of Sciences, IF – 1.42]. https://link.springer.com/article/10.1007%2FBF02703392
6. Balaji Prakash & M.R.N.Murthy. Source and target enzyme signature in serine protease inhibitor active site sequences.   Journal of Biosciences (1997), 22(5), 555 -556. [National Peer reviewed – Indian Academy of Sciences, IF – 1.42]. https://www.ias.ac.in/article/fulltext/jbsc/022/05/0555-0565
7. Balaji Prakash, S.Selvaraj, M.R.N.Murthy, Y.N.Sreerama, D. Rajagopal Rao & L.R.Gowda. Analysis of amino acid sequences of Plant Bowman-Birk Inhibitors. Journal of Molecular Evolution. (1996) 42, 560-569. .[International Peer reviewed – Springer, IF – 1.96]. https://link.springer.com/article/10.1007/BF02352286
8. Balaji Prakash, M.R.N.Murthy, Y.N.Sreerama, P.R.Rama Sarma & D.Rajagopala Rao. Crystallization and preliminary X-ray diffraction studies on a Trypsin/Chymotrypsin double headed inhibitor from horse gram seeds. Journal of Molecular Biology. (1994) 235, 364-366.  [International Peer reviewed – Elsevier, IF – 4.89]. https://www.sciencedirect.com/science/article/pii/S0022283605800415

Book Chapters.

1. Neha Vithani and Balaji Prakash$. GlmU from Mycobacterium tuberculosis – Structure, function and the role of metal ions in catalysis. Encyclopedia of Inorganic and Bioinorganic Chemistry. (2015). [International Peer reviewed – Wiley]. http://onlinelibrary.wiley.com/doi/10.1002/9781119951438.eibc2327/abstract

(Note - * refers to equal contributors, $ to co- corresponding authors).

At Ahmedabad University I will be teaching Biochemistry for 3rd Semester IMSc students and teach foundation Courses.

In the past I have taught several courses at IIT Kanpur (2002-2014) and CSIR-CFTRI, Mysore (2015-2020).

• Member of the Editorial Board, Nature Scientific Reports.
• 2019 – Member, Task force, DBT-North east region TEC, DBT, India
• 2019 – Member, Task force, DBT-North east region STAG, DBT, India
• 2019 – Member, Task force, Modern Biology, DBT, India
• Member, Protein Society.
• Member, Society of Biological Chemists.
• Member, International Union of Crystallography.
• Reviewer for manuscripts for reputed international Journals –  PNAS, Proteins, PloS ONE, FEBS Letters, GENE, Biopolymers etc.
• Reviewer for Ph.D. thesis from various institutions in the country.
• Reviewer for Project proposals from DST and DBT.

• 2004 - International Senior Research Fellow for Biomedical Science award by the Wellcome Trust, U.K. in 2004.
• 2010 - DBT National Bioscience Award for the year 2009.
• 2011 – Elected Member, Guha Research Conference (GRC), India.
• 2013 – F.N.A.Sc., Fellow of the National Academy of Sciences, Allahabad, India.

Grants:

International Funding

National