Dhruva Kumar Chakravorty

 

Assistant Professor

Department of Chemistry

342 Chemical Sciences Building

2000 Lakeshore Drive                       

The University of New Orleans

New Orleans, LA, 70148                                                                                                          

Office phone: (504) 280-6313

Email: click to email

Website: plaza.ufl.edu/dkchakravorty

 

RESEARCH SUMMARY           

Leveraging computational methods to investigate protein dynamics and enzymatic reactions for drug design

Link to Google Scholar Citation Page

 

 

EDUCATION

 

Ph.D., Physical/Computational Chemistry                                                                                            Summer 2010

The Pennsylvania State University, University Park, PA                                                               

Advisor: Professor Sharon Hammes-Schiffer

M.S., Physical Chemistry                                                                                                                         Spring 2004

St. Stephen's College, Delhi University, Delhi, India                                                          

B.S., Chemistry (with Honors)                                                                                                                  Spring 2002

St. Stephen's College, Delhi University, Delhi, India

 

 

RESEARCH EXPERIENCE

 

Postdoctoral Research                                                                                                                      2010 – 2013

    Topic: Investigating reaction pathways in zinc metalloproteins using computational tools.

    Advisor: Prof. K. M. Merz, Jr., Quantum Theory Project, The University of Florida, Gainesville

    Experimental Collaborator: Prof. D.P. Giedroc, Indiana University, Bloomington

    Computational Collaborator: Prof. C. David Sherrill, Georgia Institute of Technology, Atlanta

    Collaboration with Industry: Quantum-Bio Inc., (Merck Pharmaceuticals and Abbott Laboratories)

 

Graduate Research                                                                                                                                         2004 – 2010

    Topic: Simulations of proton transfer reactions in enzymes using hybrid quantum/classical molecular dynamics.

    Advisor: Prof. S. Hammes-Schiffer, Department of Chemistry, The Pennsylvania State University, University Park                               

 

Independent Research                                                                                                                                  2000 - 2003

    Topic: Synthesis and applications of organic molecules for non-linear optics applications.

    Advisor: Prof. T.P. Radhakrishnan, School of Chemistry, University of Hyderabad, Hyderabad, India                                                        

 

 

 

PUBLICATIONS

 

  1. D.K. Chakravorty, M. Kumarasiri, A.V. Soudackov, and S. Hammes-Schiffer, "Implementation of Umbrella Integration within the Framework of the Empirical Valence Bond Approach" Journal of Chemical Theory and Computation. 4, 1974-1980 (2008) PMCID: PMC2659676
  2. D.K. Chakravorty, A.V. Soudackov, and S. Hammes-Schiffer, "Hybrid Quantum/Classical Molecular Dynamics simulations of the Proton Transfer Reactions catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics" Biochemistry 48, 10608-10619  (2009) PMCID: PMC2783618
  3. D.K. Chakravorty, and S. Hammes-Schiffer, "Impact of Mutation on Proton Transfer Reactions in Ketosteroid Isomerase: Insights from Molecular Dynamics Simulations" Journal of the American Chemical Society 132, 7549-7555 (2010) PMCID: PMC2896286.
  4. Y. Yang, D.K. Chakravorty, K.M. Merz, Jr., "Finding a Needle in the Haystack: Computational Modeling of Mg2+ Binding in the Active Site of Protein Farnesyltransferase" Biochemistry 49, 9658-9666 (2010) PMCID: PMC3035748.
  5. D.K. Chakravorty, B. Wang, M.N. Ucisik and K.M. Merz, Jr., "Insight into the Cation-π Interaction at the Metal Binding Site of the Copper Metallochaperone CusF" Journal of the American Chemical Society, 133, 19330-19333 (2011) PMCID: PMC3227766.
  6. D.K. Chakravorty, B. Wang, C.W. Lee, D.P. Giedroc and K.M. Merz, Jr., "Simulations of Allosteric Motions in the Zinc Sensor CzrA" Journal of the American Chemical Society, 134, 3367-3376 (2012) PMID: 22007899.
  7. M.N. Ucisik, T.V. Sploettesser, D.K. Chakravorty, D.P. Giedroc and K.M. Merz, Jr., "Journal Cover Art: CzrA" Journal of the American Chemical Society, 134, (2012).
  8. C.W. Lee, D.K. Chakravorty, F.J. Chang, H. Reyes-Caballero, Y. Ye, K.M. Merz Jr., and D.P. Giedroc, "Solution Structure of Mycobacterium tuberculosis NmtR in the Apo-state: Insights into Ni(II) Mediated Allostery" Biochemistry, 51, 2619-2629 (2012) PMID: 22394357.
  9. D.K. Chakravorty, T. M. Parker, A.J. Guerra, C.D. Sherill, D.P. Giedroc and K.M. Merz, Jr., "Energetics of Zinc-mediated Interactions in the Allosteric Pathways of Metal Sensor Proteins" Journal of the American Chemical Society, 135, 30-33 (2013) PMID: 23214972.
  10. D.K. Chakravorty, B. Wang, A.J. Guerra, C.W. Lee, D.P. Giedroc and K.M. Merz, Jr., "Solution NMR-refinement of a Metal-Ion bound Protein Using Quantum Mechanical / Molecular Mechanical and Molecular Dynamics Methods" Journal of Biomolecular NMR (Accepted online article).
  11. P. Li, B. P. Roberts, D.K. Chakravorty, , and K.M. Merz, Jr. "Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent" Journal of Chemical Theory and Computation (Just Accepted article).
  12. M. N. Ucisik, D.K. Chakravorty and K.M. Merz, Jr., "Structure and Dynamics of the N-terminal Domain of the Cu(I) Binding Protein CusB" Biochemistry (Just Accepted article).

 

Manuscripts in preparation-

  1. D.K. Chakravorty, P. Li and K.M. Merz, Jr., "Metal Ion Mediated Hydrogen Bond is the Key to Conformational Dynamics in the Copper Metallochaperone CusF" (To be submitted to the Proceedings of the National Academy of Sciences / Biochemistry).
  2. L.L. Pan, D.K. Chakravorty and K.M. Merz, Jr., "Role of Sodium Binding Sites in the Allosteric Mechanism of Thrombin" (To be submitted to Biochemistry).
  3. D.K. Chakravorty, B.P. Roberts, C.W. Lee, D.P. Giedroc and K.M. Merz Jr. "Ni(II) mediated Allostery in Mycobacterium tuberculosis NmtR" (To be submitted to Biochemistry).
  4. D.K. Chakravorty, D.P. Giedroc and K.M. Merz Jr. "Role of Conserved Domains of Conformational Dynamics in ArsR/SmtB Metal Sensor Proteins" (To be submitted to PLOS one / Journal of Chemical Theory and Computation).
  5. D.K. Chakravorty, D.P. Giedroc and K.M. Merz Jr. "A Zinc-dependent Hydrogen Bond is Critical to the Allosteric Regulation in the Zinc Sensor Protein CzrA" (To be submitted to the Journal of the American Chemical Society or the Journal of Physical Chemistry (B)).
  6. L. Westerhoff, D.K. Chakravorty, J. Cribbs and K.M. Merz, Jr.,"Calculation and Prediction of NMR Chemical Shifts Using Quantum Mechanical/Molecular Mechanics methods" (To be submitted to the Journal of Medicinal Chemistry).
  7. B.P. Roberts, J. Torras, Z. Fu, D.K. Chakravorty, G.M. Seabra, K.M. Merz Jr. and S. Trickey, "PUPIL2: A Linked Approac to Multiscale Approach to Simulations of Materials and Biopolymers" (To be submitted to the Journal of Computational Chemistry).

 

 

 

GRANT-WRITING EXPERIENCE

 

1.     Worked closely with Prof. Kenneth M. Merz in writing National Institutes of Health RO1 grants.

2.     Written grants for fellowships and scholarships.

 

 

PRESENTATIONS

 

  Oral Presentations

2.     Florida ACS Annual Meeting, Innisbrook, FL (Invited Talk)                                                           May 2013

1.     245th American Chemical Society National Meeting, New Orleans, LA                                                  April 2013

2.     Florida ACS Annual Meeting, Innisbrook, FL (Invited Talk)                                                           May 2012

3.     Florida ACS Annual Meeting, Innisbrook, FL (Invited Talk)                                                           May 2011

4.     238th American Chemical Society National Meeting, Washington D.C.                                              August 2009

5.     Conference on Dynamics of Liquids and Biomolecules, Telluride, CO                                                  June 2006

6.     Lecture series on modified electrodes, Delhi University                                                                      Spring 2004

  Poster Presentations

  1. Metal Ions in Cells, Gordon Research Conference, Salve Regina University, RI                                  August 2011
  2. 236th American Chemical Society National Meeting, Philadelphia, PA                                               August 2008
  3. Conference on Protein Dynamics and Catalysis, Tarrytown, NY                                                            May 2008

 

 

 

AWARDS AND RECONGNITION

 

1.     Weyenberg Fellowship for research achievements in chemistry, The Pennsylvania State University            2009

2.     Roberts Fellowship for graduate students in chemistry, The Pennsylvania State University                          2004

3.     Deepankar Seth Scholarship for the best graduate student in chemistry, St. Stephen's College                   2003

4.     B.R. Katyal Scholarship for the best under-graduate student in chemistry, St. Stephen's College                 2002

5.     Jawaharlal Nehru Center for Advanced Scientific Research fellowship                                                          2001

6.     Science Merit Scholarship for academic performance, Delhi University                           2000, 2001, 2002, 2003   

 

 

 

    

TECHNICAL SKILLS

 

Computational and theoretical chemistry skills

 

Software and Programming skills

 

 

  Materials/Synthetic Chemistry skills

 

       Organic synthesis of potential candidates for helical superstructures

                          Creating electroluminescent devices

       Molecular coating techniques, Self Assembly growth, molecular beam deposition methods, multi-layer coating techniques

 

 

 
WORK EXPERIENCE

 

   Founder and President of Aspire Tutorials, Delhi                                                                             2002 - 2004

                          Provided personalized educational services to grade school and college students in their homes

                          Developed fast paced company with 5 employees having over 500% fiscal growth in less than two years

 

   Teaching and Mentoring

                          Mentoring two graduate students in the Merz group                                                             2011 to present

                          Mentored an undergraduate chemistry student at the Pennsylvania State University                                    2009

                          Undergraduate coursework, the Pennsylvania State University                                                          2004 – 2005

                          Worked with physically challenged and underprivileged children                                                        1999 - 2003

 

 

ADDITIONAL INFORMATION

Languages Spoken                                                                                                      English, Hindi, Bengali, Sanskrit

Citizenship                                                                                                                                                       India           

Permanent Resident:                                                                                                                    United States of America

Professional Affiliations                                                                                                        American Chemical Society