Rajeev Prabhakar


(305) 284-9372
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2003-2006Post Doctoral Emory University
2003Ph.D. Stockholm University
Computational chemistry is a fast emerging field and today is widely applied to solve complex chemical and biochemical problems in both academia and the chemical and pharmaceutical industries. In this field, highly accurate quantum chemical methods implemented in the advanced commercial software and state-of-the-art computers including supercomputing facilities are used to explore chemistry. In our research group, we apply computational approaches, namely pure quantum mechanical (QM), hybrid quantum mechanics/ molecular mechanics (QM/MM) and molecular simulations, to investigate reaction mechanisms catalyzed by both enzymatic and non-enzymatic systems.

LIST OF SPECIALTIES: Computational chemistry, enzyme catalyzed reactions, neurodegenerative disorders and drug designing


Audrey E Tolbert, Catherine S Ervin, Thomas J Paul, Vindi M. Jayasinghe-Arachchige, Leela Ruckthong, Kosh P. Neupane, Jeanne A Stuckey, Rajeev Prabhakar, and Vincent L Pecoraro Heteromeric 3-Stranded Coiled Coils Designed Using a Pb(II)(Cys)3 Template Mediated Strategy submitted (Nature Chemistry. 2018).

Searle Duay, Gaurav Sharma, Rajeev Prabhakar, Alfredo Angeles-Boza, and Eric May Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A submitted (The Journal of Physical Chemistry B. 2018).

Gaurav Sharma, Qiaoyu Hu, Vindi Jayasinghe-Arachchige, Thomas Paul, Gerhard Schenk and Rajeev Prabhakar Investigating Coordination Flexibility of Glycerophosphodiesterase (GpdQ) Through Interactions with Mono-, Di-, and Triphosphoester (NPP, BNPP, GPE, and Paraoxon) Substrates under review (Physical Chemistry Chemical Physics. 2018).

Thomas J. Paul, Tatjana Parac-Vogt, David Quiñonero, Rajeev Prabhakar. The Journal of Physical Chemistry B 7219–7232122 (29) (Investigating Polyoxometalate-Protein Interactions at Chemically Distinct Binding Sites. 2018). [Link]

Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gaurav Sharma, Thomas J. Paul, Marcus Lundberg, David Quiñonero, Tatjana N. Parac-Vogt and Rajeev Prabhakar (Journal of Computational Chemistry. 2018). [Link]

SUMMARY: In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW11O39)]4− (ZrK) have been investigated using the hybrid two‐layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392‐Glu393 site of HSA is predicted to occur in the rate‐limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392‐Glu393, Ala257‐Asp258, Lys313‐Asp314, and Arg114‐Leu115) for the hydrolysis of all four sites of HSA.

Thomas J. Paul, Gerhard Schenk, Rajeev Prabhakar Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase (GpdQ): A Molecular Dynamics Study 5797–5808122 (22) (The Journal of Physical Chemistry B. 2018). [Link]

Amir Aliyan, Thomas J. Paul, Christopher Pennington, Gaurav Sharma, Rajeev Prabhakar, Angel Martí Photochemical Identification of Molecular Binding Sites on the Surface of Amyloid-β Fibillar Aggregrates. 898-9123 (Chem. 2017). [Link]

Hyuck Jin Lee, Kyle J. Korshavn, Younwoo Nam, Juhye Kang, Thomas J. Paul, Richard A. Kerr, Il Seung Youn, Mehmet Ozbil, Kwang S. Kim, Brandon T. Ruotolo, Rajeev Prabhakar, Ayyalusamy Ramamoorthy and Mi Hee Lim Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-related Pathological Features in Alzheimer’s Disease 2706-1523 (Chemistry - A European Journal. 2017). [Link]

Zhang, Tingting; Sharma, Gaurav ; Paul, Thomas; Hoffmann, Zachary; Prabhakar, Rajeev Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis 1079-1088575 (Journal of Chemical Information and Modeling. 2017). [Link]

Faridi M, Khan S, Zhao W, Zhang K, Kumar V, Armstrong A R, Moore E, Dorschner J M, Schnaith A M, Purmalek M, Carmona-Rivera C, Irizarry-Caro J, Zhang T, Day R, Stoub D, Hoffman V, Jehangir S, Bhargava P, Lopez A, Torroella-Kouri M, Isaac B, Altintas M A, Cimbaluk D, Zloza A, Prabhakar R, Deep S, Jolly M, Koh K H, Lee H W, Reichner J, Bradshaw E, Chen J, Moita L, Yuen P, Tsai W, Niewold T, Vazquez-Padron R, Kaplan M, and Gupta V CD11b Activation Suppresses TLR-Dependent Inflammation and Autoimmunity in Systemic Lupus Erythematosus 1271-1283127.4 (The Journal of clinical investigation. 2017). [Link]