Pratul K. Agarwal, Ph.D. - Publications

Affiliations: 
2002 Pennsylvania State University, State College, PA, United States 
Area:
theoretical and computational methods for describing chemical reactions in condensed phases and at interfaces

53 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
2023 Lee E, McLeod MJ, Redzic JS, Marcolin B, Thorne RE, Agarwal P, Eisenmesser EZ. Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle. Frontiers in Molecular Biosciences. 10: 1244587. PMID 37645217 DOI: 10.3389/fmolb.2023.1244587  0.322
2022 Schröder GC, O'Dell WB, Webb SP, Agarwal PK, Meilleur F. Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Chemical Science. 13: 13303-13320. PMID 36507176 DOI: 10.1039/d2sc05031e  0.64
2021 Redzic JS, Duff MR, Blue A, Pitts TM, Agarwal P, Eisenmesser EZ. Modulating Enzyme Function Dynamic Allostery within Biliverdin Reductase B. Frontiers in Molecular Biosciences. 8: 691208. PMID 34095235 DOI: 10.3389/fmolb.2021.691208  0.328
2020 Agarwal PK, Bernard DN, Bafna K, Doucet N. Enzyme dynamics: Looking beyond a single structure. Chemcatchem. 12: 4704-4720. PMID 33897908 DOI: 10.1002/Cctc.202000665  0.357
2020 Duff MR, Redzic JS, Ryan LP, Paukovich N, Zhao R, Nix JC, Pitts TM, Agarwal P, Eisenmesser EZ. Structure, dynamics, and function of the evolutionarily changing biliverdin reductase B family. Journal of Biochemistry. PMID 32246827 DOI: 10.1093/Jb/Mvaa039  0.376
2020 Narayanan C, Bernard DN, Letourneau M, Gagnon J, Gagné D, Bafna K, Calmettes C, Couture JF, Agarwal PK, Doucet N. Insights into structural and dynamical changes experienced by human RNase 6 upon ligand binding. Biochemistry. PMID 31909602 DOI: 10.1021/Acs.Biochem.9B00888  0.404
2019 Kumar P, Agarwal PK, Brett Waddell M, Mittag T, Serpersu EH, Cuneo MJ. Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad. Angewandte Chemie (International Ed. in English). PMID 31515870 DOI: 10.1002/Anie.201908535  0.37
2019 Li J, Fortunato G, Lin J, Agarwal PK, Kohen A, Singh P, Cheatum CM. Evolution Conserves the Network of Coupled Residues in Dihydrofolate Reductase. Biochemistry. PMID 31423766 DOI: 10.1021/Acs.Biochem.9B00460  0.417
2019 Hester KP, Bhattarai K, Jiang H, Agarwal PK, Pope C. Engineering Dynamic Surface Peptide Networks on Butyrylcholinesterase for Enhanced Organophosphosphorus Anticholinesterase Catalysis. Chemical Research in Toxicology. PMID 31411024 DOI: 10.1021/Acs.Chemrestox.9B00146  0.447
2019 Bafna K, Narayanan C, Chennubhotla SC, Doucet N, Agarwal PK. Nucleotide substrate binding characterization in human pancreatic-type ribonucleases. Plos One. 14: e0220037. PMID 31393891 DOI: 10.1371/Journal.Pone.0220037  0.392
2019 Duff MR, Desai N, Craig MA, Agarwal PK, Howell EE. Crowders Steal Dihydrofolate Reductase Ligands through Quinary Interactions. Biochemistry. PMID 30724552 DOI: 10.1021/Acs.Biochem.8B01110  0.302
2018 Agarwal PK. A Biophysical Perspective on Enzyme Catalysis. Biochemistry. PMID 30507164 DOI: 10.1021/Acs.Biochem.8B01004  0.468
2018 Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential substrate recognition by maltose binding proteins influenced by structure and dynamics. Biochemistry. PMID 30204415 DOI: 10.1021/Acs.Biochem.8B00783  0.363
2018 Narayanan C, Bernard DN, Bafna K, Gagné D, Agarwal PK, Doucet N. Ligand-Induced Variations in Structural and Dynamical Properties Within an Enzyme Superfamily. Frontiers in Molecular Biosciences. 5: 54. PMID 29946547 DOI: 10.3389/Fmolb.2018.00054  0.356
2018 Duff MR, Borreguero JM, Cuneo M, Ramanathan A, He J, Kamath G, Chennubhotla CS, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK. Modulating enzyme activity by altering protein dynamics with solvent. Biochemistry. PMID 29901984 DOI: 10.1021/Acs.Biochem.8B00424  0.486
2018 Narayanan C, Bernard DN, Bafna K, Gagné D, Chennubhotla CS, Doucet N, Agarwal PK. Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily. Structure (London, England : 1993). PMID 29478822 DOI: 10.1016/J.Str.2018.01.015  0.455
2017 Bhojane PP, Duff MR, Bafna K, Agarwal PK, Stanley CB, Howell EE. Small Angle Neutron Scattering (SANS) Studies on R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini. Biochemistry. PMID 29020453 DOI: 10.1021/Acs.Biochem.7B00822  0.301
2017 Narayanan C, Bafna K, Roux LD, Agarwal PK, Doucet N. Applications of NMR and computational methodologies to study protein dynamics. Archives of Biochemistry and Biophysics. PMID 28483383 DOI: 10.1016/J.Abb.2017.05.002  0.382
2017 Norris V, Krylov SN, Agarwal PK, White GJ. Synthetic, Switchable Enzymes. Journal of Molecular Microbiology and Biotechnology. 27: 117-127. PMID 28448969 DOI: 10.1159/000464443  0.34
2017 Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Biomolecular Nmr Assignments. PMID 28271277 DOI: 10.1007/S12104-017-9736-9  0.39
2016 O'Dell WB, Agarwal PK, Meilleur F. Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angewandte Chemie (International Ed. in English). PMID 28004877 DOI: 10.1002/Anie.201610502  0.361
2016 Agarwal PK, Doucet N, Chennubhotla C, Ramanathan A, Narayanan C. Conformational Sub-states and Populations in Enzyme Catalysis. Methods in Enzymology. 578: 273-97. PMID 27497171 DOI: 10.1016/Bs.Mie.2016.05.023  0.466
2016 Gagné D, Narayanan C, Nguyen Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry. PMID 27387012 DOI: 10.1021/Acs.Biochem.6B00130  0.46
2016 Li QQ, Hao JJ, Zhang Z, Hsu I, Liu Y, Tao Z, Lewi K, Metwalli AR, Agarwal PK. Histone deacetylase inhibitor-induced cell death in bladder cancer is associated with chromatin modification and modifying protein expression: A proteomic approach. International Journal of Oncology. PMID 27082124 DOI: 10.3892/ijo.2016.3478  0.574
2015 Gagné D, French RL, Narayanan C, Simonović M, Agarwal PK, Doucet N. Perturbation of the Conformational Dynamics of an Active-Site Loop Alters Enzyme Activity. Structure (London, England : 1993). 23: 2256-2266. PMID 26655472 DOI: 10.1016/J.Str.2015.10.011  0.479
2015 Duff MR, Chopra S, Strader MB, Agarwal PK, Howell EE. Tales of Dihydrofolate Binding to R67 Dihydrofolate Reductase. Biochemistry. PMID 26637016 DOI: 10.1021/Acs.Biochem.5B00981  0.384
2014 Ramanathan A, Savol A, Burger V, Chennubhotla CS, Agarwal PK. Protein conformational populations and functionally relevant substates. Accounts of Chemical Research. 47: 149-56. PMID 23988159 DOI: 10.1021/Ar400084S  0.437
2013 Agarwal PK. Role of protein motions in function: comment on "Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments" by Cristian Micheletti. Physics of Life Reviews. 10: 35-6; discussion 39-. PMID 23157841 DOI: 10.1016/J.Plrev.2012.10.008  0.346
2012 Ramanathan A, Savol AJ, Agarwal PK, Chennubhotla CS. Event detection and sub-state discovery from biomolecular simulations using higher-order statistics: application to enzyme adenylate kinase. Proteins. 80: 2536-51. PMID 22733562 DOI: 10.1002/Prot.24135  0.386
2012 Agarwal PK, Schultz C, Kalivretenos A, Ghosh B, Broedel SE. Engineering a hyper-catalytic enzyme by photoactivated conformation modulation Journal of Physical Chemistry Letters. 3: 1142-1146. DOI: 10.1016/J.Bpj.2011.11.1505  0.475
2012 Ramanathan A, Burger VM, Savol AJ, Stanley CB, Agarwal PK, Chennubhotla CS. Integrating Theory, Simulations and Experiments to Reveal the Recognition-Specific Pathways in the Nuclear Co-Activator Binding Domain Ensemble Biophysical Journal. 102: 10a-11a. DOI: 10.1016/J.Bpj.2011.11.080  0.312
2011 Ramanathan A, Agarwal PK. Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis. Plos Biology. 9: e1001193. PMID 22087074 DOI: 10.1371/Journal.Pbio.1001193  0.473
2011 Savol AJ, Burger VM, Agarwal PK, Ramanathan A, Chennubhotla CS. QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin. Bioinformatics (Oxford, England). 27: i52-60. PMID 21685101 DOI: 10.1093/bioinformatics/btr248  0.303
2011 Borreguero JM, He J, Meilleur F, Weiss KL, Brown CM, Myles DA, Herwig KW, Agarwal PK. Redox-promoting protein motions in rubredoxin. The Journal of Physical Chemistry. B. 115: 8925-36. PMID 21608980 DOI: 10.1021/Jp201346X  0.366
2011 Ramanathan A, Savol AJ, Langmead CJ, Agarwal PK, Chennubhotla CS. Discovering conformational sub-states relevant to protein function. Plos One. 6: e15827. PMID 21297978 DOI: 10.1371/Journal.Pone.0015827  0.315
2011 Ramanathan A, Borreguero JM, Chennubhotla CS, Agarwal PK. Protein Flexibility and Energy Flow During Enzyme Catalysis Biophysical Journal. 100: 194a. DOI: 10.1016/J.Bpj.2010.12.1277  0.497
2010 Kamath G, Howell EE, Agarwal PK. The tail wagging the dog: insights into catalysis in R67 dihydrofolate reductase. Biochemistry. 49: 9078-88. PMID 20795731 DOI: 10.1021/Bi1007222  0.377
2010 Ramanathan A, Agarwal PK, Kurnikova M, Langmead CJ. An online approach for mining collective behaviors from molecular dynamics simulations. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 309-24. PMID 20377447 DOI: 10.1089/Cmb.2009.0167  0.385
2010 Ramanathan A, Savol A, Langmead C, Agarwal P, Chennubhotla SC. High-Order Correlations in Internal Protein Motions and Energetics Biophysical Journal. 98: 235a-236a. DOI: 10.1016/J.Bpj.2009.12.1276  0.415
2009 Ramanathan A, Agarwal PK. Computational identification of slow conformational fluctuations in proteins. The Journal of Physical Chemistry. B. 113: 16669-80. PMID 19908896 DOI: 10.1021/Jp9077213  0.389
2009 Agarwal PK. Evolution of enzyme fold: Linking protein dynamics and catalysis Biophysical Journal. 96: 377a. DOI: 10.1016/J.Bpj.2008.12.2829  0.489
2009 Ramanathan A, Borreguero J, Langmead CJ, Agarwal PK. Conserved Protein Flexibility And Pathways Of Energy Flow In Enzyme Catalysis Biophysical Journal. 96: 71a. DOI: 10.1016/J.Bpj.2008.12.265  0.499
2006 Agarwal PK. Enzymes: An integrated view of structure, dynamics and function. Microbial Cell Factories. 5: 2. PMID 16409630 DOI: 10.1186/1475-2859-5-2  0.486
2005 Agarwal PK. Role of protein dynamics in reaction rate enhancement by enzymes. Journal of the American Chemical Society. 127: 15248-56. PMID 16248667 DOI: 10.1021/Ja055251S  0.502
2004 Agarwal PK, Geist A, Gorin A. Protein dynamics and enzymatic catalysis: investigating the peptidyl-prolyl cis-trans isomerization activity of cyclophilin A. Biochemistry. 43: 10605-18. PMID 15311922 DOI: 10.1021/Bi0495228  0.411
2004 Agarwal PK. Cis/trans isomerization in HIV-1 capsid protein catalyzed by cyclophilin A: insights from computational and theoretical studies. Proteins. 56: 449-63. PMID 15229879 DOI: 10.1002/Prot.20135  0.337
2003 Watney JB, Agarwal PK, Hammes-Schiffer S. Effect of mutation on enzyme motion in dihydrofolate reductase. Journal of the American Chemical Society. 125: 3745-50. PMID 12656604 DOI: 10.1021/Ja028487U  0.723
2002 Agarwal PK, Billeter SR, Rajagopalan PT, Benkovic SJ, Hammes-Schiffer S. Network of coupled promoting motions in enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. 99: 2794-9. PMID 11867722 DOI: 10.1073/Pnas.052005999  0.604
2002 Agarwal PK, Billeter SR, Hammes-Schiffer S. Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis Journal of Physical Chemistry B. 106: 3283-3293. DOI: 10.1021/Jp020190V  0.668
2001 Billeter SR, Webb SP, Agarwal PK, Iordanov T, Hammes-Schiffer S. Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion. Journal of the American Chemical Society. 123: 11262-72. PMID 11697969 DOI: 10.1021/Ja011384B  0.743
2001 Billeter SR, Webb SP, Iordanov T, Agarwal PK, Hammes-Schiffer S. Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes Journal of Chemical Physics. 114: 6925-6936. DOI: 10.1063/1.1356441  0.729
2000 Webb SP, Agarwal PK, Hammes-Schiffer S. Combining electronic structure methods with the calculation of hydrogen vibrational wavefunctions: Application to hydride transfer in liver alcohol dehydrogenase Journal of Physical Chemistry B. 104: 8884-8894. DOI: 10.1021/Jp001635N  0.712
2000 Agarwal PK, Webb SP, Hammes-Schiffer S. Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase Journal of the American Chemical Society. 122: 4803-4812. DOI: 10.1021/Ja994456W  0.688
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