structural and computational biology

Raja Dey, Ph. D.

Address: ** ******** **. # **, *********, NJ 07111

E-mail: *******@*****.*** (Willing to Relocate)

Phone: 973-***-**** (home)

Linkedin URL: http://www.linkedin.com/pub/raja-dey/11/483/37a/

Google Scholar: https://scholar.google.com/citations?user=qDJ6prEAAAAJ&hl=en

SUMMARY

My research efforts have been dedicated to structure-function analysis of macromolecular complexes. Areas of expertise include: X-ray Crystallography, Computational Modeling, Biophysical Characterization, Teaching and Mentoring, Investigating NIH funded project, Reviewing Journal Articles, and Publishing Peer-reviewed Articles.

Personal Attributes: * Independent and self-motivated * Positive attitude towards new developments * Manages and mentors others well * Excellent written and oral communication skills * Strong research, analytical and problem-solving skills * Works efficiently in a team or matrix organization *

Extensive experience in protein expression in E. coli host cell, purification by liquid column chromatography, protein crystallization, x-ray data processing, structure determination and refinement, biophysical characterization of peptide or protein molecule. Expertise in small and macro molecule x-ray crystallography.

Over 10 years of experience to conduct protein production, crystallization trials, Crystal Fishing, Mounting. X-ray Diffraction Data Collection, Data Processing, Structure Determination, Refinement, and Analysis

Strong bio analytical experience in peptide/protein characterization via: Circular Dichroism, Dynamic Light Scattering, Electron Microscopy Imaging, Isothermal Titration Calorimetry, UV/Vis Spectroscopy, SDS-PAGE, and Fluorescence Anisotropy

Advanced Computational modeling, involving Homology Modeling, Molecular Dynamics Simulation, Docking (both protein-protein and protein-ligand), and Virtual Screening of large databases of small molecules

MAJOR ACHIEVEMENTS

Solved 3D molecular structures of 8 distinct macromolecular complexes and over 30 small molecules by x-ray crystallography. Design and optimization of peptide nano-particles in silico followed by in vitro.

Identified small molecule inhibitors of G13 protein using pharmacophore-based virtual screening. Discovered potential allosteric modulators of nicotinic acetylcholine receptor alpha 7 subunit and small molecule moiety that inhibit the binding of myocyte enhancer factor 2 with histone deacetylase 4.

30 Peer-reviewed Publications in Journal of Molecular Biology, Structure, Cell Reports, Nucleic Acids Research, PLoS one, Journal of Organic Chemistry, Journal of Biomolecular Structure and Dynamics, Protein Engineering, Journal of Molecular Modelling, Polyhedron, Acta Crystallographica etc.

Awarded Ph. D. in Physics, M. Phil. in Environmental Science, and M. Sc. in Physics

WORK EXPERIENCE

Senior Research Associate (Postdoctoral): Weill Cornell Medical College, Department of Physiology and Biophysics, New York, 09/2015- current

X-ray diffraction data processing and structure determination of GPCR and its complex with different G-protein subunits. Expression, purification, crystallization, x-ray data collection and structure determination of Ric8A – G-protein complex, Fascin protein and it’s complexes with small molecule inhibitors. Identified small molecule inhibitors of G13 protein alpha subunit with pharmacophore-based virtual screening of small molecule databases (Zinc, Cornell, and NIH databases) using Schrodinger.

Senior Research Associate and Instructor (Postdoctoral): University of Connecticut, Institute of Materials Science, Storrs, 08/2011- 08/2015

Expressed in BL21-DE3 bacterial host cell and purified vimentin intermediate filament (11 different constructs), utilizing Ni-NTA affinity column, HiTrap Q HP, HiTrap SP HP, and size exclusion columns. Used UNICORN 5.2 for Acta FPLC.

Design and executed crystallization experiment, studied biophysical properties using DLS, EM, CD, ITC.

Performed molecular dynamics simulation (using CHARMM) of different mutants of a short peptide that forms spherical particle with icosahedral symmetry aimed at designing nanoparticle based bio-marker.

Instructed Biophysical Chemistry for graduates and undergraduates at UCONN.

Research Associate (Postdoctoral): University of Southern California, Dept. of Molecular and Computational Biology, Los Angeles, 06/2006 – 12/2010.

Used FPLC to purify HIV-1 integrase and APE 1. Columns used are Mono S, S200, HR 75. Used different biophysical techniques e.g. DLS, MALS, SDS page to check the homogeneity of the sample. Performed fluorescence anisotropy experiment to check the small molecule binding with myocyte enhancer factor 2.

Solved and refined 3D structures of myocyte enhancer factor 2 (MEF2) both in apo form and in complex with histone deacetylase 4, p53 core domain, and GATA binding protein 3 (all in complex with DNA) by the method of x-ray crystallography. Programs used: CNS, CCP4, PHENIX, O, COOT, PYMOL.

Performed computational docking (both protein-protein and protein-ligand), and virtual screening of small molecule databases in search of small molecule that binds to nicotinic acetylcholine receptor (nAChR) and MEF2. Discovered some potential allosteric modulators of nAChR and small molecule that inhibits the binding of MEF2 with HDAC4. Programs used: Molsoft ICM

Postdoctoral Fellow: Chalmers University of Technology, Department of Chemistry and Bioscience, Sweden, 10/2003 –10/ 2005

Crystallized Bacillus Subtilis chorismate mutase, preparation of heavy atom derivative of chorismate mutase enzyme crystal, fishing and mounting crystal, x-ray diffraction data collection,

Solved and refined 3D structure of chorismate mutase enzyme from Mycobacterium Tuberculosis in apo and ligand bound form. Programs used: CCP4, CNS, O, PYMOL, DIAMOND, Insight II.

Graduate Research Assistant: University of Calcutta, Department of Physics, India. 02/1997 – 04/2002

Performed small molecule crystallization, X-ray data collection, solved and refined many small molecule compounds of biological importance,

Analysed chemical conformation of these molecules, built homology model of steroid receptors and studied their interaction with different steroid compounds, e.g. cortisol, corticosterone, deoxy-corticosterone. Programs used: SHELX, MULTAN, ORTEP, PLUTON, Insight II

EDUCATION

Ph. D. in Physics (04/2002), Calcutta University, India

Thesis Title – “Studies on Crystal and Molecular Structure of some Organic Compounds by X-ray Crystallography and Computer Modelling”

M. Phil. in Environmental Science (05/1992), Jadavpur University, India

Thesis Title – “Atmospheric boundary layer and role of convection”

B. Ed. in Education (03/1991), Calcutta University, India

Studied History of Education, Methods of Teaching Science and Mathematics

M.Sc. in Physics (08/1988), Calcutta University, India :- studied mechanics, spectroscopy, electronics, solid state physics, liquid crystal, nuclear physics, relativity, X-rays and Crystallography, Application of Crystallography to study structure-function of both small and macromolecules

B.Sc. Honors in Physics (03/1985, Calcutta University, India :- studied Chemistry(General, Inorganic, Organic, and Physical), Mathematics, and Honors in Physics

ADDITIONAL CERTIFICATES

Data Scientist’s Toolbox, R programming, Getting and Cleaning Data, and Exploratory Analysis of Data, Reproducible Research, and Statistical Inference – Jan-May, 2015, Johns Hopkins University with distinction.

Object oriented programming (3 units), Spring 2011, Los Angeles Trade Technical College, California

Micro Database Programming (3 units), Spring 2011, Los Angeles Trade Technical College, California

Advanced graduate course in ‘Practical Protein Crystallization’, February 2005, BMC, Uppsala, Sweden.

Ph. D. course in ‘Introduction to Biomolecular NMR Spectroscopy’, January 2005, Swedish NMR Centre,

Goteborg University, Sweden.

SPECIALIZED SKILLS

Laboratory

1.Molecular biology: Protein expression in bacterial cell and purification by FPLC using ion exchange, size exclusion, affinity, and Histrap columns.

2.Biophysical characterization : Fluorescence anisotropy, Dynamic light scattering (DLS), UV/Vis spectroscopy, Electron Microscopy, Circular Dichroism, ITC, SAXS, SDS-PAGE gel electrophoresis. Folding analysis of different protein and peptide nanoparticle.

3.Structural biology: Protein crystallization (hanging drop and sitting drop vapour diffusion experiments); Preparing heavy atom derivatives; Crystal fishing, mounting and storage; X-ray diffraction data collection and data processing; Structure solving and refinement using CCP4, CNS and PHENIX suits. Used many phasing methods e.g. SAD, MAD, MIR, MR etc., model building by COOT, O, and PYMOL.

Computational: Homology modeling, Molecular docking (both protein-protein and protein-ligand), virtual screening of small molecule databases, molecular dynamics simulation using Schrodinger, CHARMM, Insight II, Molsoft. Experienced in Fortran, Python, and R programing languages.

PROFESSIONAL SOCIETIES: Member of International Union of Crystallography, American Crystallographic Association, and American Chemical Society

SELECTED PUBLICATIONS

1.Viktoriya Syrovatkina, Kamela O. Alegre, Dey, Raja and Xin-Yun Huang, ”Regulation, Signaling, and Physiological Functions of G-Proteins”; J. Mol. Biol. (2016) (http://dx.doi.org/10.1016/ j.jmb.2016.08.002)

2.Dey, Raja, Yan Xia, Mu-Ping Nieh and Peter Burkhard, ”Molecular Design of a Minimal Peptide Nanoparticle”, ACS Biomaterials and Engineering (DOI:10.1021/acsbiomaterials.6b00243), 2016.

3.Tais A. P. F. Doll, Raja Dey and Peter Burkhard, Design and optimization of peptide nanoparticles. J. of Nano. Biotech. (joint first authorship);13(1):73, 2015.

4.Tais A. P. F. Doll, Senthilkumar Raman, Raja Dey and Peter Burkhard, “Nanoscale assemblies and their biomedical applications”; J. R. Soc. Interface. 10, 20120740; doi:10.1098/rsif.2012.0740, 2013.

5.Jayathilaka, Nimanthi; Han, Aidong; Gaffney, Kevin; Dey, Raja; Jarusiewicz, Jamie; Noridomi, Kaori; Philips, Michael; Lei, Xiao; He, Ju; Ye, Jun,; Gao, Tao; Petasis, Nicos; Chen, Lin; “Inhibition of the function of class IIa HDACs by blocking their interaction with MEF2”; Nucleic Acids Research, 2012, 1–11

6.Yongheng Chen, Darren L. Bates, Raja Dey, Po-Han Chen, Ana Carolina Dantas Machado, Ite A. Laird-Offringa, Remo Rohs, Lin Chen, “DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation”; Cell Reports 2, 1-10, 2012.

7.Xuli Wu, Raja Dey, Hui Wu, Zhigang Liu, Qingqing He, Xiaojuan Zeng; O R I G I N A L Studies on the interaction of -epigallocatechin-3-gallate from green tea with bovine b-lactoglobulin by spectroscopic methods and docking; International Journal of Dairy Technology. 01/2012; 65. DOI:10.1111/j.1471-0307.2012.00873.x

8.Raja Dey, Lin Chen, “In search of allosteric modulators of alpha7-nAChR by solvent density guided structure based virtual screening”; Journal of Biomolecular Structure and Dynamics, Vol 28, Issue 5, 695-715, 2011.

9.Yongqing Wu, Raja Dey, Aidong Han, Nimanthi Jayathilaka, Michael Philips, Jun Ye, Lin Chen ”Structure of MEF2A bound to DNA reveals a completely folded MADS-box/MEF2 domain that recognizes DNA and recruits transcription co-factors” JMB (joint 1st authorship), 397, 520-533, 2010.

10.Yongheng Chen, Raja Dey and Lin Chen “Crystal structure of the p53 core domain bound to a full consensus site as a self-assembled tetramer”. Structure, 18, 246-256, 2009

11.Raja Dey, Kunmei Ji, Zhaigang Liu, Lin Chen; A Cytokine-Cytokine interaction in the Assembly of Higher-Order Structure and Activation of the Interleukine3: Receptor Complex, PLoS one, Vol 4, Issue 4, e5188, 1-12, 2009

12.Morsy A. M. Abu-Youssef, Raja Dey, Yousry Gohar, Alshima'a A. Massoud, Lars Ohrstrom, Vratislav Langer, Synthesis and structure of silver complexes with nicotinate type ligands having antibacterial activities against clinically isolated antibiotic resistant pathogens, Journal of Organic Chemistry, 46(15), 5893-5903, 2007

13.Mats Ökvist, Raja Dey, Severin Sasso, Peter Kast and Ute Krengel; 1.6 Å crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: Novel fold topology revealed. JMB (Joint 1st authorship), 357, 1483-1499, 2006

14.Ute Krengel, Raja Dey, Mats Ökvist, Severin Sasso, and Peter Kast; Preliminary X-ray crystallographic analysis of the secreted chorismate mutase from Mycobacterium tuberculosis: a tricky crystallization problem solved. Acta Cryst. F62, 1-5, 2006.

15.Raja Dey and P. Roychowdhury; Homology model of human corticosteroid binding globulin : a study of its steroid binding ability and a plausible mechanism of steroid hormone release at the site of inflammation; Journal of Molecular Modelling, Vol. 9, pp. 183-189, 2003.

16.Raja Dey and P. Roychowdhury; Homology modelling of the ligand binding domain of mineralocorticoid receptor: close structural kinship with the ligand binding domain of glucocorticoid receptor and their similar binding mode with DOC (de-oxy corticosterone); Journal of Biomolecular Structure and Dynamics, Vol. 20, No. 1, pp. 21-29, 2002.

17.Raja Dey, P. Roychowdhury, C. Mukharjee; Homology modelling of the ligand-binding domain of glucocorticoid receptor: binding site interactions with cortisol and corticosterone; Protein Engineering, Vol. 14 no. 8 pp. 565-571, 2001.

REFERENCES – Available Upon Request

Contact this candidate