Udupi A. Ramagopal

Structural Biology of enzymes and immune receptors

A biological cell is a highly complex and organized soup of proteins, DNA, RNA, lipids and many other complex molecules that work in synergy. Although, the information necessary for the energy metabolism, defense,sensing the external world, and all other essential processes for the survival are hidden inside the genome of the cell, the real workhorse molecules are the proteins. These proteins can synthesize highly complex molecules essential for everyday life, act as framework for the cell shape and integrity, sense external molecules and also the possible threat from the outside world and so on. Over the course of evolution, nature has learnt all the tricks to create these nano-machines (proteins and their complexes), which are polymers made of just twenty different amino acids. We are interested in understanding these magical-machines, one at a time or when they are talking to each other, using biophysical and biochemical techniques. Since, the visible light has its own limitation to see such objects at atomic details, we use X-rays (X-ray diffraction from ordered 3D-array of these molecules, called crystals) to visualize such molecules. For example, we are interested in structure based functional characterization of key bacterial enzymes responsible for synthesis of essential small molecules for their survival. We are also interested in the molecules on the surface of the immune cells, so called “immune receptors” that recognize the external enemy like bacteria or our own cancer cells and play a critical role in the clearance of such threats.

Protein structure and their importance in biology.

Proteins are the key molecules life. They work 24/7 and are responsible for all the processes that take place in any living organism. For example, when we breathe, walk or even sleep, there are different proteins working in an optimal concentration and speed depending upon the need. Most drugs we consume are the manipulators of the function of these proteins. Understanding the structure of proteins is essential for understanding the basic biology as well as to design drugs against these proteins. Our lab tries to see these molecular machines in atomic details and also attempts to design small molecule drug against these molecules (see individual projects under the section “group members”).  We also try to tinker them for therapeutic applications. Below are some of the examples of proteins structures solved at PPISR.

  1. Raghurama P. Hegde, Fedorov, A.A., Sauder, J.M., Burley, S.K., Almo, S.C. & Ramagopal UA*, 2017, "The treasure your data may have: Phasing with unexpected weak anomalous scatterers", Acta Cryst F73, 184-195
  2. Ramagopal UA, Liu W, Garrett S, Yan Q, Srinivasan M, Wong S, Bell A, Mankikar S, Vangipuram R, Deshpande S, Korman A, Almo, SC. 2017, Structural basis for cancer immunotherapy by the first-in-class checkpoint inhibitor Ipilimumab. Answering referees, Proc. Nat. Acad. Sci. (USA), 114(21), E4223-E4232.
  3. Samanta D, Guo H, Rubinstein R, Ramagopal UA*, Almo SC, 2016, Biochemical and Structural studies reveal a canonical mode of molecular recognition between immune receptors TIGIT and nectin-2, Molecular Immunology 81, 151-159.
  4. Bhowmick T,  Ghosh S, Ramagopal UA, Day D, Ramakumar S, Nagaraja, S. 2014, Structure based inhibition provides an insight into the HU mediated regulation in Mycobacterium tuberculosis.  Nature Communications, 5, 4124.
  5. Chattopadyay K, Ramagopal UA,  Brenowitz, M, Nathenson SG, Almo SC.  2008.  Evolution of GITRL immune function: Murine GITRL exhibits previously unrecognized structural and biochemical properties within the TNF ligand superfamily. Proc. Nat. Acad. Sci. (USA), 105(2), 635-640.  News: http://stke.sciencemag.org/cgi/content/abstract/sigtrans;1/3/ec30
  6. Cao E, Ramagopal UA, Fedorov A, Fedorov E, Yan Q, Lary J, Cole J, Nathenson SG. and Almo SC. 2006. NTB-A Crystal structure: implications for homophilic interactions and signaling within the SLAM family of receptors. Immunity, 25(4), 559-570.
  7. Ramagopal, UA*., Thirumuruhan, RA., Fedorov, L., Dauter, Z., Almo, S.C.  2005.  Radiation-induced site-specific damage of mercury derivatives: phasing and implications. Acta Cryst. D61, 1289-1298.
  8. Ramagopal UA, Dauter M. and Dauter Z. 2003. Phasing on anomalous sulfurs: What is the limit? Acta Cryst. D59, 1020-1027. (Referred in the popular books such as  “Biomolecular crystallography" by Bernhard Rupp).
    (Comment: http://www.nsls.bnl.gov/newsroom/publications/newsletters/2003/03-nov.pdf)
  9. Ramagopal UA, Ramakumar S, Sahal D, Chauhan VS. 2001. De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions. Proc. Nat. Acad. Sci. (USA) 98(3):  870-874.

Sponsored projects

  • Ramalingaswami Fellowship titled “Co-stimulatory molecules:  Biology and therapeutic intervention”, Department of Biotechnology (DBT), New Delhi, India.
  • Design of modified B7-1 (CD-80) and B7-2 (CD86) molecules to create potential reagents for cancer and auto-immune disorders”, Vision Group on Science and Technology (VGST), Karnataka (Ms. Swetha, L.).
  • Structural and evolutionary investigations on antibiotic resistance conferring rRNA methyltransferases for designing novel strategies of drug development, Department of Science and Technology, India.

In-house projects

  • Structural Studies of purine Phosphoribosyltransferases from Pathogenic Bacteria (Ms. Pavithra G. C.).
  • The structure based functional characterization of an unusual restriction endonuclease KpnI (Ms. Pavithra G. C.).
  • Structural Study of proteins from the enolase superfamily (Dr. R. P. Hegde)
  • Testing the limits of macromolecular crystallographic phasing (Dr. R. P. Hegde)
  • Associate Professor (Ramalingaswami Fellow - DBT), 2014 – current, Poornaprajna Institute of Scientific Research, Bangalore, India.
  • Assistant Professor (Ramalingaswami Fellow - DBT), 2011 – 2013,  Poornaprajna Institute of Scientific Research, Bangalore, India.
  • Visiting Faculty, 2011 – Present: Albert Einstein College Of Medicine, New York, USA. http://www.einstein.yu.edu/home/faculty/profile.asp?id=9276
  • 2009-2011: Instructor (Faculty), Albert Einstein College Of Medicine, New York, USA.
  • 2005-2009: Associate of Biochemistry (Faculty), Albert Einstein College Of Medicine, New York, USA.
  • 2003-2005: Senior Research Associate, Department of Biochemistry, Albert Einstein College Of Medicine, New York, USA.
  • 2001-2003: Visiting Fellow, National Institute of Health, USA.
  • 2001: PhD, Department of Physics, Indian Institute of Science, Bangalore, India.
  • Ramalingswami fellow, DBT, India (2011 - 2016).

  • Best thesis “Kumari L. A. Meera Award and a Gold Medal”, 2001, IISc, India.

  • Visiting Fellow(2001 – 2003, NIH, USA).

  • Visiting Faculty (Albert Einstein College of Medicine, 2011 – current).

  • Proposal reviewer: Macromolecular Crystallography, APS, Argonne National Laboratory, USA.

  • Served in the "User Executive Committee 2002-2003" of National Synchrotron Light Source, Brookhaven National Laboratory, USA.

  • Jeffery Award (poster award - IUCr 2002, co-author).

  • Contributed >200 protein structures to World Wide Protein Data Bank (wwPDB).

  • Invited Instructor (2003-2010) at RapiData, a comprehensive course offered at Brookhaven National Laboratory for budding crystallographers around the world (http://www.bnl.gov/rapidata/).

  • Doctoral Advisory committee member for two students registered under Manipal University

  • Scientific Advisor “Genelon Life Science Ltd.”, Yelahanka, Bangalore 

Dr. Raghurama P. Hegde, Research Associate (PhD, IISc)

Raghurama Hegde obtained his M.Sc. in Physics from Christ College  (now Christ University), Bangalore University. During that time he was the recipient of second prize at the Prof. S. P. Bondade Memorial Lecture Contest held by the Indian Physics Association. He had qualified in the Graduate Aptitude Test in Engineering (GATE) and also recipient of a Junior Research Fellowship and Senior Research Fellowship of the Council of Scientific and Industrial Research (CSIR), India, during his Ph.D. He obtained his Ph.D. in Biocrystallography from the Department of Physics, Indian Institute of Science. After his Ph.D., he was a Research Fellow at the Protein Chemistry Laboratory, Department of Biological Sciences, National University of Singapore, Singapore before he joined the Division of Biological Sciences, PPISR as a Research Associate.

He has worked on two projects: (i) Structural Study of proteins from the enolase superfamily. (ii) Testing the limits of macromolecular crystallographic phasing. In the first project we have determined the crystal structures of three proteins from the enolase superfamily involved in bacterial metabolism. In the second project using X-ray diffraction data with weak anomalous signal we show how we can use the weak anomalous signals, from serendipitous anomalous scatterers observed in crystals and from native sulphurs, obtained using X-ray energies away from their absorption edges, for de novo phasing.  He is currently working on the structural studies of a putative rRNA methyltranferase from Sinorhizobium meliloti.

Ms. Pavithra G. C. (Graduate Student)

Pavithra obtained M. Sc. in Microbiology from Bangalore University.

Purine phosphoribosyltransferase is a glycosyltransferase that catalyzes the reaction between purine and PRPP to synthesize respective purine monophosphate (AMP/GMP) with the release of pyrophosphate (PP). PRTasespresent in bacteria, yeast, plants as well as mammals and are involved in purine salvage. In many pathogenic bacteria that lack, so called de novo pathway, salvage pathway is the only way to produce purine nucleotides, an essential component of DNA synthesis and also a precursor for ATP/GTP. We are perusing structural and functional characterization of PRTases from few pathogenic bacteria, which are lacking the de novo synthesis and hence are expected to be potential drug targets.

Ms. Swetha L. (Graduate Student)

I did my B.Sc.Ed at the Regional Institute of Education, Mysore and masters in Zoology at Sri Venkateswara University, Tirupati where I am a recipient of Gold medal. I am also a recipient of CSIR-JRF (2012) and qualified Graduate Aptitude Test in Engineering (GATE-2012) and Andrapradesh State Elligibility (AP-SET-2012). I joined the structural biology group at PPISR in 2013 and currently I am a senior research fellow here.

Boosting the body’s immune system to fight against an ailment is often referred to as immunotherapy. Modulation of T-cell co-stimulatory/inhibitory pathways has been proven to be one of the main immunotherapeutic approach in the treatment of cancer. CD28/CTLA-4: B7-1/B7-2 family of molecules being one of the key proteins in the T-cell co-stimulatory/ inhibitory pathway are most explored targets for immune check-point inhibitors. This project aims to modify human B7-2 protein, aided by the CD28 and CTLA-4 structure analysis, to make it a better immune-modulator than the existing antibody based drugs.

Mr. Shankar Kundapura

The T-lymphocyte cells (T-cells) are the sentinels of the cell-mediated immune response. They play a vital role in eliminating specific challenges to our body such as tumor cells, infectious agents and the like. However, their actions are very nuanced and complex. One such example is of the immune checkpoint receptors present on T-cells and few other immune related cells. These immune checkpoint receptors modulate the extent of T-cell activity. These receptors are responsible for maintaining a delicate balance between the autoimmunity and diseased state. 

One such immune checkpoint receptor is of particular interest namely, programmed cell death protein-1 (PD-1). This receptor-ligand pathway is responsible for dampening the T-cell immune response. The tumor cells exploit this pathway to escape immune surveillance by the T-cells. A myriad of antibodies have been used to remove this advantage enjoyed by the tumor cells, to various degrees of success. However, issues of toxicity and unassailable cost of these antibodies demand a cheaper and safer alternative. An attempt is being made to address these issues by rationally and minimally modifying the receptors and employing them as an alternative to antibodies.