Prof. Manisha Goel's Lab

Our lab research expertise includes Structural Biology, Computational Biology and Bioinformatics. We aim to understand the mechanistics of cellular processes and biological pathways. For exploring these questions, we use various biochemical, biophysical techniques along with in-silico tools. Our current research avenues include:

• Human protein (mis)folding diseases: archaeal proteostasis machinery as the model
• Virulence factors as drug targets: understanding the role of evolutionary divergence
• Prosequences as Intra-molecular chaperones (IMCs): role in protein folding memory
• Literature text mining based hypothesis generation: network creation, to replace manual “literature review”
• Novel biophysical assays for chaperone activity: NTA based methods
• Role of mechanical forces in initiating protein folding: cell free translation systems

1. Supervision of Doctoral Thesis :   4 awarded , 3 ongoing
2. Supervision of MPhil thesis:  3 awarded
3. Mentorship projects:  DSKothari PDF, DST-WoSA, CSIR-SRA, DBT-BioCARE, ICMR-RA, DST-SERB

Research papers published in Refereed/Peer-Reviewed Journals

1. Singhal N, Sharma A, Aswal M, Singh N, Kumar M, Goel M. Identification of binding partners of CsaA – an archaeal chaperonic protein of Picrophilus torridus. Protein Pept Lett. 2020 Nov 26. doi: 10.2174/0929866527999201126205131. Epub ahead of print. PMID: 33243110.
2. Yadav A, Sharma V, Pal J, Gulati P, Goel M, Chandra U, Bansal N, Saha S. DNA replication protein Cdc45 directly interacts with PCNA via its PIP box in Leishmania donovani and the Cdc45 PIP box is essential for cell survival. PLoS Pathog. 2020; 16(5):e1008190. Published 2020 May 15. doi:10.1371/journal.ppat.1008190
3. Singhal N, Sharma A, Kumari S, Garg, A, Rai, R, Singh N, Kumar M, Goel M. Biophysical and Biochemical Characterization of Nascent Polypeptide-Associated Complex of Picrophilus torridus and Elucidation of Its Interacting Partners. Front Microbiol. 2020;11:915. Published 2020 May 26. doi:10.3389/fmicb.2020.00915 PMID: 32528429 
4. Kaushik V, Prasad S, Goel M. Biophysical and biochemical characterization of a thermostable archaeal cyclophilin from Methanobrevibacter ruminantium. Int J Biol Macromol. 2019 Jul 29;139:139-152. doi: 10.1016/j.ijbiomac.2019.07.149. [Epubahead of print] PubMed PMID: 31369788  
5. Rani S, Sharma A, Goel M. (2018) Insights into archaeal chaperone machinery: anetwork-based approach. Cell Stress Chaperones Nov;23(6):1257-1274 
6. Kaushik V, Verma VV, Goel M. (2018) Functional divergence and comparative in-silico study of Cas4 proteins of DUF83 class. J Mol Recognit. 31(5):e2694.  
7. Rani S, A Sharma, Goel M. Navigating the structure-function-evolutionary relationship of CsaA chaperone in archaea. (2018) Critical Reviews in Microbiology, 44(3):274-289. 
8. Kumari S, Pal RK, Gupta R, Goel M. High Resolution X-ray Diffraction Dataset for Bacillus licheniformis Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility. Protein J. 2017 Feb;36(1):7-16. PubMed PMID: 28120227. 
9. Kumar S, Jain KK, Rani S, Bhardwaj KN, Goel M, Kuhad RC. In-Vitro Refolding and Characterization of Recombinant Laccase (CotA) From Bacillus pumilus MK001 and Its Potential for Phenolics Degradation. (2016) Mol Biotechnol. Dec;58(12):789-800. PubMed PMID: 27771851. 
10. Rani S, Srivastava A, Kumar M, Goel M. (2016) CrAgDb–a database of annotated chaperone repertoire in arachaeal genomes. FEMS Microbiol Lett. Mar; 363 (6). 
11. Singh Y, Gupta N, Verma VV, Goel M, Gupta R. (2016) Selective disruption of disulphide bonds lowered activation energy and improved catalytic efficiency in TALipB from Trichosporon asahii MSR54: MD simulations revealed flexible lid and extended substrate binding area in the mutant. Biochem Biophys Res Commun. Mar 25;472(1):223-30. 
12. Verma VV, Gupta R, Goel M. (2015) Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies. Biol Direct. Sep 14;10:49 
13. Ranjan P, Kashyap R.S, Goel M, Veetil S.K, Kateriya S (2014) Cellular organelles facilitate dimerization of a newly identified Arf fromChlamydomonas reinhardtii. J. of Phycology, 50(6), 1137-1145. 
14. Srivastava A, Singhal N, Goel M, Virdi JS, Kumar M (2014) CBMAR: a comprehensive Beta-lactamase molecular annotation resource. Database (Oxford). Doi: 10.1093/database/bau111. Print 2014. 
15. Srivastava A, Singhal N, Goel M, Virdi JS, Kumar M (2014) Identification of family specific fingerprints in β-lactamase families. Scientific World Journal. 2014:980572. ISSN: 2356-6140 (Print) ISSN: 1537-744X 
16. Minakhin, L., Goel M., Berdygulova, Z., Ramanculov, E., Florens, L., Glazko, G., Karamychev, V.N., Slesarev, A.I., Kozyavkin, S.A., Khromov, I., Ackermann, H.W., Washburn, M., Mushegian, A., Severinov, K. (2008) Genome comparison and proteomic characterization of Thermus thermophilus bacteriophages P23-45 and P74-26: siphoviruses with triplex-forming sequences and the longest known tails. J Mol Biol. 378(2):468-80.  
17. Roux, M.M., Radeke, M.J., Goel M., Mushegian, A., Foltz, K.R. (2008) 2DE identification of proteins exhibiting turnover and phosphorylation dynamics during sea urchin egg activation. Dev. Biol. 313(2):630-47. 
18. Savalia, D., Westblade, L., Goel M., Florens, L., Kemp, P., Akulenko, N., Pavlova, O., Ian Molineux, I., Washburn, M., Ackermann, H.W., Mushegian, A., Gabisonia, T., Severinov, K. (2008) Genomic and Proteomic Analysis of Phi32, a Novel Phage of E. coli  J. Mol. Biol. 377(3):774-89. 
19. Sea Urchin Genome Sequencing Consortium; Mushegian, A., Goel M., (2006) The genome of the sea urchin Strongylocentrotus purpuratus. Science. 314(5801):941-52.  
20. Goel M., Mushegian, A. (2006) Intermediary metabolism in sea urchin: the first inferences from the genome sequence. Dev Biol. 300(1):282-92. 
21. Bradham, C.A., Foltz, K.R., Beane, W.S., Arnone, M.I., Rizzo, F., Coffman, J.A., Mushegian, A., Goel M., Morales, J., Geneviere, A.M., Lapraz, F., Robertson, A.J., Kelkar, H., Loza-Coll, M., Townley, I.K., Raisch, M., Roux, M.M., Lepage, T., Gache, C., McClay, D.R., Manning, G. (2006) The sea urchin kinome: a first look. Dev Biol. 300(1):180-93. 
22. Goel M., Damai, R.S., Sethi, D.K., Kaur, K.J., Maiya, B.G., Swamy, M.J. and Salunke D.M. (2005) Crystal Structures of the PNA-Porphyrin Complex in the Presence and Absence of Lactose: Mapping the Conformational Changes on Lactose Binding, Interacting Surfaces, and Supramolecular Aggregations. Biochemistry 44(15):5588-96. 
23. Goel M.*, Krishnan, L.*, Kaur, S., Kaur, K.J. and Salunke, D.M. (2004) Plasticity within the Antigen-Combining Site May Manifest as Molecular Mimicry in the Humoral Immune Response. J Immunol. 173(12):7358-67. (* Equal contribution). 
24. Goel M., Anuradha P., Kaur, K.J., Maiya B.G., Swamy, M.J. and Salunke, D.M. (2004) Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction. Acta Crystallogr D Biol Crystallogr. 60(Pt 2):281-8. 
25. Goel M., Jain, D., Kaur, K.J., Kenoth, R., Maiya, B.G., Swamy, M.J., Salunke, D.M. (2001) Functional equality in the absence of structural similarity: An added dimension to molecular mimicry. J. Biol. Chem  276:39277-39281. 
26. Kaur, K., Jain, D., Goel M. and Salunke, D.M. (2001) Immunological Implications of Structural Mimicry between a Dodecapeptide and a Carbohydrate moiety Vaccine. 19:3124-3130. 
27. Jain, D., Kaur, K., Goel M. and Salunke, D.M. (2000) Structural Basis of Functional   Mimicry between Carbohydrate and Peptide Ligands of ConA. Biochem. Biophys. Res. Commun. 272:843-849

ONGOING:

1. ICMR (Nov 2020 – Oct 2023) The role of prosequences in modulating the structure of proteins. (~ 33 Lakhs)

COMPLETED:

1. DST-SERB: (Mar 2020 – Mar 2023) Characterization of the functional specificity of archaeal Cas4 (CRISPR associated protein 4) proteins for potential applications in genome editing strategies. (~ 50 Lakhs)
2. ICMR (July 2019- June 2022) Accelerating drug discovery path by delineating the structural differences leading to functional divergence in virulence factor proteins found in pathogenic bacteria. (~ 58 lakh)
3. CSIR (July 2018- June 2021) Archaeal FKBPs model systems for understanding their role in protein folding and disease: in-silico analysis and structural characterization (~34 lakh)
4. ICMR (July 2017- June 2020) Exploring the role of HSP70 (DnaK, DnaJ & GrpE) in protein folding diseases: Using archaea as model systems (~ 44 lakh)
5. RGYI (Jun 2012 – Dec 2016)(Rapid grant for Young Investigator) from DBT: Crystallographic structure determination of archaeal CRISPR-CAs proteins
6. UGC (2012-2015): Computational analysis of Cas proteins in Picrophilus torridus in comparison to other thermoacidophiles and mesophiles and their role in driving CRISPR function.
7. ICMR (2012-2015): Comparative genomics of B-lactamase genes including in-silico analysis to identify sequences for B-lactamase inhibitors. (With Dr. JS Virdi, Microbiology & Dr. Manish Kumar, Biophysics).
8. CSIR (2011-2014): Crystal structure determination and functional analysis of Gamma Glutamyl transpeptidase (GGT) from Bacillus Licheniformis ER-15. (With Dr. Rani Gupta, Microbiology).
9. DU-DST (2011-2012): Biodiversity of Environmental Virus Microbiome by Comparative Metagenomics. (With Dr. Rajeev Kaul, Microbiology).