Publications

(In-Print/Accepted as of Oct 2021)
(CSUN student names underlined)

Link to all Publications listed in PubMed
  1. Development of Enhanced Conformational Sampling Methods to Probe the Activation Landscape of GPCRs; Abrol R*, Serrano E, and Santiago LJ (2021). Membrane Proteins (Advances in Protein Chemistry and Structural Biology), 128 Ed. by Rossen Donev (in press). [PMID: ] (Link)
  2. The complex role of the N-terminus and acidic residues of HdeA as pH-dependent switches in its chaperone function; Pacheco S, Widjaja MA, Gomez JS, Crowhurst KA*, and Abrol R* (2020). Biophysical Chemistry, 264:106406. [PMID: 32593908] (Link)
  3. Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins; Youkharibache P*, Tran A, and Abrol R* (2020). Journal of Molecular Evolution, 88(4):319-344. [PMID: 32189026] (Link)
  4. Understanding G protein selectivity of muscarinic acetylcholine receptors using computational methods; Santiago LJ and Abrol R* (2019). International Journal of Molecular Sciences, 20(21):E5290. [PMID: 31653051] (Link)
  5. HER3-targeted protein chimera forms endosomolytic capsomeres and self-assembles into stealth nucleocapsids for systemic tumor homing of RNA interference in vivo; Alonso-Valenteen F, Pacheco S, Srinivas D, Rentsendorj A, Chu D, Lubow J, Sims J; Miao T, Mikhael S, Hwang JY, Abrol R*, Medina-Kauwe L* (2019). Nucleic Acids Research, 47(21):11020-11043. [PMID: 31617560] (Link)
  6. A beetle antifreeze protein protects lactate dehydrogenase under freeze-thawing; Rodriguez C, Sajjadi S, Abrol R*, Wen X* (2019). International Journal of Biological Macromolecules, 136:1153-1160. [PMID: 31226372] (Link)
  7. Chiral Graphs: Reduced Representations of Ligand Scaffolds for Stereoselective Biomolecular Recognition, Drug Design, and Enhanced Exploration of Chemical Structure Space; Mikhael S, Abrol R* (2019). ChemMedChem, 14(8):798-809. [PMID: 30821046]. (Link) (Invited)(Communication)
  8. Ethanol Induced Disordering of Pancreatic Acinar Cell Endoplasmic Reticulum: An ER Stress/Defective Unfolded Protein Response Model; Waldron RT, Su HY, Piplani H, Capri J, Cohn W, Whitelegge JP, Faull KF, Sakkiah S, Abrol R, Yang W, Zhou B, Freeman MR, Pandol SJ, Lugea A (2018). Cell Mol Gastroenterol Hepatol, 5(4):479-497. [PMID: 29930975]
  9. The 3D Structure of Human DP Prostaglandin G-Protein-Coupled Receptor Bound to Cyclopentanoindole Antagonist, Predicted Using the DuplexBiHelix Modification of the GEnSeMBLE Method; Shankar V, Goddard WA 3rd, Kim SK, Abrol R, Liu F (2018). Journal of chemical theory and computation, 14(3):1624-1642. [PMID: 29268008]
  10. Resistance to receptor-blocking therapies primes tumors as targets for HER3-homing nanobiologics; Sims JD, Taguiam JM, Alonso-Valenteen F, Markman J, Agadjanian H, Chu D, Lubow J, Abrol R, Srinivas D, Jain A, Han B, Qu Y, Mirzadehgan P, Hwang JY, Rentsendorj A, Chung A, Lester J, Karlan BY, Gray HB, Gross Z, Giuliano A, Cui X, Medina-Kauwe LK (2018). Journal of Controlled Release, 271:127-138. [PMID: 29288681]
  11. Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth; Griffith AR, Rogers CJ, Miller GM, Abrol R, Hsieh-Wilson LC, Goddard WA 3rd. (2017). Proc Natl Acad Sci, 114(52):13697-13702. [PMID: 29229841]
  12. Activation mechanism of the G protein-coupled sweet receptor heterodimer with sweeteners and allosteric agonists; Kim SK, Chen Y, Abrol R, Goddard WA 3rd, Guthrie B. (2017), Proc Natl Acad Sci, 114(10):2568-2573. [PMID: 28228527]
  13. Identifying multiple active conformations in the G protein-coupled receptor activation landscape using computational methods; Dong S, Goddard WA 3rd*, Abrol R* (2017), G Protein Coupled Receptors Part A (Methods in Cell Biology Book Series), Ed. Arun K. Shukla (Elsevier), Vol.142, pp. 173-186. [PMID: 28964335] (Invited Chapter)
  14. Conformational and Thermodynamic Landscape of GPCR Activation From Theory and Computation; Dong SS, Goddard WA 3rd*, Abrol R* (2016), Biophysical Journal, 110(12):2618-29. [PMID: 27332120]
  15. Structure-Based Sequence Alignment of the Transmembrane Domains of all Human GPCRs: Phylogenetic, Structural and Functional Implications; Cvicek V, Goddard WA 3rd*, Abrol R* (2016), PLoS Computational Biology, 12(3):e1004805. [PMID: 27028541]
  16. Computational Prediction and Biochemical Analyses of New Inverse Agonists for the CB1 Receptor; Scott CE, Ahn KH, Graf ST, Goddard WA 3rd, Kendall DA, Abrol R (2016). J Chem Inf Model, 56(1):201-12. [PMID: 26633590]
  17. FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer; Han B, Qu Y, Jin Y, Yu Y, Deng N, Wawrowsky K, Zhang X, Li N, Bose S, Wang Q, Sakkiah S, Abrol R, Jensen TW, Benjamin B, Tanaka H, Johnson J, Gao B, Hao J, Liu Z, Buttyan R, Ray PS, Hung MC, Giuliano AE, Cui X (2015). Cell Reports, 13(5):1046-58. [PMID: 26565916]
  18. The interaction of N-glycans in Fcγ receptor I α-chain with Escherichia coli K1 outer membrane protein A for entry into macrophages: experimental and computational analysis; Krishnan S, Liu F, Abrol R, Hodges J, Goddard WA 3rd, Prasadarao NV (2014). J Biol Chem, 289(45):30937-49. [PMID: 25231998]
  19. Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor; Abrol R*, Trzaskowski B, Goddard WA 3rd*, Nesterov A, Olave I, Irons C (2014). Proc Natl Acad Sci, 111(36):13040-5. [PMID: 25157173]
  20. The SuperBiHelix Method for Predicting the Pleiotropic Ensemble of G-Protein Coupled Receptor Conformations; Bray JK, Abrol R*, Goddard WA 3rd*, Trzaskowski B, Scott CE (2013). Proc Nat Acad Sci, 111(1):E72-8. [PMID: 24344284]
  21. The glove-like structure of the conserved membrane protein TatC provides insight into signal sequence recognition in twin-arginine translocation; Ramasamy S, Abrol R, Suloway CJ, Clemons WM Jr. (2013). Structure 21(5):777-88. [PMID: 23583035].
  22. Use of G-protein coupled and uncoupled CCR5 receptors by CCR5 inhibitor-resistant and -sensitive human immunodeficiency virus type 1 variants; Berro R, Yasmeen A, Abrol R, Trzaskowski B, Abi-Habib S, Grunbeck A, Lascano D, Goddard WA 3rd, Klasse PJ, Sakmar TP, Moore JP (2013). J Virology, 87(12):6569-81. [PMID: 23468486].
  23. Computationally-predicted CB1 cannabinoid receptor mutants show distinct patterns of salt-bridges that correlate with their level of constitutive activity reflected in G protein coupling levels, thermal stability, and ligand binding; Ahn KH, Scott CE, Abrol R, Goddard WA 3rd, Kendall DA (2013). Proteins, 81(8):1304-17. [PMID: 23408552]
  24. Conformational Ensemble View of G Protein-Coupled Receptors and the Effect of Mutations and Ligand Binding; Abrol R, Kim SK, Bray JK, Trzaskowski B, Goddard WA 3rd (2013). G Protein-Coupled Receptors (Methods in Enzymology), Ed. Conn PM (Elsevier, Oxford), Vol.520, pp. 31-48. [PMID: 23332694] (Invited Chapter)
  25. Molecular basis for dramatic changes in cannabinoid CB1 G protein-coupled receptor activation upon single and double point mutations; Scott CE, Abrol R, Ahn KH, Kendall DA, Goddard WA 3rd (2013). Protein Science, 22(1):101-13. [PMID: 23184890]
  26. The Predicted Structure of Agonist-Bound Glucagon-Like Peptide 1 Receptor, a Class B G Protein-Coupled Receptor; Kirkpatrick A, Heo J, Abrol R, Goddard WA 3rd (2012). Proc Nat Acad Sci, 109(49):19988-93. [PMID: 23169631]
  27. Structure Prediction of G Protein-Coupled Receptors and Their Ensemble of Functionally Important Conformations; Abrol R, Griffith AR, Bray JK, Goddard WA 3rd (2012). Membrane Protein Structure: Methods and Protocols (Methods in Molecular Biology), Eds. Vaidehi N and Klein-Seetharaman J (Humana, New York), Vol.914, pp. 237-54. [PMID: 22976032] (Invited Paper)
  28. Identification and Characterization of an Activating F229V Substitution in the V2 Vasopressin Receptor in an Infant with NSIAD.; Carpentier E, Greenbaum LA, Rochdi D, Abrol R, Goddard WA 3rd, Bichet DG, Bouvier M. (2012). J Am Soc Nephrol, 23(10):1635-40. [PMID: 22956819]
  29. The 3D structure prediction of TAS2R38 bitter receptors bound to agonists phenylthiocarbamide (PTC) and 6-n-Propylthiouracil (PROP); Tan J, Abrol R, Trzaskowski B, Goddard WA 3rd (2012). J Chem Inf Model, 52:1875-85. [PMID: 22656649]
  30. Molecular basis for the interplay of apoptosis and proliferation mediated by Bcl-xL:Bim interactions in pancreatic cancer cells; Abrol R, Edderkaoui M, Goddard WA 3rd, Pandol SJ (2012). Biochem Biophys Res Commun, 422(4):596-601. [PMID: 22609401]
  31. Genetically Encoded Photo-cross-linkers Map the Binding Site of an Allosteric Drug on a G Protein-Coupled Receptor: Grunbeck A, Huber T, Abrol R, Trzaskowski B, Goddard WA 3rd, Sakmar TP (2012). ACS Chem Biol, 7(6):967-72. [PMID: 22455376]
  32. BiHelix: Towards de novo Structure Prediction of an Ensemble of G-Protein Coupled Receptor Conformations; Abrol R, Bray JK, Goddard WA 3rd (2012). Prot Struc Func Bioinf, 80(2):505-18. [PMID: 22173949]
  33. First-Principles-Based Multiscale, Multiparadigm Molecular Mechanics and Dynamics Methods for Describing Complex Chemical Processes; Jaramillo-Botero A, Nielsen R, Abrol R, Su J, Pascal T, Mueller J, Goddard WA 3rd (2012). Top Curr Chem, 307:1-42. [PMID: 21243466] (Invited Review)
  34. Characterizing and Predicting the Functional and Conformational Diversity of Seven-Transmembrane Proteins; Abrol R, Kim SK, Bray JK, Griffith AR, Goddard WA 3rd (2011). Methods, 55(4):405-14. [PMID: 22197575] (Invited Paper)
  35. Structure-based prediction of subtype-selectivity of Histamine H3 receptor selective antagonists in the clinical trials; Kim SK, Fristrup P, Abrol R, Goddard WA 3rd (2011). J Chem Inf Model, 51(12):3262-74. [PMID: 22035233]
  36. G Protein-Coupled Receptors: Conformational 'Gatekeepers' of Transmembrane Signal Transduction and Diversification; Abrol R, Goddard WA 3rd (2011). Extracellular and Intracellular Signalling, Eds. Adams JD and Parker KK, pp.188-229 (RSC, Cambridge). (Invited Review)
  37. Novel Purine-Based Fluoroaryl-1,2,3-Triazoles as Neuroprotecting Agents: Synthesis, Neuronal Cell Culture Investigations, and CDK5 Docking Studies; Nair N, Kudo W, Smith MA, Abrol R, Goddard WA 3rd, Reddy VP (2011). Bioorg Med Chem Lett, 21:3957-61. [PMID: 21641213]
  38. Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches; Rogers CJ, Clark PM, Tully SE, Abrol R, Garcia KC, Goddard WA 3rd, Hsieh-Wilson LC (2011). Proc Natl Acad Sci U S A, 108(24):9747-52. [PMID: 21628576]
  39. Predicted structures of agonist and antagonist bound complexes of adenosine A3 receptor, Kim SK, Riley L, Abrol R, Jacobson KA, Goddard WA 3rd (2011). Proteins: Structure, Function, and Bioinformatics, 79(6):1878-97. [PMID: 21488099]
  40. Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors; Kim SK, Li Y, Abrol R, Heo J, Goddard WA 3rd (2011). J Chem Inf Model, 51(2):420-33. [PMID: 21299232]
  41. Experimental validation of the predicted binding site of Escherichia coli K1 outer membrane protein A to human brain microvascular endothelial cells: identification of critical mutations that prevent E. coli meningitis; Pascal TA, Abrol R, Mittal R, Wang Y, Prasadarao NV, Goddard WA 3rd (2010). J Biol Chem, 285(48):37753-61. [PMID: 20851887]
  42. Prediction of the three-dimensional Structure for the Rat Urotensin II G-Protein-Coupled Receptor and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat from Atomistic Simulations; Kim SK, Li Y, Park C, Abrol R, Goddard WA 3rd (2010). ChemMedChem, 5(9):1594-608. [PMID: 20683923]
  43. Predicted 3D structures for adenosine receptors bound to ligands: Comparison to the crystal structure; Goddard WA 3rd, Kim SK, Li Y, Trzaskowski B, Griffith AR, Abrol R (2010). J Struct Biol, 170(1):10-20. [PMID: 20079848]
  44. Rottlerin Stimulates Apoptosis in Pancreatic Cancer Cells through Interactions with Proteins of the Bcl-2 Family; Ohno I, Eibl G, Odinokova IV, Edderkaoui M, Damoiseaux RD, Yazbec M, Abrol R, Goddard WA 3rd, Yokosuka O, Pandol SJ, Gukovskaya AS (2010). Am J Physiol Gastrointest Liver Physiol, 298(1):G63-73. [PMID: 19762431]
  45. Multiscale-Multiparadigm Modeling and Simulation of Nanometer Scale Systems and Processes for Nanomedical Applications; Jaramillo-Botero A, Abrol R, van Duin A, Goddard WA 3rd (2009). Nanomedicine: A Systems Engineering Approach, Eds. Zhang M and Xi N, pp.245-300 (Pan Stanford Publishing). Invited review
  46. Nonadiabatic effects in the H + H2 exchange reaction: accurate quantum dynamics calculations at a state-to-state level; Chu TS, Han KL, Hankel M, Balint-Kurti GG, Kuppermann A, Abrol R (2009). J Chem Phys, 130(14):144301. [PMID: 19368439]
  47. Computational studies of the structure and function of two lipid-activated GPCRs; Niemer RK, Abrol R, Goddard WA 3rd (2008). J Recept Sig Transd, 28(1-2), 138-139.
  48. 3-Dimensional Structures of G-Protein Coupled Receptors and Binding Sites of Agonists and Antagonists; Goddard WA 3rd, Abrol R (2007). J Nutr, 137(6 Suppl 1), 1528S-1538S. [PMID: 17513420]
  49. Geometric phase effects in H3 predissociation; Lepetit B, Abrol R, Kuppermann A (2007). Phys Rev A, 040702(R).
  50. Predictions of CCR1 Chemokine Receptor Structure and BX471 Antagonist Binding Followed by Experimental Validation; Vaidehi N, Schlyer S, Trabanino RJ, Floriano WB, Abrol R, Sharma S, Kochanny M, Koovakat S, Dunning L, Liang M, Fox JM, de Mendonca FL, Pease JE, Goddard WA 3rd, Horuk R (2006). J Biol Chem, 281(37):27613-20. [PMID: 16837468]
  51. Biological Chiral Recognition: A Substrate's Perspective; Sundaresan V, Abrol R (2005). Chirality, 17(Suppl):S30-9. [PMID: 15736174]
  52. Multiple potential energy surface quantum reaction dynamics; Kuppermann A, Abrol R (2004). Nonadiabatic Transitions in Quantum Systems, Eds. Osherov VI and Ponomarev LI (IPCP, Chernogolovka), pp.10.
  53. Towards a general model for protein-substrate stereoselectivity; Sundaresan V, Abrol R (2002). Protein Sci, 11(6): 1330-9. [PMID: 12021432]
  54. Quantum reaction dynamics for multiple electronic states; Kuppermann A, Abrol R (2002). The Role of Degenerate States in Chemistry: A Special Volume of Advances in Chemical Physics, Eds. Baer M and Billing GD, 124:283-322.
  55. An optimal adiabatic to diabatic transformation of the 12A' and 22A' states of H3; Abrol R,Kuppermann A (2002). J Chem Phys, 116(3):1035-62.
  56. Accurate First-Derivative Non-adiabatic Couplings for the H3 system; Abrol R, Shaw A, Yarkony DR, Kuppermann A (2001). J Chem Phys, 115(10):4640-59.
  57. A Quantum and Semiclassical Study of Dynamical Resonances in C + NO -> CN + O Reaction; Abrol R, Wiesenfeld L, Lambert B, Kuppermann A (2001). J Chem Phys, 114(17):7461-70.
  58. Reduced Potential Energy Curves for Diatomic Molecules and their respective Cations; Abrol R, Harbola M, and Sathyamurthy N (1999). Chem Phys Lett, 312(2):341-5.
  59. Computation of Vapor Pressure; Abrol R (1995). J Chem Ed, 72(12):1083-5.