Rajeev Prabhakar - Publications

Affiliations: 
Chemistry University of Miami, Coral Gables, FL 

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Das A, Sharma G, Kamatham N, Prabhakar R, Sen P, Ramamurthy V. Ultrafast Solvation Dynamics Reveal that Octa Acid Capsule's Interior Dryness Depends on the Guest. The Journal of Physical Chemistry. A. PMID 31276410 DOI: 10.1021/acs.jpca.9b04626  0.44
2019 Raj AM, Sharma G, Prabhakar R, Ramamurthy V. Space Constrained Stereoselective Geometric Isomerization of 1,2-Diphenylcyclopropane and Stilbenes in an Aqueous Medium. Organic Letters. PMID 31247756 DOI: 10.1021/acs.orglett.9b01176  0.44
2019 Otolski CJ, Anthony Raj MR, Sharma G, Prabhakar R, Ramamurthy V, Elles CG. Ultrafast trans→ cis Photoisomerization Dynamics of Alkyl-Substituted Stilbenes in a Supramolecular Capsule. The Journal of Physical Chemistry. A. PMID 31140802 DOI: 10.1021/acs.jpca.9b03285  0.44
2019 Duay SS, Sharma G, Prabhakar R, Angeles-Boza AM, May ER. Molecular Dynamics Investigation into the Effect of Zinc(II) on the Structure and Membrane Interactions of the Antimicrobial Peptide Clavanin A. The Journal of Physical Chemistry. B. PMID 30908921 DOI: 10.1021/acs.jpcb.8b11496  0.44
2019 Sharma G, Hu Q, Jayasinghe-Arachchige VM, Paul TJ, Schenk G, Prabhakar R. Investigating coordination flexibility of glycerophosphodiesterase (GpdQ) through interactions with mono-, di-, and triphosphoester (NPP, BNPP, GPE, and paraoxon) substrates. Physical Chemistry Chemical Physics : Pccp. PMID 30785142 DOI: 10.1039/c8cp07031h  0.44
2018 Jayasinghe-Arachchige VM, Hu Q, Sharma G, Paul TJ, Lundberg M, Quinonero D, Parac-Vogt TN, Prabhakar R. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study. Journal of Computational Chemistry. PMID 30238478 DOI: 10.1002/jcc.25528  0.44
2018 Paul TJ, Parac-Vogt T, Quiñonero D, Prabhakar R. Investigating Polyoxometalate-Protein Interactions at Chemically Distinct Binding Sites. The Journal of Physical Chemistry. B. PMID 29975530 DOI: 10.1021/acs.jpcb.8b02931  0.44
2018 Paul TJ, Schenk G, Prabhakar R. Formation of Catalytically Active Binuclear Center of Glycerophosphodiesterase (GpdQ): A Molecular Dynamics Study. The Journal of Physical Chemistry. B. PMID 29723477 DOI: 10.1021/acs.jpcb.8b02046  0.44
2017 Zhang T, Sharma G, Paul TJ, Hoffmann Z, Prabhakar R. Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. Journal of Chemical Information and Modeling. PMID 28398040 DOI: 10.1021/acs.jcim.6b00781  0.44
2017 Faridi MH, Khan SQ, Zhao W, Lee HW, Altintas MM, Zhang K, Kumar V, Armstrong AR, Carmona-Rivera C, Dorschner JM, Schnaith AM, Li X, Ghodke-Puranik Y, Moore E, Purmalek M, ... ... Prabhakar R, et al. CD11b activation suppresses TLR-dependent inflammation and autoimmunity in systemic lupus erythematosus. The Journal of Clinical Investigation. PMID 28263189 DOI: 10.1172/JCI88442  0.44
2017 Lee HJ, Korshavn KJ, Nam Y, Kang J, Paul TJ, Kerr RA, Youn IS, Ozbil M, Kim KS, Ruotolo BT, Prabhakar R, Ramamoorthy A, Lim MH. Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-Related Pathological Features in Alzheimer's Disease. Chemistry (Weinheim An Der Bergstrasse, Germany). 23: 2706-2715. PMID 28004889 DOI: 10.1002/chem.201605401  0.84
2016 Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Physical Chemistry Chemical Physics : Pccp. 18: 24790-24801. PMID 27711373 DOI: 10.1039/c6cp02097f  1
2016 Tootoonchi MH, Sharma G, Calles J, Prabhakar R, Kaifer AE. Cooperative Self-Assembly of a Quaternary Complex Formed by Two Cucurbit[7]uril Hosts, Cyclobis(paraquat-p-phenylene) and a "Designer" Guest. Angewandte Chemie (International Ed. in English). PMID 27533594 DOI: 10.1002/anie.201606038  0.44
2016 Paul TJ, Hoffmann Z, Wang C, Shanmugasundaram M, de Joannis J, Shekhtman A, Lednev IK, Yadavalli VK, Prabhakar R. Structural and Mechanical Properties of Amyloid beta Fibrils: A Combined Experimental and Theoretical Approach. The Journal of Physical Chemistry Letters. PMID 27387853 DOI: 10.1021/acs.jpclett.6b01066  1
2015 Derrick JS, Kerr RA, Nam Y, Oh SB, Lee HJ, Earnest KG, Suh N, Peck KL, Ozbil M, Korshavn KJ, Ramamoorthy A, Prabhakar R, Merino EJ, Shearer J, Lee JY, et al. A Redox-Active, Compact Molecule for Cross-Linking Amyloidogenic Peptides into Nontoxic, Off-Pathway Aggregates: In Vitro and In Vivo Efficacy and Molecular Mechanisms. Journal of the American Chemical Society. 137: 14785-97. PMID 26575890 DOI: 10.1021/jacs.5b10043  0.84
2015 Song ES, Ozbil M, Zhang T, Sheetz M, Lee D, Tran D, Li S, Prabhakar R, Hersh LB, Rodgers DW. An Extended Polyanion Activation Surface in Insulin Degrading Enzyme. Plos One. 10: e0133114. PMID 26186535 DOI: 10.1371/journal.pone.0133114  0.84
2015 Libardo MD, Paul TJ, Prabhakar R, Angeles-Boza AM. Hybrid peptide ATCUN-sh-Buforin: Influence of the ATCUN charge and stereochemistry on antimicrobial activity. Biochimie. 113: 143-55. PMID 25891844 DOI: 10.1016/j.biochi.2015.04.008  1
2015 Zhang T, Ozbil M, Barman A, Paul TJ, Bora RP, Prabhakar R. Theoretical insights into the functioning of metallopeptidases and their synthetic analogues. Accounts of Chemical Research. 48: 192-200. PMID 25607542 DOI: 10.1021/ar500301y  1
2014 Barman A, Prabhakar R. Computational Insights into Substrate and Site Specificities, Catalytic Mechanism, and Protonation States of the Catalytic Asp Dyad of β -Secretase. Scientifica. 2014: 598728. PMID 25309776 DOI: 10.1155/2014/598728  1
2014 Mondal B, Zhang T, Prabhakar R, Captain B, Ramamurthy V. Role of hydrogen bonds in molecular packing of photoreactive crystals: templating photodimerization of protonated stilbazoles in crystalline state with a combination of water molecules and chloride ions. Photochemical & Photobiological Sciences : Official Journal of the European Photochemistry Association and the European Society For Photobiology. 13: 1509-20. PMID 25096970 DOI: 10.1039/c4pp00221k  1
2014 Zhang T, Zhu X, Prabhakar R. Mechanistic insights into metal (Pd2+, Co2+, and Zn2+)-β-cyclodextrin catalyzed peptide hydrolysis: a QM/MM approach. The Journal of Physical Chemistry. B. 118: 4106-14. PMID 24713044 DOI: 10.1021/jp502229s  0.56
2013 Elton ES, Zhang T, Prabhakar R, Arif AM, Berreau LM. Pb(II)-promoted amide cleavage: mechanistic comparison to a Zn(II) analogue. Inorganic Chemistry. 52: 11480-92. PMID 24066688 DOI: 10.1021/ic401782x  1
2013 Cook NP, Ozbil M, Katsampes C, Prabhakar R, Martí AA. Unraveling the photoluminescence response of light-switching ruthenium(II) complexes bound to amyloid-β. Journal of the American Chemical Society. 135: 10810-6. PMID 23845146 DOI: 10.1021/ja404850u  0.84
2013 Barman A, Prabhakar R. Elucidating the catalytic mechanism of β-secretase (BACE1): a quantum mechanics/molecular mechanics (QM/MM) approach. Journal of Molecular Graphics & Modelling. 40: 1-9. PMID 23337572 DOI: 10.1016/j.jmgm.2012.12.010  1
2013 Liu Y, Mukherjee A, Nahumi N, Ozbil M, Brown D, Angeles-Boza AM, Dooley DM, Prabhakar R, Roth JP. Experimental and computational evidence of metal-O2 activation and rate-limiting proton-coupled electron transfer in a copper amine oxidase. The Journal of Physical Chemistry. B. 117: 218-29. PMID 23240607 DOI: 10.1021/jp3121484  1
2013 Choudhury R, Barman A, Prabhakar R, Ramamurthy V. Hydrocarbons depending on the chain length and head group adopt different conformations within a water-soluble nanocapsule: 1H NMR and molecular dynamics studies. The Journal of Physical Chemistry. B. 117: 398-407. PMID 23215251 DOI: 10.1021/jp3090815  1
2012 Ozbil M, Barman A, Bora RP, Prabhakar R. Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions. The Journal of Physical Chemistry Letters. 3: 3460-9. PMID 26290973 DOI: 10.1021/jz301597k  1
2012 Kurouski D, Washington J, Ozbil M, Prabhakar R, Shekhtman A, Lednev IK. Disulfide bridges remain intact while native insulin converts into amyloid fibrils. Plos One. 7: e36989. PMID 22675475 DOI: 10.1371/journal.pone.0036989  1
2012 Barman A, Prabhakar R. Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study. Journal of Chemical Information and Modeling. 52: 1275-87. PMID 22545704 DOI: 10.1021/ci200611t  1
2012 Zhu X, Bora RP, Barman A, Singh R, Prabhakar R. Dimerization of the full-length Alzheimer amyloid β-peptide (Aβ42) in explicit aqueous solution: a molecular dynamics study. The Journal of Physical Chemistry. B. 116: 4405-16. PMID 22448932 DOI: 10.1021/jp210019h  1
2012 Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 17: 209-22. PMID 21918843 DOI: 10.1007/s00775-011-0843-2  1
2011 Vetrivel KS, Barman A, Chen Y, Nguyen PD, Wagner SL, Prabhakar R, Thinakaran G. Loss of cleavage at β'-site contributes to apparent increase in β-amyloid peptide (Aβ) secretion by β-secretase (BACE1)-glycosylphosphatidylinositol (GPI) processing of amyloid precursor protein. The Journal of Biological Chemistry. 286: 26166-77. PMID 21642424 DOI: 10.1074/jbc.M111.260471  1
2011 Barman A, Schürer S, Prabhakar R. Computational modeling of substrate specificity and catalysis of the β-secretase (BACE1) enzyme. Biochemistry. 50: 4337-49. PMID 21500768 DOI: 10.1021/bi200081h  1
2011 Echeverria V, Zeitlin R, Burgess S, Patel S, Barman A, Thakur G, Mamcarz M, Wang L, Sattelle DB, Kirschner DA, Mori T, Leblanc RM, Prabhakar R, Arendash GW. Cotinine reduces amyloid-β aggregation and improves memory in Alzheimer's disease mice. Journal of Alzheimer's Disease : Jad. 24: 817-35. PMID 21321389 DOI: 10.3233/JAD-2011-102136  1
2011 Kulasekharan R, Choudhury R, Prabhakar R, Ramamurthy V. Restricted rotation due to the lack of free space within a capsule translates into product selectivity: photochemistry of cyclohexyl phenyl ketones within a water-soluble organic capsule. Chemical Communications (Cambridge, England). 47: 2841-3. PMID 21253635 DOI: 10.1039/c0cc05337f  1
2011 Cai X, Majumdar S, Fortman GC, Cazin CS, Slawin AM, Lhermitte C, Prabhakar R, Germain ME, Palluccio T, Nolan SP, Rybak-Akimova EV, Temprado M, Captain B, Hoff CD. Oxygen binding to [Pd(L)(L')] (L= NHC, L' = NHC or PR3, NHC = N-heterocyclic carbene). synthesis and structure of a paramagnetic trans-[Pd(NHC)2(η(1)-O2)2] complex. Journal of the American Chemical Society. 133: 1290-3. PMID 21204538 DOI: 10.1021/ja1103348  1
2010 Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which one among aspartyl protease, metallopeptidase, and artificial metallopeptidase is the most efficient catalyst in peptide hydrolysis? The Journal of Physical Chemistry. B. 114: 10860-75. PMID 20669962 DOI: 10.1021/jp104294x  1
2010 Bora RP, Prabhakar R. Elucidation of interactions of Alzheimer amyloid beta peptides (Abeta40 and Abeta42) with insulin degrading enzyme: a molecular dynamics study. Biochemistry. 49: 3947-56. PMID 20380468 DOI: 10.1021/bi1002103  0.84
2010 Jayaraj N, Maddipatla MV, Prabhakar R, Jockusch S, Turro NJ, Ramamurthy V. Closed nanocontainer enables thioketones to phosphoresce at room temperature in aqueous solution. The Journal of Physical Chemistry. B. 114: 14320-8. PMID 20356085 DOI: 10.1021/jp911698s  1
2010 Bora RP, Ozbil M, Prabhakar R. Elucidation of insulin degrading enzyme catalyzed site specific hydrolytic cleavage of amyloid beta peptide: a comparative density functional theory study. Journal of Biological Inorganic Chemistry : Jbic : a Publication of the Society of Biological Inorganic Chemistry. 15: 485-95. PMID 20033747 DOI: 10.1007/s00775-009-0617-2  0.84
2010 Kumar A, Zhu X, Walsh K, Prabhakar R. Theoretical insights into the mechanism of selective Peptide bond hydrolysis catalyzed by [Pd(H(2)O)(4)](2+). Inorganic Chemistry. 49: 38-46. PMID 19958017 DOI: 10.1021/ic901071v  0.56
2009 Bora RP, Prabhakar R. Translational, rotational and internal dynamics of amyloid beta-peptides (Abeta40 and Abeta42) from molecular dynamics simulations. The Journal of Chemical Physics. 131: 155103. PMID 20568886 DOI: 10.1063/1.3249609  0.84
2009 Germain ME, Temprado M, Castonguay A, Kryatova OP, Rybak-Akimova EV, Curley JJ, Mendiratta A, Tsai YC, Cummins CC, Prabhakar R, McDonough JE, Hoff CD. Coordination-mode control of bound nitrile radical complex reactivity: intercepting end-on nitrile-Mo(III) radicals at low temperature. Journal of the American Chemical Society. 131: 15412-23. PMID 19919164 DOI: 10.1021/ja905849a  1
2009 Singh R, Barman A, Prabhakar R. Computational insights into aspartyl protease activity of presenilin 1 (PS1) generating Alzheimer amyloid beta-peptides (Abeta40 and Abeta42). The Journal of Physical Chemistry. B. 113: 2990-9. PMID 19708161 DOI: 10.1021/jp811154w  1
2009 Orville AM, Lountos GT, Finnegan S, Gadda G, Prabhakar R. Crystallographic, spectroscopic, and computational analysis of a flavin C4a-oxygen adduct in choline oxidase. Biochemistry. 48: 720-8. PMID 19133805 DOI: 10.1021/bi801918u  1
2009 Barman A, Taves W, Prabhakar R. Insights into the mechanism of methionine oxidation catalyzed by metal (Cu(2+), Zn(2+), and Fe(3+)) - amyloid beta (Abeta) peptide complexes: A computational study. Journal of Computational Chemistry. 30: 1405-13. PMID 19037857 DOI: 10.1002/jcc.21167  1
2008 Triguero L, Singh R, Prabhakar R. Comparative molecular dynamics studies of wild-type and oxidized forms of full-length Alzheimer amyloid beta-peptides Abeta(1-40) and Abeta(1-42). The Journal of Physical Chemistry. B. 112: 7123-31. PMID 18476733 DOI: 10.1021/jp801168v  0.64
2008 Triguero L, Singh R, Prabhakar R. Molecular dynamics study to investigate the effect of chemical substitutions of methionine 35 on the secondary structure of the amyloid beta (Abeta(1-42)) monomer in aqueous solution. The Journal of Physical Chemistry. B. 112: 2159-67. PMID 18220385 DOI: 10.1021/jp0771872  0.64
2004 Prabhakar R, Siegbahn PEM. A Theoretical Study of the Mechanism for the Biogenesis of Cofactor Topaquinone in Copper Amine Oxidases Journal of the American Chemical Society. 126: 3996-4006. PMID 15038754 DOI: 10.1021/ja034721k  1
2003 Prabhakar R, Siegbahn PEM. A comparison of the mechanism for the reductive half-reaction between pea seedling and other copper amine oxidases (CAOs) Journal of Computational Chemistry. 24: 1599-1609. PMID 12926004 DOI: 10.1002/jcc.10282  1
2003 Prabhakar R, Siegbahn PEM, Minaev BF. A theoretical study of the dioxygen activation by glucose oxidase and copper amine oxidase Biochimica Et Biophysica Acta - Proteins and Proteomics. 1647: 173-178. PMID 12686129 DOI: 10.1016/S1570-9639(03)00090-6  1
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