Structural Biology – Macromolecular Crystallography
Chromatin Structural Biology
Histone pr
oteins 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 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. Ranjith Padinhateeri, IIT Bombay, India (chromatin biophysics)
- 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. Umasankar PK, RGCB – Trivandrum, India (intracellular trafficking pathways)
- 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 www.dvasulab.com
Our Group:

Group Members
1.
Ms. Archana Samal (UGC-SRF) – 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-SRF) – 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-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.
- Joined our group at ILS as a Project JRF in January 2020.
- Current research interest: Chromatin & nucleoplasmins
4.
Mr. Ketul Saharan (UGC-SRF) – 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
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.
Dr. Chinmayee Mohapatra (DST Woman Scientist – WOS-A)
- 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 postdoctoral fellow in April 2014.
- Currently a Woman Scientist under DST WOS-A scheme
- Current research interest: Structure of plant DNMTs
7.
Dr. Aritreyee Datta (DBT-RA; Postdoctoral Fellow)
- 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.
- Currently a postdoctoral fellow as a DBT-RA
- Current research interest: Structure of parasitic HATs and HDACs
8.
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.
- Currently a Senior Research Associate under the CSIR-SRA scheme.
- Current research interest: Infectious disease structural biology
9.
Mr. Swabhiman Sahu (X-ray Diffraction Facility In-Charge)
- PGDCA, Softech, Cuttack, 2017.
- BSc Honors (Zoology), Ravenshaw University, Cuttack, 2018.
- MSc (Life Sciences), Jawaharlal Nehru University, New Delhi, 2020.
- Joined ILS as the X-ray Diffraction Facility In-Charge in April 2022.
10.
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.
Group Alumni:
1.
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 PhD 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 University of Texas, El Paso, USA.
2.
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 PhD scholar in April 2014 with DBT-JRF.
- PhD 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.
3.
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
- Current position: Postdoctoral researcher at University of Vermont, Burlington, USA.
4.
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.
- Current position: Postdoctoral researcher at Yale University, New Haven, USA.
5.
Dr. 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.
- Current position: Postdoctoral researcher at Cedars-Sinai Medical Center, Los Angeles, USA.
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.
- Current position: Scientist in private sector at Baroda.
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.
- Current position: Postdoctoral researcher at the University of Bergen, Norway