Publications
2016
Fe(II)/Fe(III) Redox Process Can Significantly Modulate the Conformational Dynamics and Electrostatics of Pirin in NF-κB Regulation. Arghya Barman and Donald Hamelberg, ACS Omega, 2016, 1, 837–842 (link)
Mechanism of peptide hydrolysis by aspartyl and metalloproteases, homas Paul, Arghya Barman, Mehmet Ozbil, Ram P Bora, Tingting Zhang, Gaurav Sharma, Zachary Hoffmann, and Rajeev Pabhakar, Physical Chemistry Chemical Physics, 2016, DOI: 10.1039/C6CP02097F (IF: 4.449) (link)
Coupled dynamics and entropic contribution to allosteric mechanism of Pin1. Arghya Barman and Donald Hamelberg. Journal of Physical Chemistry B, 2016, 120, 8405-8415 (IF: 3.302) (link)
Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins, Arghya Barman, Crystal Lynn Smitherman, Michael Gregory Souffrant, Giovanni Gadda, and Donald Hamelberg, Journal of Chemical Information and. Modeling, 2016, 56, 139-147(IF: 4.068) (link)
2015
Pushing the limits of the molecular mechanics force field to probe weak CH--π interactions in proteins. Arghya Barman, Bruce Batiste and Donald Hamelberg. Journal of Chemical Theory and Computation. 2015, 11, 1854-1863(IF: 5.310) (link)
An Iron Reservoir to the Catalytic Metal: The Rubredoxin Iron in an Extradiol Dioxygenase. Fange Liu, Jiafeng Geng, Ryan H. Gumpper, Arghya Barman, Ian Davis, Andrew Ozarowski, Donald Hamelberg, and Aimin Liu, Journal of Molecular Biology, 2015, DOI:10.1074/jbc.M115.650259 (IF: 4.600) (link)
Loss of intra-molecular electrostatic interactions and limited conformational space may promote self-association of cis-tau peptide. Arghya Barman and Donald Hamelberg. Proteins: Structure Function and Bioinformatics 2015, 83,436-444. (IF: 2.921) (link)
Theoretical Insights into the Functioning of Metallopeptidases and Their Synthetic Analogues. Tingting Zhang, Mehmet Ozbil, Arghya Barman, Thomas J. Paul, Ram Prasad Bora, and Rajeev Prabhakar. Accounts of Chemical Research 2015,48,192-200. (IF: 24.348) (link)
2014
Cysteine mediated dynamic hydrogen-bonding network in the active site of Pin1. Arghya Barman and Donald Hamelberg. Biochemistry 2014, 53, 3839-3850 (IF: 3.194) (link)
Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”. Manish Paul, Mousumi Hazra, Arghya Barman and Saugata Hazra, Journal of Biomolecular Structure and Dynamics, 2014, 32, 928-949 (IF: 2.983) (link)
Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl isomerases. Safia Tork Ladani, Michael Souffrant, Arghya Barman and Donald Hamelberg. Biochimica et Biophysica Acta. 2014. doi:10.1016/j.bbagen.2014.12.023. (IF: 3.829) (link)
Computational Insights into Substrate and Site Specificities, Catalytic Mechanism and Protonation States of the Catalytic Asp Dyad of β-Secretase (BACE1). Arghya Barman and Rajeev Prabhakar. Scientifica, vol. 2014, Article ID 598728, 11 pages, 2014. doi:10.1155/2014/598728). (IF: 1.210) (link)
2013
Elucidating the Catalytic mechanism of β-secretase enzyme in the presence of surrounding protein environment: A QM/MM study. Arghya Barman and Rajeev Prabhakar Journal of Molecular Graphics and Modelling. 2013, 40, 1-9. (IF: 2.022) (link)
Hydrocarbons Depending on the Chain Length and Head Group Adopt Different Conformations within a Water-Soluble Nanocapsule: 1H NMR and Molecular Dynamics Studies. Rajib Choudhury, Arghya Barman, Rajeev Prabhakar and V. Ramamurthy Journal of Physical Chemistry B 2013, 117, 398-407. (IF: 3.377) (link)
2012
Protonation states of the catalytic dyad of β-secretase (BACE1) in presence of chemically diverse inhibitors: Insights from molecular docking study. Arghya Barman and Rajeev Prabhakar Journal of Chemical Information and Modeling 2012, 52 (5), 1275-1287. (IF: 4.068) (link)
Computational Insights into Dynamics of Protein Aggregation and Enzyme−Substrate Interactions. Mehmet Ozbil, Arghya Barman, Ram Prasad Bora and Rajeev Prabhakar Journal of Physical Chemistry Letter (Perspective) 2012, 3, 3460−3469. (IF: 6.687) (link)
Mechanism of Peptide Hydrolysis by Co-catalytic Metal Centers Containing Leucine Aminopeptidase Enzyme: A DFT Approach. Xiaoxia Zhu, Arghya Barman, Mehmet Ozbil, Tingting Zhang, Shanghao Li and Rajeev Prabhakar. Journal of Biological Inorganic Chemistry 2012, 17(2), 209-222. (IF: 3.164) (link)
Dimerization of the Full-Length Alzheimer’s Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A molecular Dynamics Study. Xiaoxia Zhu, Ram Prasad Bora, Arghya Barman, Rajiv Singh and Rajeev Prabhakar Journal of Physical Chemistry B 2012, 116(15), 4405-4416. (IF: 3.377) (link)
2011
Computational Modeling of Substrate Specificity and Catalysis of the β-secretase (BACE1) enzyme. Arghya Barman, Stephan Schürer, Rajeev Prabhakar. Biochemistry 2011, 50, 4337-4349. (IF: 3.194) (link)
Loss of cleavage at ß’-site contributes to the apparent increase of Aß secretion by BACE1-GPI processing of APP. Kulandaivelu S. Vetrivel, Arghya Barman, Ying Chen, Phuong D. Nguyen, Steven L. Wagner, Rajeev Prabhakar, and Gopal Thinakaran Journal Biological Chemistry 2011, 286, 26166-26177. (IF: 4.600) (link)
Cotinine modulates nicotinic receptors, reduces β-amyloid aggregation, and improves Alzheimer’s pathology in mice. Valentina Echeverria, Ross Zeitlin, Sarah Burgess, Arghya Barman, Garima Thakur, Hideyo Inouye, Edmundo Feris, Magorzota Mamcarz, Li Wang, Steven D. Buckingham, Daniel A Kirschner, Takashi Mori, Roger M. Leblanc, Rajeev Prabhakar, David Sattelle, Roger L. Papke, and Gary W. Arendash. Journal of Alzheimer’s Disease 2011, Volume 24, Number 4, 817-835. (IF: 3.612) (link)
2010
Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? Ram P Bora, Arghya Barman, Xiaoxia Zhu, Mehmet Ozbil, Rajeev Prabhakar Journal of Physical Chemistry B 2010, 114, 10860–10875. (IF: 3.377) (link)
Insights into the Mechanism of Methionine Oxidation Catalyzed by Metal (Cu2+, Zn2+ and Fe3+) -Amyloid Beta (Aβ) Peptide Complexes: A Computational Study. Arghya Barman, Woody Taves, and Rajeev Prabhakar, Journal of Computational Chemistry 2009, 30(9), 1405-1413. (IF: 3.601) (link)
2009
Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). Rajiv Singh, Arghya Barman and Rajeev Prabhakar Journal of Physical Chemistry B 2009, 113, 2990-2999. (IF: 3.377) (link)
Modeling the self-assembly dynamics of macromolecular protein aggregates underlying neurodegenerative disorders. Zhenyuan Zhao, Rajiv Singh, Arghya Barman, Neil F. Johnson, and Rajeev Prabhakar Computational and Theoretical Nanoscience 2009, 6(6), 1338-1351. (IF: 1.032) (link)
2016
Fe(II)/Fe(III) Redox Process Can Significantly Modulate the Conformational Dynamics and Electrostatics of Pirin in NF-κB Regulation. Arghya Barman and Donald Hamelberg, ACS Omega, 2016, 1, 837–842 (link)
Mechanism of peptide hydrolysis by aspartyl and metalloproteases, homas Paul, Arghya Barman, Mehmet Ozbil, Ram P Bora, Tingting Zhang, Gaurav Sharma, Zachary Hoffmann, and Rajeev Pabhakar, Physical Chemistry Chemical Physics, 2016, DOI: 10.1039/C6CP02097F (IF: 4.449) (link)
Coupled dynamics and entropic contribution to allosteric mechanism of Pin1. Arghya Barman and Donald Hamelberg. Journal of Physical Chemistry B, 2016, 120, 8405-8415 (IF: 3.302) (link)
Conserved Hydration Sites in Pin1 Reveal a Distinctive Water Recognition Motif in Proteins, Arghya Barman, Crystal Lynn Smitherman, Michael Gregory Souffrant, Giovanni Gadda, and Donald Hamelberg, Journal of Chemical Information and. Modeling, 2016, 56, 139-147(IF: 4.068) (link)
2015
Pushing the limits of the molecular mechanics force field to probe weak CH--π interactions in proteins. Arghya Barman, Bruce Batiste and Donald Hamelberg. Journal of Chemical Theory and Computation. 2015, 11, 1854-1863(IF: 5.310) (link)
An Iron Reservoir to the Catalytic Metal: The Rubredoxin Iron in an Extradiol Dioxygenase. Fange Liu, Jiafeng Geng, Ryan H. Gumpper, Arghya Barman, Ian Davis, Andrew Ozarowski, Donald Hamelberg, and Aimin Liu, Journal of Molecular Biology, 2015, DOI:10.1074/jbc.M115.650259 (IF: 4.600) (link)
Loss of intra-molecular electrostatic interactions and limited conformational space may promote self-association of cis-tau peptide. Arghya Barman and Donald Hamelberg. Proteins: Structure Function and Bioinformatics 2015, 83,436-444. (IF: 2.921) (link)
Theoretical Insights into the Functioning of Metallopeptidases and Their Synthetic Analogues. Tingting Zhang, Mehmet Ozbil, Arghya Barman, Thomas J. Paul, Ram Prasad Bora, and Rajeev Prabhakar. Accounts of Chemical Research 2015,48,192-200. (IF: 24.348) (link)
2014
Cysteine mediated dynamic hydrogen-bonding network in the active site of Pin1. Arghya Barman and Donald Hamelberg. Biochemistry 2014, 53, 3839-3850 (IF: 3.194) (link)
Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein “CheY”. Manish Paul, Mousumi Hazra, Arghya Barman and Saugata Hazra, Journal of Biomolecular Structure and Dynamics, 2014, 32, 928-949 (IF: 2.983) (link)
Computational perspective and evaluation of plausible catalytic mechanisms of peptidyl-prolyl isomerases. Safia Tork Ladani, Michael Souffrant, Arghya Barman and Donald Hamelberg. Biochimica et Biophysica Acta. 2014. doi:10.1016/j.bbagen.2014.12.023. (IF: 3.829) (link)
Computational Insights into Substrate and Site Specificities, Catalytic Mechanism and Protonation States of the Catalytic Asp Dyad of β-Secretase (BACE1). Arghya Barman and Rajeev Prabhakar. Scientifica, vol. 2014, Article ID 598728, 11 pages, 2014. doi:10.1155/2014/598728). (IF: 1.210) (link)
2013
Elucidating the Catalytic mechanism of β-secretase enzyme in the presence of surrounding protein environment: A QM/MM study. Arghya Barman and Rajeev Prabhakar Journal of Molecular Graphics and Modelling. 2013, 40, 1-9. (IF: 2.022) (link)
Hydrocarbons Depending on the Chain Length and Head Group Adopt Different Conformations within a Water-Soluble Nanocapsule: 1H NMR and Molecular Dynamics Studies. Rajib Choudhury, Arghya Barman, Rajeev Prabhakar and V. Ramamurthy Journal of Physical Chemistry B 2013, 117, 398-407. (IF: 3.377) (link)
2012
Protonation states of the catalytic dyad of β-secretase (BACE1) in presence of chemically diverse inhibitors: Insights from molecular docking study. Arghya Barman and Rajeev Prabhakar Journal of Chemical Information and Modeling 2012, 52 (5), 1275-1287. (IF: 4.068) (link)
Computational Insights into Dynamics of Protein Aggregation and Enzyme−Substrate Interactions. Mehmet Ozbil, Arghya Barman, Ram Prasad Bora and Rajeev Prabhakar Journal of Physical Chemistry Letter (Perspective) 2012, 3, 3460−3469. (IF: 6.687) (link)
Mechanism of Peptide Hydrolysis by Co-catalytic Metal Centers Containing Leucine Aminopeptidase Enzyme: A DFT Approach. Xiaoxia Zhu, Arghya Barman, Mehmet Ozbil, Tingting Zhang, Shanghao Li and Rajeev Prabhakar. Journal of Biological Inorganic Chemistry 2012, 17(2), 209-222. (IF: 3.164) (link)
Dimerization of the Full-Length Alzheimer’s Amyloid β-Peptide (Aβ42) in Explicit Aqueous Solution: A molecular Dynamics Study. Xiaoxia Zhu, Ram Prasad Bora, Arghya Barman, Rajiv Singh and Rajeev Prabhakar Journal of Physical Chemistry B 2012, 116(15), 4405-4416. (IF: 3.377) (link)
2011
Computational Modeling of Substrate Specificity and Catalysis of the β-secretase (BACE1) enzyme. Arghya Barman, Stephan Schürer, Rajeev Prabhakar. Biochemistry 2011, 50, 4337-4349. (IF: 3.194) (link)
Loss of cleavage at ß’-site contributes to the apparent increase of Aß secretion by BACE1-GPI processing of APP. Kulandaivelu S. Vetrivel, Arghya Barman, Ying Chen, Phuong D. Nguyen, Steven L. Wagner, Rajeev Prabhakar, and Gopal Thinakaran Journal Biological Chemistry 2011, 286, 26166-26177. (IF: 4.600) (link)
Cotinine modulates nicotinic receptors, reduces β-amyloid aggregation, and improves Alzheimer’s pathology in mice. Valentina Echeverria, Ross Zeitlin, Sarah Burgess, Arghya Barman, Garima Thakur, Hideyo Inouye, Edmundo Feris, Magorzota Mamcarz, Li Wang, Steven D. Buckingham, Daniel A Kirschner, Takashi Mori, Roger M. Leblanc, Rajeev Prabhakar, David Sattelle, Roger L. Papke, and Gary W. Arendash. Journal of Alzheimer’s Disease 2011, Volume 24, Number 4, 817-835. (IF: 3.612) (link)
2010
Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? Ram P Bora, Arghya Barman, Xiaoxia Zhu, Mehmet Ozbil, Rajeev Prabhakar Journal of Physical Chemistry B 2010, 114, 10860–10875. (IF: 3.377) (link)
Insights into the Mechanism of Methionine Oxidation Catalyzed by Metal (Cu2+, Zn2+ and Fe3+) -Amyloid Beta (Aβ) Peptide Complexes: A Computational Study. Arghya Barman, Woody Taves, and Rajeev Prabhakar, Journal of Computational Chemistry 2009, 30(9), 1405-1413. (IF: 3.601) (link)
2009
Computational Insights into Aspartyl Protease Activity of Presenilin 1 (PS1) Generating Alzheimer Amyloid β-Peptides (Aβ40 and Aβ42). Rajiv Singh, Arghya Barman and Rajeev Prabhakar Journal of Physical Chemistry B 2009, 113, 2990-2999. (IF: 3.377) (link)
Modeling the self-assembly dynamics of macromolecular protein aggregates underlying neurodegenerative disorders. Zhenyuan Zhao, Rajiv Singh, Arghya Barman, Neil F. Johnson, and Rajeev Prabhakar Computational and Theoretical Nanoscience 2009, 6(6), 1338-1351. (IF: 1.032) (link)
Presentations
2016: Poster Presentation (ACS 251st National Meeting, San Diego, CA)
“Conserved hydration site in Pin1 with unique water localization motif”.
Attended (7th South East Enzyme Conference, Atlanta, GA, USA)
2014: Oral Presentation (FAME 2014, Annual ACS meeting Florida, Innisbrook, FL) (Invited Talk)
“Cysteine mediated dynamic hydrogen bonding network in Pin1”.
2012: Oral Presentation (ACS 243rd National Meeting, San Diego, CA)
“Insights into the substrate recognition and catalysis by β-secretase (BACE1) enzyme: A combined computational approach”.
2011: Oral Presentation (FAME 2011, Annual ACS meeting Florida, Innisbrook, FL)
“Computational insights into substrate recognition and reactivity of ß-Secretase (BACE1) enzyme”.
2010: Oral Presentation (FAME 2010, Annual ACS meeting Florida, Innisbrook, FL)
“Computational insights into the differential substrate recognition and catalysis by the ß-Secretase (BACE1) enzyme”.
2009: Oral Presentation (FAME 2009, Annual ACS meeting Florida, Orlando, FL)
“Generation of Alzheimer’s Amyloid β peptides (Aβ40 and Aβ42) by aspartyl protease activity of presenilin I”.
2008: Poster presentation (FAME 2008, Annual ACS meeting Florida, Orlando, FL)
“Mechanism of metal catalyzed Methionine oxidation of Amyloid beta peptide”.
2016: Poster Presentation (ACS 251st National Meeting, San Diego, CA)
“Conserved hydration site in Pin1 with unique water localization motif”.
Attended (7th South East Enzyme Conference, Atlanta, GA, USA)
2014: Oral Presentation (FAME 2014, Annual ACS meeting Florida, Innisbrook, FL) (Invited Talk)
“Cysteine mediated dynamic hydrogen bonding network in Pin1”.
2012: Oral Presentation (ACS 243rd National Meeting, San Diego, CA)
“Insights into the substrate recognition and catalysis by β-secretase (BACE1) enzyme: A combined computational approach”.
2011: Oral Presentation (FAME 2011, Annual ACS meeting Florida, Innisbrook, FL)
“Computational insights into substrate recognition and reactivity of ß-Secretase (BACE1) enzyme”.
2010: Oral Presentation (FAME 2010, Annual ACS meeting Florida, Innisbrook, FL)
“Computational insights into the differential substrate recognition and catalysis by the ß-Secretase (BACE1) enzyme”.
2009: Oral Presentation (FAME 2009, Annual ACS meeting Florida, Orlando, FL)
“Generation of Alzheimer’s Amyloid β peptides (Aβ40 and Aβ42) by aspartyl protease activity of presenilin I”.
2008: Poster presentation (FAME 2008, Annual ACS meeting Florida, Orlando, FL)
“Mechanism of metal catalyzed Methionine oxidation of Amyloid beta peptide”.