Dr. Dileep Vasudevan

Academics

Degree	University/Institution
M.F.Sc. (Master of Fisheries Science – Fishery Microbiology)	University of Agricultural Sciences (UAS, Bangalore), College of Fisheries, Mangalore, India.
Ph.D. (Biological Sciences – Protein X-ray Crystallography)	Department of Biological Sciences, National University of Singapore (NUS), Singapore.

Work Experience

Position	University/Organisation	Period
Scientist	Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram	June 2023 onwards
Scientist	Institute of Life Sciences (ILS), Bhubaneswar	December 2012 onwards (On Lien at ILS from June 2023)
Postdoctoral Fellow at Disease Biology Unit	Novartis Institute for Tropical Diseases (NITD), Singapore	April 2011- November 2012
Postdoctoral Fellow at School of Biological Sciences	Nanyang Technological University (NTU), Singapore	February 2006 – March 2011

Awards & Recognition

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

Research

Details
Structural Biology [https://www.DVasuLab.com] Over the initial years, we have gained a certain sense of directionality with respect to our science. Details of our current focus areas can be seen below: *(1) Chromatin Structural Biology:* Histone proteins package eukaryotic DNA into chromatin. The dynamic DNA-protein complex called nucleosomes forms 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. A 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 than isolated studies focusing on the interaction of protein factors with individual histone(s) or DNA. In this context, we work on some nucleosome-interacting proteins. Around the theme of chromatin structural biology, another of our interests is histone chaperones. Histone chaperones are a group of proteins that bind histones and regulate nucleosome assembly. The mode of action of several histone chaperones is not well-understood. Also, it is not completely clear 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. A major interest in this direction has been nucleoplasmins. Our endeavors with histone chaperones have gotten us to initiate structural characterization work on certain histone deacetylases (HDACs) as well! (2) 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 that help in the 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 work from ILS has shown that the structure of ClpD is quite different from that of ClpC in its N-terminus. Our interest in 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. (3) Infectious Disease Structural Biology: A couple of our chromatin structural biology and Clp machinery projects have infectious disease flavor. In addition, we also work on proteins from bacteria, fungi, viruses, and parasites that are infectious to humans. We have recently started working on candidate proteins from the pathogens that infect cultured shrimps. Over and above these, additional structural biology projects are being taken up from time to time collaboratively. Our collaborators @ ILS: Dr. Balachandran Ravindran (immunology) Dr. Narottam Acharya (yeast genome instability) Dr. Soma Chattopadhyay (virology) Dr. Tushar Kant Beuria (bacterial cell division) Dr. V. Arun Nagaraj (plasmodium biology) 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. Aline V. Probst, CNRS, France (histone variants and chaperones) Prof. Anil Grover, University of Delhi-South Campus, India (plant stress tolerance) Prof. Jagneshwar Dandapat, Utkal University – Bhubaneswar, India (immunology) Prof. Rabindra Behera, NIT – Rourkela, India (ferritin nanocages) Prof. Meenu Kapoor, Indraprastha University – New Delhi, India (plant DNMTs) Dr. Devinder Sehgal, NII – New Delhi, India (bacterial virulence) Dr. Bhavani Shankar Sahu, NBRC – Manesar, India (vesicle biogenesis) Dr. Rahul Modak, KIIT University – Bhubaneswar, India (bacterial deacetylases) Dr. Subhendu K. Otta, CIBA – Chennai, India (shrimp pathogens) Dr. Insaf Ahmed Qureshi, University of Hyderabad, Hyderabad – India (Leishmania proteins) 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 https://DVasuLab.com

Details

Structural Biology [https://www.DVasuLab.com]

Over the initial years, we have gained a certain sense of directionality with respect to our science. Details of our current focus areas can be seen below:

(1) Chromatin Structural Biology: Histone proteins package eukaryotic DNA into chromatin. The dynamic DNA-protein complex called nucleosomes forms 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.

A 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 than isolated studies focusing on the interaction of protein factors with individual histone(s) or DNA. In this context, we work on some nucleosome-interacting proteins.

Around the theme of chromatin structural biology, another of our interests is histone chaperones. Histone chaperones are a group of proteins that bind histones and regulate nucleosome assembly. The mode of action of several histone chaperones is not well-understood. Also, it is not completely clear 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. A major interest in this direction has been nucleoplasmins. Our endeavors with histone chaperones have gotten us to initiate structural characterization work on certain histone deacetylases (HDACs) as well!

(2) 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 that help in the 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 work from ILS has shown that the structure of ClpD is quite different from that of ClpC in its N-terminus. Our interest in 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.

(3) Infectious Disease Structural Biology: A couple of our chromatin structural biology and Clp machinery projects have infectious disease flavor. In addition, we also work on proteins from bacteria, fungi, viruses, and parasites that are infectious to humans. We have recently started working on candidate proteins from the pathogens that infect cultured shrimps.

Over and above these, additional structural biology projects are being taken up from time to time collaboratively.

Our collaborators @ ILS:

Dr. Balachandran Ravindran (immunology)
Dr. Narottam Acharya (yeast genome instability)
Dr. Soma Chattopadhyay (virology)
Dr. Tushar Kant Beuria (bacterial cell division)
Dr. V. Arun Nagaraj (plasmodium biology)

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. Aline V. Probst, CNRS, France (histone variants and chaperones)
Prof. Anil Grover, University of Delhi-South Campus, India (plant stress tolerance)
Prof. Jagneshwar Dandapat, Utkal University – Bhubaneswar, India (immunology)
Prof. Rabindra Behera, NIT – Rourkela, India (ferritin nanocages)
Prof. Meenu Kapoor, Indraprastha University – New Delhi, India (plant DNMTs)
Dr. Devinder Sehgal, NII – New Delhi, India (bacterial virulence)
Dr. Bhavani Shankar Sahu, NBRC – Manesar, India (vesicle biogenesis)
Dr. Rahul Modak, KIIT University – Bhubaneswar, India (bacterial deacetylases)
Dr. Subhendu K. Otta, CIBA – Chennai, India (shrimp pathogens)
Dr. Insaf Ahmed Qureshi, University of Hyderabad, Hyderabad – India (Leishmania proteins)

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 https://DVasuLab.com

Publications

Details
Laxmi N. Mishra, Christophe Thiriet, Dileep Vasudevan. 2023. Editorial: Chromatin structure and function. Frontiers in Genetics 14: 1140534. Ruchir C. Bobde, Ashish Kumar, Dileep Vasudevan. 2022. Plant-specific HDT family histone deacetylases are nucleoplasmins. The Plant Cell 34(12): 4760-77. Ajit K. Singh, Ketul Saharan, Somanath Baral, Dileep Vasudevan. 2022. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. Biochimica et Biophysica Acta – Gene Regulatory Mechanisms 1865(7): 194872. Saikat De, Soumyajit Ghosh, Supriya S. Keshry, Chandan Mahish, Chinmayee Mohapatra, Ankeeta Guru, Prabhudutta Mamidi, Ankita Datey, Sweta S. Pani, Dileep Vasudevan, Tushar K. Beuria, Subhasis Chattopadhyay, Bharat B. Subudhi, Soma Chattopadhyay. 2022. MBZM-N-IBT, a novel small molecule, restricts chikungunya virus infection by targeting nsP2 protease activity in vitro, in vivo, and ex vivo. Antimicrobial Agents and Chemotherapy e0046322. Ajit K. Singh, Ketul Saharan, Somanath Baral, Dileep Vasudevan. 2022. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. bioRxiv 489347. [pre-print article] Aritreyee Datta, Shaikh N. Hossain, Chinmayee Mohapatra^#, Dileep Vasudevan^#. 2022. Structural insights into proteins from White spot syndrome virus: perspectives on structure-based anti-viral strategies. Reviews in Aquaculture 2022: 1-12. Ajit K. Singh, Ketul Saharan, Somanath Baral, Sheng Luan, Dileep Vasudevan. 2022. Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain. International Journal of Biological Macromolecules 206: 670-80. Ruchir C. Bobde, Ketul Saharan, Somanath Baral, Surajit Gandhi, Archana Samal, Rajivgandhi Sundaram, Ashish Kumar, Ajit K. Singh, Aritreyee Datta, Dileep Vasudevan. 2021. In vitro characterization of histone chaperones using analytical, pull-down and chaperoning assays. Journal of Visualized Experiments [JoVE] 63218. Shyla Gopalakrishnan, Soumya K. Uma, Gayathri Mohan, Amrutha Mohan, Geetha Shanmugam, Vineeth T.V. Kumar, Sreekumar J, Sivakumar K. Chandrika, Dileep Vasudevan, Sai R.C. Nori, Shijulal N. Sathi, Sanil George and Tessy T. Maliekal. 2021. SSTP1, a host defense peptide, exploits the immunomodulatory IL6 pathway to induce apoptosis in cancer cells. Frontiers in Immunology 12: 740620. Premlata Kumari, Rajivgandhi Sundaram, Kodavati Manohar, Dileep Vasudevan^#, Narottam Acharya^#. 2021. Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA. Journal of Biological Chemistry* 297(1): 100911. 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 595(9): 1328-1349. 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. 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. 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. 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. Rajivgandhi Sundaram, Dileep Vasudevan. 2020. Structural basis of nucleosome recognition and modulation. BioEssays 42(9): 1900234. 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. Ashish Kumar, Dileep Vasudevan. 2020. Structure-function relationship of H2A-H2B specific plant histone chaperones. Cell Stress and Chaperones 25(1): 1-17. 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). Supriya Borah, Dileep Vasudevan, Rajeeb K. Swain. 2019. C-type lectin family XIV members and angiogenesis. Oncology Letters 18: 3954-3962. 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. 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. 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* 449629. [pre-print article] 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. 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. 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. 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 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. [* Co-first authors] [^# Co-corresponding authors]

Details

Laxmi N. Mishra, Christophe Thiriet, Dileep Vasudevan. 2023. Editorial: Chromatin structure and function. Frontiers in Genetics 14: 1140534.
Ruchir C. Bobde*, Ashish Kumar*, Dileep Vasudevan. 2022. Plant-specific HDT family histone deacetylases are nucleoplasmins. The Plant Cell 34(12): 4760-77.
Ajit K. Singh*, Ketul Saharan*, Somanath Baral, Dileep Vasudevan. 2022. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. Biochimica et Biophysica Acta – Gene Regulatory Mechanisms 1865(7): 194872.
Saikat De, Soumyajit Ghosh, Supriya S. Keshry, Chandan Mahish, Chinmayee Mohapatra, Ankeeta Guru, Prabhudutta Mamidi, Ankita Datey, Sweta S. Pani, Dileep Vasudevan, Tushar K. Beuria, Subhasis Chattopadhyay, Bharat B. Subudhi, Soma Chattopadhyay. 2022. MBZM-N-IBT, a novel small molecule, restricts chikungunya virus infection by targeting nsP2 protease activity in vitro, in vivo, and ex vivo. Antimicrobial Agents and Chemotherapy e0046322.
Ajit K. Singh*, Ketul Saharan*, Somanath Baral, Dileep Vasudevan. 2022. The plant nucleoplasmin AtFKBP43 needs its extended arms for histone interaction. bioRxiv 489347. [pre-print article]
Aritreyee Datta*, Shaikh N. Hossain*, Chinmayee Mohapatra^#, Dileep Vasudevan^#. 2022. Structural insights into proteins from White spot syndrome virus: perspectives on structure-based anti-viral strategies. Reviews in Aquaculture 2022: 1-12.
Ajit K. Singh*, Ketul Saharan*, Somanath Baral, Sheng Luan, Dileep Vasudevan. 2022. Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain. International Journal of Biological Macromolecules 206: 670-80.
Ruchir C. Bobde*, Ketul Saharan*, Somanath Baral, Surajit Gandhi, Archana Samal, Rajivgandhi Sundaram, Ashish Kumar, Ajit K. Singh, Aritreyee Datta, Dileep Vasudevan. 2021. In vitro characterization of histone chaperones using analytical, pull-down and chaperoning assays. Journal of Visualized Experiments [JoVE] 63218.
Shyla Gopalakrishnan*, Soumya K. Uma, Gayathri Mohan, Amrutha Mohan, Geetha Shanmugam, Vineeth T.V. Kumar, Sreekumar J, Sivakumar K. Chandrika, Dileep Vasudevan, Sai R.C. Nori, Shijulal N. Sathi, Sanil George and Tessy T. Maliekal*. 2021. SSTP1, a host defense peptide, exploits the immunomodulatory IL6 pathway to induce apoptosis in cancer cells. Frontiers in Immunology 12: 740620.
Premlata Kumari*, Rajivgandhi Sundaram*, Kodavati Manohar*, Dileep Vasudevan^#, Narottam Acharya^#. 2021. Interdomain connecting loop and J loop structures determine cross-species compatibility of PCNA. Journal of Biological Chemistry 297(1): 100911.
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 595(9): 1328-1349.
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.
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.
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.
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.
Rajivgandhi Sundaram, Dileep Vasudevan. 2020. Structural basis of nucleosome recognition and modulation. BioEssays 42(9): 1900234.
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.
Ashish Kumar, Dileep Vasudevan. 2020. Structure-function relationship of H2A-H2B specific plant histone chaperones. Cell Stress and Chaperones 25(1): 1-17.
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).
Supriya Borah, Dileep Vasudevan, Rajeeb K. Swain. 2019. C-type lectin family XIV members and angiogenesis. Oncology Letters 18: 3954-3962.
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.
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.
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 449629. [pre-print article]
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

[* Co-first authors] [^# Co-corresponding authors]

Group

Details

Our Group Members:

	Ms. Archana Samal (UGC-SRF) – Ph.D. 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 Ph.D. scholar in March 2020. Current research interest: Chromatin structural biology
	Mr. Surajit Gandhi (UGC-SRF) – Ph.D. scholar BSc (Zoology), Banwarilal Bhalotia College, Asansol, 2016. MSc (Zoology), University of Burdwan, Purba Bardhaman, 2018. Joined our group at ILS as a Ph.D. scholar in February 2020. Current research interest: Chromatin & infectious disease structural biology
	Mr. Ketul Saharan (UGC-SRF) – Ph.D. 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 Ph.D. scholar in March 2019. His Ph.D. is registered with RCB, Faridabad. EMBO Scientific Exchange Grant (SEG) Fellow at NTU Singapore (Sept-Dec 2022) Current research interest: Chromatin & HDACs
	Dr. Dharma Rao Tompa (Project-RA; Postdoctoral Fellow) BSc (Biochemistry), Andhra University, Visakhapatnam, 2009. MSc (Biochemistry & Molecular Biology), Central University of Kerala, Kasaragod, 2012. Ph.D. (Structural Biology and Molecular Biophysics), SASTRA University, Thanjavur, 2019. Post-doc at ICGEB, New Delhi, 2021-2022. Joined ILS as a post-doc in September 2022. Current research interest: Chromatin and infectious disease structural biology
	Mr. Manoj Kumar Barik (Laboratory Technician) DMLT from JRN Rajasthan Vidyapeeth University (2019) Lab Technician in a private diagnostic laboratory in Bhubaneswar (2019-2021) Trainee Lab Technician from March to December 2021 in our group. Joined ILS as a Lab Technician in January 2022.
	Mr. Vicky Kumar (XRD Facility In-Charge) BSc (Industrial Microbiology) Honors, Langat Singh College, Muzaffarpur, 2019. MSc (Biotechnology), DBT-RGCB, Thiruvananthapuram, 2022. Joined our group in ILS as the XRD Facility In-charge in February 2023.
	Mr. Purushottam Patnaik (AUC Facility In-Charge) BSc (Zoology), Vikram Deb Autonomous College, Jeypore, Berhampur University, 2020. MSc (Microbiology), College of Pharmaceutical Sciences, Berhampur, 2022. Joined our group in ILS as the AUC Facility In-charge in February 2023.

Group Alumni:

	Dr. Ruchir Chandrakant Bobde 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 Ph.D. scholar in January 2017. PhD from ILS (RCB Faridabad) (Jan 2017 – Apr 2023). While with us, he worked on the theme of chromatin & HDACs
	Dr. Manas Kumar Jagdev 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. Registered for Ph.D. in Nov 2017. PhD from ILS (Utkal University) (Nov 2017 – Feb 2022). With us, he worked on plant & mycobacterial Clp chaperone machinery proteins. Current position: Postdoctoral researcher at the University of Texas, El Paso, USA.
	Dr. Rajivgandhi Sundaram 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 in ILS as a Ph.D. scholar in April 2014 with DBT-JRF. Ph.D. from ILS (Manipal Academy of Higher Education) (Apr 2014 – Aug 2021). With us, he worked on plant histone chaperones and PCNA. Current position: Postdoctoral researcher at Johns Hopkins University, Baltimore, USA.
	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 Ph.D. scholar in April 2014 with DBT-JRF. Ph.D. from ILS (Manipal Academy of Higher Education) (Apr 2014 – Sept 2020). With us, he worked on plant FKBP-nucleoplasmins. Current position: Postdoctoral researcher at the University of Vermont, Burlington, USA.
	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 Ph.D. scholar in September 2013 with DBT-JRF. Ph.D. from ILS (Manipal Academy of Higher Education) (Sept 2013 – Sept 2020). With us, he worked on plant chromatin and histone chaperones. Current position: Postdoctoral researcher at Yale University, New Haven, USA.
	Dr. Supriya Borah (co-supervisory) BSc (Agriculture), Assam Agricultural University, Jorhat, 2010. MSc (Agricultural Biotechnology), UAS, Dharwad, 2012. Ph.D. 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. Current position: DBT-RA at CDFD, Hyderabad
	Dr. Shaikh Nausad Hossain (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. Ph.D. (Structural Biology), University of Queensland, Australia, 2013. Postdoctoral fellow at Okinawa Institute of Science and Technology (OIST), Japan, 2013-2016. Visiting postdoctoral fellow at NISER, Bhubaneswar, 2017-2018. Joined our group at ILS as an institutional postdoctoral fellow in July 2018. CSIR-SRA from December 2019 – December 2022. With us, he worked on the broad theme of infectious disease structural biology
	Dr. Chinmayee Mohapatra (Postdoctoral Fellow) BSc Honors (Botany) Utkal University, Bhubaneswar, 2005. MSc (Biotechnology), Utkal University, Bhubaneswar, 2007. Ph.D. (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 postdoctoral fellow in April 2014. Postdoc with our group in ILS under various schemes from Apr 2014 to Feb 2023. With us, she worked on Clp chaperone machinery proteins.
	Dr. Aritreyee Datta (Postdoctoral Fellow) BSc (Biotechnology), Bangalore University, 2007. MSc (Biotechnology), KIIT University, 2010. Ph.D. (Biotechnology), University of Kolkata, 2017. SRF in Bose Institute, Kolkata, 2012-2017. Joined our group at ILS as a postdoctoral fellow in August 2017. Postdoc with our group in ILS from Aug 2017 to Oct 2022. While with us, she worked on chromatin and infectious disease thematic projects.
	Dr. Sushil Kumar (Postdoctoral Fellow) BSc (Biology), University of Allahabad, 2001. MSc (Bioinformatics), University of Allahabad, 2005. MTech (Biotechnology), West Bengal University of Technology, Kolkata, 2007. Ph.D. (Structural Biology), JNU, New Delhi, 2015. JRF/SRF in CCMB, Hyderabad, 2008-2015. Postdoc with 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. Current position: Scientist with Biocon, Chennai
	Dr. Vipul Panchal (Project fellow) BSc (Chemistry – Honors), MS University, Baroda, 2008. MSc (Biochemistry), MS University, Baroda, 2010. Ph.D. 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. Current position: Postdoctoral researcher at the University of Bergen, Norway
	Mr. Somanath Baral (Project-SRF) 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. Project JRF with us from January 2020 to June 2022. While with us, he worked on the theme of chromatin & nucleoplasmins.

Grants

Details

Funding agency	Title of the project	Duration
DBT	Bioactive Bhubaneswar Biophysical Characterization Facility	4 years; from December 2019 (*ongoing*)
SERB	Unraveling the function of plant FKBP nucleoplasmins through structural studies	3 years; from December 2019 (*completed*)
DBT	Structural characterization of White Spot Syndrome Viral enzymes involved in viral nucleotide synthesis	3 years; from January 2018 (*completed*)
CSIR	Structural basis of dengue virus capsid protein interaction with the human death domain-associated protein DAXX	3 years; from October 2015 (*completed*)
SERB	Host nucleosomes forming a docking station for Dengue virus capsid protein C – a structural analysis	3 years; from October 2015 (*completed*)
DBT	Structural characterization of Influenza A virus matrix protein M1 interaction with host nucleosomes	3 years; from November 2014 (*completed*)

Contacts

Email	Address	Fax	Office
dileep@ils.res.in	DBT-Institute of Life Sciences, Nalco Square, Chandrasekharpur, Bhubaneswar-751023, India	+91 674 2300728	+91-674-2304291

Highlights

Details
ESRF Highlights 2020 features the work that DVasuLab did at their facility and got published in NAR in 2020! Indian Structural Biology groups are getting featured in ESRF Highlights for the first time! https://www.esrf.eu/home/UsersAndScience/Publications/Highlights/esrf-highlights-2020.html Our publication in the Plant Cell journal got highlighted in this “In Brief” article https://academic.oup.com/plcell/advance-article/doi/10.1093/plcell/koac277/6696235

Details

ESRF Highlights 2020 features the work that DVasuLab did at their facility and got published in NAR in 2020! Indian Structural Biology groups are getting featured in ESRF Highlights for the first time! https://www.esrf.eu/home/UsersAndScience/Publications/Highlights/esrf-highlights-2020.html

Our publication in the Plant Cell journal got highlighted in this “In Brief” article

https://academic.oup.com/plcell/advance-article/doi/10.1093/plcell/koac277/6696235

Positions

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

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