Educational Qualification:

1. Ph.D. (Protein X-ray Crystallography) (2007): Department of Biological Sciences, National University of Singapore (NUS), Singapore.
2. M.F.Sc. (Master of Fisheries Science – Microbiology) (2001): University of Agricultural Sciences (UAS, Bangalore), College of Fisheries, Mangalore, India.
3. B.F.Sc. (Bachelor of Fisheries Science) (1999): Kerala Agricultural University (KAU, Thrissur), College of Fisheries, Panangad, Cochin, India.

Work Experience:

1. Scientist at Institute of Life Sciences (ILS), Bhubaneswar, India, December 2012 onwards
2. Postdoctoral Fellow at Disease Biology Unit, Novartis Institute for Tropical Diseases (NITD), Singapore, April 2011- November 2012
3. Postdoctoral Fellow at School of Biological Sciences, Nanyang Technological University (NTU), Singapore, February 2006 – March 2011

Memberships:

1. International Union of Crystallography (IUCr) Associate
2. Indian Crystallographic Association (ICA)
3. Indian Biophysical Society (IBS)
4. Society of Biological Chemists, India (SBCI)
5. Electron Microscope Society of India (EMSI)
6. Professional Fisheries Graduates Forum (PFGF)

Honours and Fellowship:

1. National University of Singapore Research Scholarship for pursuing Ph.D. (2002-2006).
2. Certificate of Appreciation from Professional Fisheries Graduates Forum (PFGF), India for Masters degree thesis (2002).
3. Indian Council of Agricultural Research (ICAR) JRF for pursuing Masters degree (1999 – 2001)

Ph.D. Guideship:

1. Regional Centre for Biotechnology, Faridabad (Biotechnology; Adjunct Assistant Professor)
2. Utkal University, Bhubaneswar (Biotechnology & Life Sciences)
3. Manipal Academy of Higher Education, Manipal (Biotechnology)
4. KIIT University, Bhubaneswar (Biotechnology)

Structural Biology – Macromolecular Crystallography

Chromatin Structural Biology

Histone proteins package eukaryotic DNA into chromatin. The dynamic DNA-protein complex called nucleosomes form the basic element of chromatin. All eukaryotic genomic processes, both natural and pathological, including transcription, replication, recombination, repair, chromosome segregation, carcinogenesis and viral infection can be fully understood only in the context of nucleosomes. The core of a nucleosome, called the nucleosome core particle (NCP) consists of fourteen turns of B-form DNA around an octamer of histone proteins, as can be seen in the image.

Nucleosome is known to be the binding platform for several protein factors. In order for a protein to gain access to chromosomal DNA/histone proteins, it needs to interact and/or compete with the histone proteins/DNA of the nucleosome. Studies involving nucleosomes are of greater significance as compared to isolated studies focusing on interaction of protein factors with individual histone(s) or DNA. So in addition to a couple of stand-alone chromatin structural biology projects, we are also looking at projects which combine the themes of chromatin biology and infectious diseases. In this regard, our group is interested in proteins from certain viruses for which nucleosome form a docking station. A combined biochemical, biophysical and crystallographic approach on complexes of host nucleosomes and interacting viral proteins is expected to reveal details of the interactions, thereby explaining several previously unknown mechanisms involved in the life cycle of the viruses. This understanding could probably be a step towards the identification of suitable drug candidates against those viruses that target viral replication.

Around the theme of chromatin structural biology, another of our interest is histone chaperones. Histone chaperones are a group of proteins that bind histones and regulate nucleosome assembly. Mode of action of several histone chaperones is not well-understood. Also, it is not completely clear regarding what decides the specificity of certain histone chaperones for H3-H4, H2A-H2B or histone variants. In order to better understand these molecular machines, we work on a few projects dealing with the structural characterization of some important, but poorly characterized histone chaperones.

Structural Biology of Clp Machinery Proteins

The caseinolytic protease (Clp) machinery is present in bacteria, plants and other eukaryotes. These proteases usually associate with Clp chaperone proteins which help in ATP-dependent unfolding of substrates which need to be taken in for proteolysis by the proteases. ClpD is a Clp-associated chaperone unique to plants. Plant ClpC and ClpD proteins both get localized into chloroplast stroma. However, our recent work has revealed that the structure of ClpD is quite different from ClpC in its N-terminus. Our interest on plant Clp machinery proteins is to understand their distinct roles in protein homeostasis and stress response. In addition, we also work on mycobacterial Clp chaperones due to their importance as a target in anti-mycobacterial research.

Infectious Disease Structural Biology

A couple of our chromatin structural biology and Clp machinery projects have infectious disease flavour. In addition, we also work on proteins involved in bacterial cell division, as well as proteins from infectious fungal and viral pathogens. More recently, we have started working on candidate proteins from the dreaded White Spot Syndrome Virus (WSSV) that infects cultured shrimps.

Over and above these, additional crystallographic projects are being taken up from time to time, on a collaborative basis.

Our in-house collaborators:

• Dr. Balachandran Ravindran (immunology)
• Dr. Soumen Chakraborty (leukemia)
• Dr. Santhibhusan Senapati (tumor microenvironment)
• Dr. Narottam Acharya (yeast genome instability)
• Dr. Soma Chattopadhyay (virology)
• Dr. Tushar Kant Beuria (bacterial cell division)

Other major collaborators:

• Prof. Kim Lewis, North Eastern University, Boston, USA (antibacterials)
• Prof. Sheng Luan, University of California at Berkeley, USA (plant FKBPs)
• Prof. Klaas van Wijk, Cornell University, USA (plant protein homeostasis)
• Prof. Claudia Jonak, Austrian Inst. of Technology, Austria (plant stress factors)
• Prof. Anil Grover, University of Delhi-South Campus, India (plant stress tolerance)
• Prof. Jagnehswar Dandapat, Utkal University, India (immunology)
• Prof. Rabindra Behera, NIT-Rourkela, India (ferritin nanocages)
• Prof. Anirban Bhunia, Bose Institute, Kolkata (protein NMR)
• Dr. Devinder Sehgal, National Institute of Immunology, New Delhi (bacterial virulence)
• Prof. Meenu Kapoor, Guru Gobind Singh Indraprastha University, New Delhi (plant DNMTs)

As we have technical expertise in making nucleosome core particles and nucleosomal arrays, our group is open to collaborative projects dealing with nucleosome binding factors.

To know more about our group, please have a look at www.dvasulab.com

Publications:

1. Rajivgandhi Sundaram, Kodavati Manohar, Shraddheya K. Patel, Narottam Acharya^#, Dileep Vasudevan^#. 2021. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. FEBS Letters (Accepted; Available online).
2. Sunanda Mallick, Ashish Kumar, Hiren Dodia, Cyrus Alexander, Dileep Vasudevan, Tushar K. Beuria. 2021. Biochemical characterization of an E. coli cell division factor FtsE shows ATPase cycles similar to the NBDs of ABC-transporters. Bioscience Reports 41(1): BSR20203034.
3. Manas K. Jagdev, Jagneshwar Dandapat, Dileep Vasudevan. 2021. Recombinant expression, purification and SAXS analysis of Arabidopsis thaliana ClpC1. International Journal of Biological Macromolecules 167: 1273-1280.
4. Vipul Panchal*, Sushil Kumar*, Shaikh N. Hossain^#, Dileep Vasudevan^#. 2021. Structure analysis of thymidylate synthase from white spot syndrome virus reveals WSSV-specific structural elements. International Journal of Biological Macromolecules 167: 1168-1175.
5. Sunil K. Raghav, Arup Ghosh, ..…. Dileep Vasudevan, Amol R. Suryawanshi, Rupesh Dash, Shantibhusan Senapati, Tushar K. Beuria, Rajeeb K. Swain, Soma Chattopadhyay S, Gulam H. Syed, Anshuman Dixit, Punit Prasad, Sanghamitra Pati, Ajay Parida. 2020. Analysis of Indian SARS- CoV-2 genomes reveals prevalence of D614G mutation in Spike protein eliciting increase in interaction with TMPRSS2 and virus infectivity. Frontiers in Microbiology 11: 594928.
6. Rajivgandhi Sundaram, Dileep Vasudevan. 2020. Structural basis of nucleosome recognition and modulation. BioEssays 42(9): 1900234.
7. Ajit K. Singh, Aritreyee Datta, Jobichen Chacko, Sheng Luan, Dileep Vasudevan. 2020. AtFKBP53 – a chimeric histone chaperone with functional nucleoplasmin and PPIase domains. Nucleic Acids Research 48(3): 1531–1550.
8. Ashish Kumar, Dileep Vasudevan. 2020. Structure-function relationship of H2A-H2B specific plant histone chaperones. Cell Stress and Chaperones 25(1): 1-17.
9. Voddu Suresh*, Rajivgandhi Sundaram*, Pujarini Dash*, Surendra C. Sabat, Debasish Mohapatra, Sneha Mohanty, Dileep Vasudevan^#, Shantibhusan Senapati^#. 2019. Macrophage migration inhibitory factor of Syrian golden hamster shares structural and functional similarity with human counterpart and promotes pancreatic cancer. Scientific Reports 9: 15507 (2019).
10. Supriya Borah, Dileep Vasudevan, Rajeeb K. Swain. 2019. C-type lectin family XIV members and angiogenesis. Oncology Letters 18: 3954-3962.
11. Ashish Kumar, Ajit K. Singh, Ruchir C. Bobde, Dileep Vasudevan. 2019. Structural characterization of Arabidopsis thaliana NAP1-Related Protein 2 (AtNRP2) and comparison with its homolog AtNRP1. Molecules 24(12). pii: E2258.
12. Santhosh Gatreddi, Vijaykumar Pillalamarri, Dileep Vasudevan, Anthony Addlagatta, Insaf A. Qureshi. 2019. Unraveling structural insights of ribokinase from Leishmania donovani. International Journal of Biological Macromolecules 136: 253-265.
13. Pujarini Dash*, Rajivgandhi Sundaram*, Voddu Suresh*, Surendra C. Sabat, Debasish Mohapatra, Sneha Mohanty, Dileep Vasudevan^#, Shantibhusan Senapati^#.2018. Macrophage migration inhibitory factor (MIF) of Syrian golden hamster (Mesocricetus auratus) has similar structure and function as human MIF and promotes pancreatic tumor growth in vivo. bioRxiv [pre-print article]
14. Chinmayee Mohapatra, Manas K. Jagdev, Dileep Vasudevan. 2017. Arabidopsis ClpD N-terminal domain is highly divergent from ClpC1. XXIV IUCr Congress Abstract. Acta Crystallographica A A73 A2, C246.
15. Dileep Vasudevan, Manas K. Jagdev, Chinmayee Mohapatra. 2017. Structural basis of mycobacterial inhibition by natural products targeting ClpC1. XXIV IUCr Congress Abstract. Acta Crystallographica A A73 A2, C228.
16. Biswamaitree Subhadarshanee*, Abhinav Mohanty*, Manas K. Jagdev, Dileep Vasudevan, Rabindra K. Behera. 2017. Surface charge dependent separation of modified and hybrid ferritin in native PAGE: impact of lysine 104. Biochimica et Biophysica Acta – Proteins and Proteomics 1865(10): 1267-1273.
17. Chinmayee Mohapatra*, Manas K. Jagdev*, Dileep Vasudevan. 2017. Crystal structures reveal N-terminal Domain of Arabidopsis thaliana ClpD to be highly divergent from that of ClpC1. Scientific Reports 7: 44366
18. Dileep Vasudevan*, Gayathri Gopalan*, Ashish Kumar, Veder J. Garcia, Sheng Luan, Kunchithapadam Swaminathan. 2015. Plant immunophilins: a review of their structure-function relationship. Biochimica et Biophysica Acta– General Subjects 1850(10): 2145-2158.
19. Dileep Vasudevan, Srinivasa P. S. Rao, Christian G. Noble.2013. Structural basis of mycobacterial inhibition by Cyclomarin A. Journal of Biological Chemistry 288(43): 30883-30891.
20. Dileep Vasudevan*, Aigen Fu*, Sheng Luan, Kunchithapadam Swaminathan. 2012. Crystal structure of Arabidopsis thaliana cyclophilin 38 reveals a previously uncharacterized immunophilin fold and a possible autoinhibitory mechanism. The Plant Cell 24(6): 2666-2674.
21. Eugene Y. D.Chua*, Dileep Vasudevan*, Gabriela E. Davey, Bin Wu, Curt A. Davey. 2012. The mechanics behind DNA sequence-dependent properties of the nucleosome. Nucleic Acids Research 40(13): 6338-6352.
22. Dileep Vasudevan, Eugene Y. D. Chua, Curt A. Davey. 2010. Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. Journal of Molecular Biology 403(1): 1-10.
23. Ong S. Michelle*, Dileep Vasudevan*, Curt A. Davey.2010. Divalent metal- & High Mobility Group N protein- dependent nucleosome stability and conformation. Journal of Nucleic Acids 2010: 143890.
24. Bin Wu*, Mohideen A. Kareem*, Dileep Vasudevan, Curt A. Davey. 2010. Structural insight into the sequence-dependence of nucleosome positioning. Structure 18(4): 528-536.
25. Ou Li, Dileep Vasudevan, Curt A. Davey, Peter Droge. 2006. High-level expression of DNA architectural factor HMGA2 and its association with nucleosomes in human embryonic stem cells. Genesis 44(11): 523-529.
26. Dileep Vasudevan, Gayathri Gopalan, Zengyong He, Sheng Luan, Kunchithapadam Swaminathan. 2005. Expression, purification, crystallization & preliminary X-ray diffraction analysis of Arabidopsis thaliana cyclophilin 38. Acta Crystallographica F 61(12): 1087-1089.
27. Dileep V, Kumar HS, Kumar Y, Nishibuchi M, Karunasagar I, Karunasagar I. 2003. Application of polymerase chain reaction for detection of Vibrio parahaemolyticus associated with tropical seafood and coastal environment. Letters in Applied Microbiology 36(6): 423-427.

[* Equal contributors] [^# Co-corresponding authors]

Our Group:

Group Members

  1.     Ms. Archana Samal (UGC-JRF) – PhD scholar

• BSc Honors (Botany) Honors, Shailabala Women’s College, Cuttack, 2016.
• MSc (Life Sciences), Central University of Punjab, Bathinda, 2018.
• Project JRF at Utkal University (Feb 2019 – Nov 2019).
• Joined our group at ILS as a PhD scholar in March 2020.
• Current research interest: Chromatin structural biology

2.   Mr. Surajit Gandhi (UGC-JRF) – PhD scholar

• BSc (Zoology), Banwarilal Bhalotia College, Asansol, 2016.
• MSc (Zoology), University of Burdwan, Purba Bardhaman, 2018.
• Joined our group at ILS as a PhD scholar in February 2020.
• Current research interest: Chromatin & infectious disease structural biology

3.     Mr. Somanath Baral (Project-JRF)

• BSc Honors (Botany), Utkal University, Bhubaneswar, 2015.
• MSc (Botany), Berhampur University, Berhampur, 2017.
• MPhil (Botany), Berhampur University, Berhampur, 2019.
• Project JRF, IIT Kharagpur, May 2019 – December 2019.
• Joined our group at ILS as a Project JRF in January 2020.
• His PhD is registered with KIIT University, Bhubaneswar.
• Current research interest: Chromatin & nucleoplasmins

4.      Mr. Ketul Saharan (UGC-JRF) – PhD scholar

• BSc (Biotechnology), Government National College, Sirsa, 2014.
• MSc (Botany), Kurukshetra University, Kurukshetra, 2016.
• JRF at School of Life Sciences, JNU, New Delhi, Aug 2017 – Feb 2019.
• Joined our group at ILS as a PhD scholar in March 2019.
• His PhD is registered with RCB, Faridabad.
• Current research interest: Chromatin & HDACs
  

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 5.     Mr. Ruchir Chandrakant Bobde (SRF) – PhD scholar

• BSc (Chemistry, Microbiology, Biotechnology), RTM Nagpur University, 2013.
• MSc (Biotechnology), RTM Nagpur University, 2016.
• Trainee at ACTREC, Navi Mumbai, Jan 2016 – Mar 2016.
• Project staff at ICAR-CICR, Nagpur, Oct 2016 – Jan 2017.
• Joined our group at ILS as a PhD scholar in January 2017.
• His PhD is registered with RCB, Faridabad.
• Current research interest: Chromatin & HDACs

6.     Mr. Rajivgandhi Sundaram (DBT-SRF) – PhD scholar

• BSc (Biotechnology), Tiruvalluvar University, Vellore, 2010.
• MSc (Biotechnology), Periyar University, Salem, 2012.
• DMLT, Microtech Insitute of Paramedical Science and Research, Salem, 2011.
• Junior Executive in Biocon Research Limited, Bangalore, 2012-2013.
• JRF in School of Biological Sciences, NISER, Bhubaneswar, 2013-2014.
• Joined our group at ILS as a PhD scholar in April 2014.
• His PhD is registered with MAHE, Manipal.
• Current research interest: Chromatin & histone chaperones

7.      Mr. Manas Kumar Jagdev (SRF) – PhD scholar

• BSc (Biotechnology), Utkal University, Bhubaneswar, 2009.
• MSc (Industrial Biotechnology), Siksha ‘O’ Anusandhan University, 2011.
• Research trainee in Imgenex India Pvt. Ltd., Bhubaneswar, 2011-2012.
• Microbiologist in Sambit Aqua, Cuttack, 2012-2013.
• Chemist/Microbiologist in Spring Resources Pvt Ltd, Cuttack, 2013.
• Joined our group at ILS as a Lab Technician in September 2013.
• Upgraded to project SRF in December 2015.
• His PhD is registered with Utkal University.
• Current research interest: Bacterial & plant chaperones

8.     Dr. Mrs. Chinmayee Mohapatra (Post-Doctoral Fellow)

• BSc Honors (Botany) Utkal University, Bhubaneswar, 2005.
• MSc (Biotechnology), Utkal University, Bhubaneswar, 2007.
• PhD (Cell & Molecular Biology), Utkal University, Bhubaneswar, 2014.
• BCIL trainee in Imgenex India Pvt. Ltd., Bhubaneswar, 2007-2008.
• JRF/SRF in CIFA, Bhubaneswar, 2008-2014.
• Joined our group at ILS as a postdoc in April 2014.
• Current research interest: Structure of Chikungunya Virus proteins

9.      Dr. Mrs. Aritreyee Datta (DBT-RA)

• BSc (Biotechnology), Bangalore University, 2007.
• MSc (Biotechnology), KIIT University, 2010.
• PhD (Biotechnology), University of Kolkata, 2017.
• SRF in Bose Institute, Kolkata, 2012-2017.
• Joined our group at ILS as a post-doctoral fellow in August 2017.
• Current research interest: Structure of Viral ubiquitin ligase enzymes

10.     Dr. Shaikh Nausad Hossain (CSIR- SRA; Postdoctoral Fellow)

• BSc (Biotechnology), Bangalore University, 2005.
• Diploma (Genetic Engineering), JIVAS, Bangalore, 2005.
• Project JRF at PGIMER, Chandigarh, 2005-2006.
• MSc (Molecular Biology), University of Queensland, Australia, 2008.
• Research Assistant, University of Queensland, Australia, 2008-2009.
• PhD (Structural Biology), University of Queensland, Australia, 2013.
• Post-doctoral fellow at Okinawa Institute of Science and Technology (OIST), Japan, 2013-2016.
• Visiting post-doctoral fellow at NISER, Bhubaneswar, 2017-2018.
• Joined our group at ILS as a post-doctoral fellow in July 2018.
• Current research interest: Infectious disease structural biology

Group Alumni:

1.     Dr. Ajit Kumar Singh

• BSc (Biotechnology), Bangalore University, 2010.
• MSc (Biotechnology), Bangalore University, 2012.
• Trainee/Junior Executive in Biocon Research Limited, Bangalore, 2012-2013.
• JRF in Fermentation Technology Department, CFTRI, Mysore, 2013-2014.
• Joined our group in ILS as a PhD scholar in April 2014 with DBT-JRF.
• PhD from ILS (Manipal Academy of Higher Education) (Apr 2014 – Sept 2020).
• With us, he worked on plant FKBP-nucleoplasmins
• He is currently a post-doctoral fellow at the Virginia Commonwealth University, USA.

2.    Dr. Ashish Kumar 

• BSc Honors (Biotechnology), Patna University, Patna, 2011.
• MSc (Biotechnology), Babasaheb Bhimrao Ambedkar University, Lucknow, 2013.
• Joined our group in ILS as a PhD scholar in September 2013 with DBT-JRF.
• PhD from ILS (Manipal Academy of Higher Education) (Sept 2013 – Sept 2020).
• With us, he worked on plant chromatin and histone chaperones

3.    Dr. Mrs. Supriya Borah – (co-supervisory)

• BSc (Agriculture), Assam Agricultural University, Jorhat, 2010.
• MSc (Agricultural Biotechnology), UAS, Dharwad, 2012.
• PhD on co-supervisory from our group in ILS (Manipal Academy of Higher Education) (Feb 2013 – Oct 2019).
• While with us, she worked on Clec14a protein that is involved in angiogenesis.

4.    Dr. Sushil Kumar (Post-Doctoral Fellow)

• BSc (Biology), University of Allahabad, 2001.
• MSc (Bioinformatics), University of Allahabad, 2005.
• MTech (Biotechnology), West Bengal University of Technology, Kolkata, 2007.
• PhD (Structural Biology), JNU, New Delhi, 2015.
• JRF/SRF in CCMB, Hyderabad, 2008-2015.
• Postdoc in our group in ILS from May 2015 to May 2018.
• While with us, he worked in the broad area of Chromatin & Infectious Disease Structural Biology.
• Currently on a short career break, waiting for fellowship application results.

5.    Dr. Vipul Panchal (Project fellow)

• BSc (Chemistry – Honors), MS University,  Baroda, 2008.
• MSc (Biochemistry), MS University, Baroda, 2010.
• PhD from CSIR-IGIB, New Delhi, 2019.
• Project Fellow in our group at ILS from May 2018 to June 2019.
• While with us he worked on certain viral enzymes involved in nucleotide synthesis.
• Currently a Postdoc at University of Bergen, Norway

• We are not accepting MSc dissertation, PhD or post-doc applications at the moment!
• For any query, feel free to write to Dileep at: dileep [at] ils [dot] res [dot] in