CV_Sourav_Roy
- 1. Sourav Roy Male, Indian, Born on 16/12/1984 Research Associate Macromolecular Crystallography, Protein Folding, Biophysics Saha Institute of Nuclear Physics Email: sourav.roy@saha.ac.in/srvryt@gmail.com Office Address: Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics 1/AF, BidhanNagar, Kolkata - 700064, India Email: sourav.roy@saha.ac.in srvryt@gmail.com Phone No: +91-7278354430 +91-8274991248 Residential Address: 141-V, South Sinthee Road Kolkata-700050 West Bengal India Research Interests: I always had a strong motivation to understand how proteins carry out the specific functions ranging from chaperone to signaling. What are the unique structural features involved in such functions and what alterations cause them to dodge their responsibility? These are the questions that have intrigued me and crossed my mind on several occasions. Thus, I have developed a keen interest in solving crystal structure of proteins and to draw structural correlations to various functions, in active collaboration from bio-physical and bioinformatics tools. The specific orientation of key structural units and often residues confer stability and important spatial orientations (for biomolecular recognition) to proteins essential for its functions, such features and problems could most potently be addressed once the structural details are known. Interaction between proteins and ligands (drugs/substrates) is another such domain that has invoked my research interests. Such interactions can be best understood by structural biology (X-ray or NMR) coupled with bio-physical tools (ITC, DSC etc). To this effect I have solved two mutant crystal structures of cyclophilin from leishmania donovani and have also done isothermal titration calorimetry to study the nature of interaction between phosphoglucokinase (source: leishmania major) and suramin. I may mention that, protein unfolding has also been an area of research during my PhD tenure in which I have studied the nature of intermediate states in cyclophilin during equilibrium unfolding by guanidinium chloride. I had also employed molecular dynamics simulation at high temperatures to probe specific patterns in the unlocking of side chains in the protein interiors with cyclophilin from leishmania donovani as a model system. A sizeable amount of my research experience also revolves around MD simulation of proteins (especially their unfolding pathways and characterizing them). During my PhD tenure I have done MD unfolding simulations of proteins and have employed surface contact network based novel metrics to analyze the unfolding trajectories. In these studies we have also laid out 1 | P a g e
- 2. criteria to demarcate between the DMG (dry molten globule), WMG (wet molten globule) and TS (transition state) state ensembles based on solvent accessibility and the novel metrics. An important conclusion of this study was the disruption of key persistent contacts (which could serve as hubs) near the transition state of the molecule. Executive Summary: Can work hard individually or in a group; preparation of research reports and manuscripts. Identify biophysical and protein crystallography problems and solve them independently. Thesis Title: “Protein folding and conformational stability studies on cyclophilin and its mutants” Publications: 1) Equlibrium unfolding of cyclophilin: Characterization of intermediate state(s). Sourav Roy, Sankar Basu, Alok. K. Datta, Dhananjay Bhattacharyya, Rahul Banerjee* and Dipak Dasgupta*. International Journal of Biological Macromolecules, Volume 69, August 2014, Pages 353-360. doi: http://dx.doi/10.1016/j.ijbiomac.2014.05.063. 2) The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics. Sourav Roy, Sankar Basu, Dipak Dasgupta, Dhananjay Bhattacharyya* and Rahul Banerjee*. (Under minor revision, Plos One) Publications during MSc Project Work Anion formation by electron impact from CF4 S.V.K. Kumar, M. A. Rahman and Sourav Roy. International Journal of Mass Spectrometry. Vol. 277, 1-3, 2008, 57-61. Participation in conferences 1) ‘National workshop on Biocalorimetry’, organized by Saha Institute of Nuclear Physics, 2009 2) ‘International Conference on Physics Biology Interface’ organized by Saha Institute of Nuclear Physics, Kolkata and Indian Biophysical Society, Kolkata, 2009. 3) ‘Recent Advances in Chemical and Physical Biology’ organized by Saha Institute of Nuclear Physics and the Mechanobiology Institute, Singapore. 4) ‘International Conference on Protein Folding and Dynamics’ organized by the National Centre for Biological Sciences, Bangalore, 2012 2 | P a g e
- 3. 5) ‘National conference and workshop on Fluorescence Correlation Spectroscopy’ organized by Saha Institute of Nuclear Physics and Tata Institute of Fundamental Research, 2013 6) ‘Annual conference of the Indian Biophysical Society MADALS’ organized by Saha Institute of Nuclear Physics, 2014 Poster Presentations ‘Purification and Initial Crystallisation trials of Adenosine Kinase and Topoisomerase (II) from Leishmania Donovani ’ presented at International Conference on Physics Biology Interface’ organized by Saha Institute of Nuclear Physics, Kolkata and Indian Biophysical Society, Kolkata, 2009. ‘Protein folding and conformational stability studies on cyclophilin and its mutants’ presented at ‘International Conference on Protein Folding and Dynamics’ organized by the National Centre for Biological Sciences, Bangalore, 2012. ‘ Unfolding molecular dynamics simulation of cyclophilin characterization of the set of unfolding events’ presented at National conference and workshop on Fluorescence Correlation Spectroscopy organized by Saha Institute of Nuclear Physics and Tata Institute of Fundamental Research, 2013. ‘ Denaturant induced equilibrium unfolding of cyclophilin from leishmania donovani: Characterization of intermediate states’ presented at ‘Annual conference of the Indian Biophysical Society MADALS’ organized by Saha Institute of Nuclear Physics, 2014. Oral Presentation in ‘National Symposium on Frontiers of Biology’ held at Saha Institute of Nuclear Physics, 2015. Skills and Areas of Expertise: Bio-physical spectroscopy: Equilibrium experimental protein folding/unfolding techniques involving fluorescence, absorbtion spectoscopy, far-near UV circular dichroism spectroscopy, dynamic light scattering and bio-calorimetric techniques of differential scanning calorimetry and isothermal titration calorimetry. Protein Purification and Macromolecular Crystallography: Protein purification to homogeneity from bacterial systems through affinity column chromatography (Ni-NTA), maintenance and working with insect cell culture, 3 | P a g e
- 4. transformation of plasmids into expression systems, SDS Page and setting up of crystallisation trials by hanging drop vapour diffusion methods, crytsallization of proteins, capillary mounting of protein crystals, data collection of proteins and protein bound to ligands and structure solution using molecular replacement methods using Amore and Molrep from CCP4 suite of programs. Manual adjustments of protein side chains to fit electron densities using program Coot and O. Refinement of protein structures using CNS and Refmac. Solution of two mutant crystal structures of cyclophilin V33A and L120A with pdb codes 4S1J and 4S1E. I have also had experience in carrying out peptidyl-prolyl cis-trans isomerase enzymatic assay for cyclophilin with ala-ala-pro-phe-p-nitroanilide as the substrate. Molecular dynamics simulation techniques Experience in performing and analysis of Molecular Dynamics Simulations of proteins under native and denaturing conditions (elevated temperatures) Familiar with running Bioinformatics and Simulation Packages like NAMD, CHARMM, AMBER, Dali Server, Reduce, Modeller, Stride, DSSP, VMD and others. Programming in Fortran 77/90/95 and execution of shell scripts for downstream computational analyses. Softwares and Programs Molecular Visualization: Pymol, Rasmol, Swiss-PDB viewer Plotting: GNU plot, Origin, MATLAB, GraphPad Prism Computational: Fortran 77/90/95, MATLAB, shell scripting Pictorial Representation: Photoshop, Corel Draw, Cytoscape X-ray Crystallography: CCP4, Refmac, Coot, O, CNS, Phenix Awards and Honors: Qualified CSIR-NET lecturer-ship in the joint CSIR-UGC National Eligibility Test (NET) held in December 2008. Qualified Joint Entrance Screening Test (JEST) for admission into PhD programme 2007, Rank 74. Secured Rank #1 in the Pune-University MSc Entrance Examination 2006. Educational Qualification 4 | P a g e
- 5. Course/Degree Year of Completion Institution/Board Percentage/CGPA PhD(Life Sciences) 2015 Saha Institute of Nuclear Physics N/A Post MSc Associate ship Degree 2009 Saha Institute of Nuclear Physics 76.3 MSc (Physics) Specialisation: Biophysics 2008 University of Pune, Dept. of Physics 4.4 out of 6 BSc (Physics) 2006 St: Xavier’s College 58.3 XII Standard 2003 St: Joseph’s College 84.6 X Standard 2001 WWA Cossipore English School 91.8 References: 1. Prof. Rahul Banerjee Crystallography and Molecular Biology Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: rahul.banerjee@saha.ac.in 2. Prof. Dhananjay Bhattacharyya Computational Science Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: dhananjay.bhattacharyya@saha.ac.in 3. Prof. Dipak Dasgupta Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: dipak.dasgupta@saha.ac.in 4. Prof. Umesh Singh Indian Institute of Chemical Biology Kolkata-700032 India Email:umesh.singh@iicb.res.in 5 | P a g e
- 6. Course/Degree Year of Completion Institution/Board Percentage/CGPA PhD(Life Sciences) 2015 Saha Institute of Nuclear Physics N/A Post MSc Associate ship Degree 2009 Saha Institute of Nuclear Physics 76.3 MSc (Physics) Specialisation: Biophysics 2008 University of Pune, Dept. of Physics 4.4 out of 6 BSc (Physics) 2006 St: Xavier’s College 58.3 XII Standard 2003 St: Joseph’s College 84.6 X Standard 2001 WWA Cossipore English School 91.8 References: 1. Prof. Rahul Banerjee Crystallography and Molecular Biology Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: rahul.banerjee@saha.ac.in 2. Prof. Dhananjay Bhattacharyya Computational Science Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: dhananjay.bhattacharyya@saha.ac.in 3. Prof. Dipak Dasgupta Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics Kolkata-700064 India Email: dipak.dasgupta@saha.ac.in 4. Prof. Umesh Singh Indian Institute of Chemical Biology Kolkata-700032 India Email:umesh.singh@iicb.res.in 5 | P a g e