Faculty & Staff
Contact
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Email
deepeshn.bt.ls@msruas.ac.in
- Phone deepeshn.bt.ls@msruas.ac.in
- Websites
Dr. Deepesh Nagarajan
Assistant Professor
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School/College
Faculty of Life and Allied Health Sciences
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Department
Department of Biotechnology
Dr. Deepesh Nagarajan is an Assistant Professor in the Department of Biotechnology at the M.S. Ramaiah University of Applied Sciences. He completed a Bachelor of Science from St. Xavier’s College (Mumbai), followed by an integrated PhD in Biochemistry from Indian Institute of Science (IISc) (2010–2017). He served as a research associate at IISc before completing a postdoctoral fellowship at the University of Washington’s Baker Lab (2019–2022).
His recent contributions include being part of an international team at the University of Washington's Baker Lab that computationally designed versatile, self-assembling proteins capable of forming various 2D and 3D shapes, an architectural approach published in Nature. Additionally, his team discovered "peptidomelanin," a metal-chelating biomolecule found in fungi with potential applications in environmental remediation and metal extraction, the findings of which were published in ACS Omega. His older work extends to the design of antimicrobial peptides to combat multidrug-resistant bacteria.
Qualifications
- PhD in Biochemistry
Indian Institute of Science (Bangalore) , 2018
- MSc in Biology
Indian Institute of Science (Bangalore) , 2012
- BSc Microbiology
St. Xaviers College (Mumbai) , 2010
Experience
Total Years of Experience
7 Years
Academic Experience
- 1 year as a Research Associate (2018–2019) in Prof. Nagasuma Chandra’s lab, IISc.
- 3 years as a Postdoctoral Fellow (2019–2022) in the Baker Lab, University of Washington, Seattle.
- 3 years as an Assistant Professor at BT/FLAHS/MSRUAS.
- Antibiotics and their mechanisms of action (Springer, 2024 edition) Edited by Dr. Deepesh Nagarajan
National Conference Papers
- Deepesh Nagarajan, Nagasuma Chandra. PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding sites. 2013 National Conference on Parallel Computing Technologies (PARCOMPTECH), 1 6
International Journal Papers
- Deepesh Nagarajan, Natasha Roy, Omkar Kulkarni, Neha Nanajkar, Akshay Datey, Sathyabaarathi Ravichandran, Chandrani Thakur, Indumathi V Aprameya, Siddhartha P Sarma, Dipshikha Chakravortty, Nagasuma Chandra. Ω76: A designed antimicrobial peptide to combat carbapenem and tigecycline resistant Acinetobacter baumannii. Science Advances (2019) 5(7), eaax1946.
- Huddy, Timothy F., Yang Hsia, Ryan D. Kibler, Jinwei Xu, Neville Bethel, Deepesh Nagarajan, Rachel Redler et al. Blueprinting extendable nanomaterials with standardized protein blocks. Nature (2024) 627(8005), 898–904.
- Alexis Courbet, Jesse Hansen, Yang Hsia, Neville Bethel, Young Jun Park, Chunfu Xu, Adam Moyer, Scott Boyken, George Ueda, Una Nattermann, Deepesh Nagarajan, Daniel Adriano Silva, William Sheffler, Joel Quispe, Neil King, Philip Bradley, David Veesler, Justin Kollman, David Baker, Ashley Nord. Computational design of mechanically coupled axle–rotor protein assemblies. Science (2022) 376(6591), 383–390.
- Rakshita Sukruth Kolipakala, Suranjana Basu, Senjuti Sarkar, Beneta Merin Biju, Daniela Salazar, Likhit Reddy, Pushya Pradeep, Muniraj Krishnaveni Yuvapriya, Shrijita Nath, Riley Gall, Anish Hemanth Samprathi, Harshitha Balaji, Eeshaan AB Koundinya, Aparna Shetye, Deepesh Nagarajan. Fungal Peptidomelanin: A Novel Biopolymer for the Chelation of Heavy Metals. ACS Omega (2024) 9(34), 36353–36370.
- Srivatsan S., Pramanik S., Pradeep P., Sarkar S., Chandrappa S.P., Gall R., et al., Nagarajan D. A broad-spectrum copper oxidase synthesizes fungal peptidomelanin. ACS Omega (2025).
- Pushya Pradeep, Rakshita Sukruth Kolipakala, Deepesh Nagarajan. The genome of Aspergillus niger strain melanoliber. Microbiology Resource Announcements (2025) 14(3), e00809-24.
- SM L., Pradeep P., Nagarajan D., KN H., MY S., Gurikar C. The whole-genome sequence of the halotolerant nitrogen-fixing bacterium Azotobacter salinestris strain AZT-41. Microbiology Resource Announcements (2025), e00695-25.
- Rampur S., VK M.K., Pelli P.R., Sarkar S., Pramanik S., Majumder U., et al., Nagarajan D. The distribution of groundwater uranium in Chintamani village, Karnataka, India. F1000Research (2025) 14, 321.
- Jayakumar Pallavi, Harshita Snehal, Rakshita Sukruth Kolipakala, Daniela Salazar, Mrunal Hanbar, Larina Bejoy Chiramel, Khushi Alok Jha, Sai Bhumica Lakshmi Venkatesh, Tanishka Dayanand Shetty, Navya Madhusudan, Amrutha Mohan, Amulia John, Naomi Deep D’souza, Priyanka Sheet, Deepesh Nagarajan. A complete morphological characterization of all life stages of the phorid fly Megaselia scalaris. Scientific Reports (2023) 13:22933.
- Srivarshini Ganesan, Nidhi Mittal, Akash Bhat, Rachana S. Adiga, Ananthakrishnan Ganesan, Deepesh Nagarajan, Raghavan Varadarajan. Improved prediction of stabilizing mutations in proteins by incorporation of mutational effects on ligand binding. Proteins: Structure, Function, and Bioinformatics (2024) 0:1–12.
- Deepesh Nagarajan, Tushar Nagarajan, Natasha Roy, Omkar Kulkarni, Sathyabaarathi Ravichandran, Madhulika Mishra, Dipshikha Chakravortty, Nagasuma Chandra. Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates. Journal of Biological Chemistry (2018) 293(10), 3492–3509.
- Deepesh Nagarajan, Sujeesh Sukumaran, Geeta Deka, Kiran Krishnamurthy, Hanudatta S. Atreya, Nagasuma Chandra. Design of a heme binding peptide motif adopting a β-hairpin conformation. Journal of Biological Chemistry (2018) 293(24), 9412–9422.
- Deepesh Nagarajan, Geeta Deka, Megha Rao. Design of symmetric TIM barrel proteins from first principles. BMC Biochemistry (2015) 16(1), 1–22.
- Deepesh Nagarajan, Tushar Nagarajan, Neha Nanajkar, Nagasuma Chandra. A uniform in vitro efficacy dataset to guide antimicrobial peptide design. Data (2019) 4(1), 27.
- Neha Nanajkar, Lekhana S. Mruthyunjaya, Deepesh Nagarajan. A Simple Radioassay to Detect Nanoscale Membrane Disruption. Methods and Protocols (2023) 6(2), 23.
- Sumith Kumar, Bipul C. Karmakar, Deepesh Nagarajan, Asish K. Mukhopadhyay, Richard D. Morgan, Desirazu N. Rao. N4-cytosine DNA methylation regulates transcription and pathogenesis in Helicobacter pylori. Nucleic Acids Research (2018) 46(7), 3429–3445.
- Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma Chandra. ABS–Scan: In silico alanine scanning mutagenesis for binding site residues. F1000Research (2014) 3.
- Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma Chandra. PLIC: Protein–ligand interaction clusters. Database (2014).
- Chandrani Thakur, Ashutosh Tripathi, Sathyabaarathi Ravichandran, Akshatha Shivananjaiah, Anushree Chakraborty, Sreekala Varadappa, Nagaraj Chikkavenkatappa, Deepesh Nagarajan, Sharada Lakshmi Narasimhaiah, Amit Singh, Nagasuma Chandra. A new blood-based RNA signature (R9) for monitoring tuberculosis treatment. iScience (2022).
- Bedobroto Biswas, Naik Shalini Ashok, Deepesh Nagarajan, Md Zaffar Iqubal. Assessment of Biofilm Formation among Clinical Isolates of Escherichia coli. Microbial Research Journal International (2020) 30(1), 26–32.
- Deepesh Nagarajan, Neha Nanajkar. The TIM barrel fold. WikiJournal of Science (2020) 4.
- Aida Jameei, Deepesh Nagarajan, Mohsen Sarikhani, Nagasuma Chandra, Anjali A. Karande. Development and Characterization of a Potent TNF-α Blocking Agent. Monoclonal Antibodies in Immunodiagnosis and Immunotherapy (2019) 38(4), 145–156.
- Pushya Pradeep, Deepesh Nagarajan. Conserved Structural Motifs across Diverse Vitamin B12 Binding Proteins. Journal of Bioinformatics and Systems Biology (2019) 6(4), 312–326.
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