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

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
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
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.
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.
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.
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.
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).
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.
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.
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).
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).
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-

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).
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).
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).
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).
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)).
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).
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. 245^th 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. 238^th 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

Metal Ions in Cells, Gordon Research Conference, Salve Regina University, RI August 2011
236^th American Chemical Society National Meeting, Philadelphia, PA August 2008
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

Molecular dynamics (MD) simulations of enzymatic reactions and protein conformational dynamics
Quantum Mechanical/ Molecular Mechanical (QM/MM) methods
Structure Validation Methods: NMR refinement and X-ray crystallography
Developing bonded and non-bonded metal ion force fields for MD simulations
Umbrella sampling methods
NMR structure determination from experimental information
Calculations of target and ligand observed NMR chemical shifts
Calculation of rates and free energies of for enzymatic and non-enzymatic reactions
Calculations of transmission coefficients and quantum nuclear contributions to free energies of reaction
Impact of mutations on structure and rates of enzymatic reactions
Analyze effect of pKa and pH variations on rates of reactions
Docking substrate and drug molecules
Protein-ligand and Protein-DNA interactions
Electrostatic analysis
Quantum mechanical calculations of optimized structures and transition states in enzymatic and non-enzymatic reactions
Analysis of non-bonding energetic contributions

Software and Programming skills

Electronic structure programs: Gaussian, Jaguar (Schrodinger) and Molpro
Molecular Dynamics packages: DLPOLY, AMBER, Schrodinger suite, GROMACS and GROMOS94
Semi-Empirical programs: MOPAC and COSMOS
Docking Programs: Glide and Haddock
Cambridge Crystallographic Database software
Programming Languages: FORTRAN90 and C++
Scripting Languages: shell scripting languages and Perl
Extensive use of Wolfram Mathematica
Co-developer of PUPIL, a quantum mechanical / molecular mechanical program
Wrote programs to obtain structural information from trajectories: RMSF, RMSD, Average Structures
Wrote programs to implement Umbrella Integration and the Weighted Histogram Analysis Method (WHAM) to calculate free energies of reaction
Visualization software: Maestro, Visual Molecular Dynamics (VMD), MOLDEN, Chimera and Pymol
Electrostatics software: Advance Poisson Boltzmann Solver (APBS), DCQTP.
Protein structure software: Prime, JACKAL software (Honig Lab), Roberta, Prime, Haddock
Protein structure software: Prime, JACKAL software Familiar with Windows, Mac and Linux operating systems

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