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. 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. Joo-Won Suh, Myongji University, S. Korea (anti-TB agents)
- 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)
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 Photo:
Group Members
1. 
Mr. Ruchir Chandrakant Bobde (JRF) – 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 ILS as a PhD scholar in January 2017.
- Current research interest: Chromatin & associated chaperones
2. 
Mr. Ajit Kumar Singh (DBT-SRF) – PhD scholar
- 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 ILS as a PhD scholar in April 2014.
- Current research interest: Chromatin, Chaperones & Viral Structural Proteins
3. 
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 ILS as a PhD scholar in April 2014.
- Current research interest: Chromatin, Chaperones & Viral Structural Proteins
4. 
Mr. Ashish Kumar (DBT-SRF) – PhD scholar
- BSc Honors (Biotechnology), Patna University, Patna, 2011.
- MSc (Biotechnology), Babasaheb Bhimrao Ambedkar University, Lucknow, 2013.
- Joined ILS as a PhD scholar in September 2013.
- Current research interest: Chromatin, Chaperones & Viral Structural Proteins
5. 
Ms. Supriya Borah (DBT-SRF) – PhD scholar (co-supervision)
- BSc (Agriculture), Assam Agricultural University, Jorhat, 2010.
- MSc (Agricultural Biotechnology), UAS, Dharwad, 2012.
- Joined ILS as a PhD student in February 2013.
- Current research interest: Proteins involved in angiogenesis
6. 
Mr. Manas Kumar Jagdev (SERB project SRF)
- 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 ILS as a Lab Technician in September 2013.
- Upgraded to project SRF in December 2015.
- Current research interest: Bacterial & Plant Chaperone Proteins
7. 
Mr. Vipul Panchal (DBT project SRF)
- BSc (Chemistry – Honors), MS University, Baroda, 2008.
- MSc (Biochemistry), MS University, Baroda, 2010.
- Completing PhD from CSIR-IGIB, New Delhi.
- Joined ILS as a project SRF in May 2018.
- Current research interest: Viral enzymes involved in nucleotide synthesis
8. 
Ms. Sudeshna Sen (Laboratory technician)
- BSc (Botany), SB Women’s College, Cuttack, 2015.
- Laboratory Demonstrator (Botany), Sukinda Govt. College, Jajpur, 2015-2016.
- Joined ILS as a Lab Technician in October 2016
9. 
Dr. Mrs. Aritreyee Datta (SERB N-PDF)
- BSc (Biotechnology), Bangalore University, 2007.
- MSc (Biotechnology), KIIT University, 2010.
- PhD (Biotechnology), University of Kolkata, 2017.
- SRF in Bose Institute, Kolkata, 2012-2017.
- Joined ILS as a post-doctoral fellow in August 2017.
- Current research interest: Structure of Viral Ubiquitin Ligase enzymes
10. 
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.
- 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 ILS as an institutional post-doctoral fellow in July 2018.
- Current research interest: Chromatin and Infectious Disease Structural Biology
Positions/Vacancies:
We cannot accommodate any more project trainees / MSc project students until June 2019.
A PhD student vacancy is available for Jan-Feb 2019 intake. For details, please refer to: https://www.ils.res.in/advertisements-notice/ – under the link “Advertisement for PhD Program”.
Postdoctoral candidates interested to get sponsorship for a national scheme like DBT-RA or N-PDF are welcome to discuss about the possibility when the respective applications are open.
For any specific query, you could contact Dileep at: dileepvasudevan@gmail.com
Group Alumni:
1. 
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 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.
2. 
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.
- ILS Institutional postdoc from April 2014 to July 2014.
- Postdoc in ILS with DBT-RA fellowship from July 2014 to June 2016.
- Postdoc in ILS with SERB N-PDF from July 2016 to June 2018.
- While with us, she worked on Bacterial & Plant Protease Machinery Proteins.
- Currently working as a Guest Faculty at Ravenshaw University.
We cannot accommodate any more project trainees / MSc project students until June 2019.
A PhD student vacancy is available for Jan-Feb 2019 intake. For details, please refer to: https://www.ils.res.in/advertisements-notice/ – under the link “Advertisement for PhD Program”.
Postdoctoral candidates interested to get sponsorship for a national scheme like DBT-RA or N-PDF are welcome to discuss about the possibility when the respective applications are open.
For any specific query, you could contact Dileep at: dileepvasudevan@gmail.com
