Publications:

    2024

  1. Narkhede, Y., Saxena, R., Sharma, T., Conarty, J.P., Ramirez, V.T., Motsa, B.B., Amiar, S., Li, S., Chapagain, P.P., Wiest, O. and Stahelin, R.V., 2024. Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Science 33(5), p.e4978 (2024). Link

  2. Colbert, B.M., Lanting, C., Smeal, M., Blanton, S., Dykxhoorn, D.M., Tang, P.C., Getchell, R.L., Velde, H., Fehrmann, M., Thorpe, R. and Chapagain, P., 2024. The natural history and genotype–phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. Human Genetics pp.1-14 (2024). Link

  3. Motsa, B.B., Sharma, T., Ciofi, M., Chapagain, P.P. and Stahelin, R.V., 2024. Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particlesJournal of Biological Chemistry (2024). Link

  4. Cioffi, M.D., Husby, M.L., Gerstman, B.S., Stahelin, R.V. and Chapagain, P.P., Role of phosphatidic acid lipids on plasma membrane association of the Ebola virus matrix protein VP40. Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1869, 159464 (2024). Link

  5. Gressett, T.E., Hossen, M.L., Talkington, G., Volic, M., Perez, H., Tiwari, P.B., Chapagain, P. and Bix, G., Molecular interactions between perlecan LG3 and the SARS‐CoV‐2 spike protein receptor binding domain. Protein Science 33(1), e4843 (2024). Link [ Featured on the journal cover ]

    6. 2023

  6. Yuan, M., Mahmud, I., Katsushima, K., Joshi, K., Saulnier, O., Pokhrel, R., Lee, B., Liyanage, W., Kunhiraman, H., Stapleton, S. and Gonzalez-Gomez, I., 2023. miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. TActa Neuropathologica Communications 11(1), 203. (2023). Link

  7. Deng, Z., Chapagain, P. and Leng, F., Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase.The Journal of Biological Chemistry 299(12) (2023). Link

  8. Stebliankin, V., Shirali, A., Baral, P., Shi, J., Chapagain, P., Mathee, K., & Narasimhan, G. Evaluating protein binding interfaces with transformer networks. Nature Machine Intelligence 5, 1042–1053 (2023). Link

  9. Angel J. Magaña, Jan Sklenicka, Clemencia Pinilla, Marc Giulianotti, Prem Chapagain, Radleigh Santos, Maria Soledad Ramirez and Marcelo E. Tolmasky Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation RSC Med. Chem. (2023).[ Featured on the journal cover ] Link

  10. Sharma, T., Gerstman, B., and Chapagain, P.* Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding Int. J. Mol. Sci. 24(16) (2023). Link

  11. Narkhede, Y.B., Bhardwaj, A., Motsa, B.B., Saxena, R., Sharma, T., Chapagain, P.P., Stahelin, R.V. and Wiest, O. Elucidating Residue-Level Determinants Affecting Dimerization of Ebola Virus Matrix Protein Using High-Throughput Site Saturation Mutagenesis and Biophysical Approaches. The Journal of Physical Chemistry B. 127, 29, 6449–6461 (2023). Link

  12. Vashist, A., Raymond, A.D., Chapagain, P., Vashist, A., Arias, A.Y., Kolishetti, N. and Nair, M., Multi-functional auto-fluorescent nanogels for theranostics. Journal of NeuroVirology 11(1), 252–257 (2023). Link

  13. Katsushima, K., Pokhrel, R., Mahmud, I., Yuan, M., Murad, R., Baral, P., Zhou, R., Chapagain, P., Garrett, T., Stapleton, S. and Jallo, G., 2023. The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas. Acta Neuropathologica Communications 11(1), p.38(2023). Link

  14. Balbin, C.A., Nunez-Castilla, J., Stebliankin, V., Baral, P., Sobhan, M., Cickovski, T., Mondal, A.M., Narasimhan, G., Chapagain, P., Mathee, K. and Siltberg-Liberles, J., 2023. Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes, ImmunoInformatics 9, p.100023 (2023). Link

  15. Tsegay, P.S., Hernandez, D., Qu, F., Olatunji, M., Mamun, Y., Chapagain, P. and Liu, Y., 2023. RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. Nucleic Acids Research 51,166-181. (2023). Link

  16. Mukherjee, S., Manna, P., Douglas, N., Chapagain, P.P. and Jimenez, R., Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness. The Journal of Physical Chemistry B 1, 52–61 (2023). Link

  17. Thapa B, Adhikari NP, Tiwari PB, Chapagain PP. A 5′-Flanking C/G Pair at the Core Region Enhances the Recognition and Binding of Kaiso to Methylated DNA. Journal of Chemical Information and Modeling 63, 7, 2095–2103 (2023). Link

    18. 2022

  18. Alfonso, E., Deng, Z., Boaretto, D., Hood, B., Vasile, S., Smith, L., Chambers, J., Chapagain, P., Leng, F., Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay. ACS Pharmacol. Transl. Sci., 5, 10 (2022). [ Featured on the journal cover ]. Link

  19. Alfonso, E.E., Troche, R., Deng, Z., Annamalai, T., Chapagain, P., Tse-Dinh, Y.C. and Leng, F., 2022. Potent inhibition of bacterial DNA gyrase by digallic acid and other gallate derivatives. ChemMedChem, (2022). Link

  20. Pokhrel, R., Shakya, R., Baral, P., Chapagain P., Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. Journal of Chemical Information and Modeling, (2022). [ Featured on the journal cover ]. Link

  21. Norris, M.J., Husby, M.L., Kiosses, W.B., Yin, J., Saxena, R., Rennick, L.J., Heiner, A., Harkins, S.S., Pokhrel, R., Schendel, S.L., Hastie, K.M., Sara Landeras-Bueno†, S., Li Z., Lee B., Chapagain P.P., Maisner A., Duprex W.P., Stahelin R.V., and Saphire E.O., Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. Science Advances,8(29), p.eabn1440 (2022). [ Featured on the journal cover ]. Link

  22. Baral, P., Pavadai, E., Zhou, Z., Xu, Y., Tison, C.K., Pokhrel, R., Gerstman, B.S. and Chapagain, P.*, Immunoinformatic screening of Marburgvirus epitopes and computational investigations of epitope-allele complexes. International Immunopharmacology, 111, 109109 (2022). Link

  23. Barrios, A., Diaz, M.M., Perezo, E., Hossen, M.L., Chapagain, P. and Moon, J.H., Effects of Sidechain Isomerism on Polymer-based Non-Covalent Protein Delivery. Chemical Communications, (2022). Link

  24. Devadoss, D., Acharya, A., Manevski, M., Houserova, D., Cioffi, M.D., Pandey, K., Nair, M., Chapagain, P., Mirsaeidi, M., Borchert, G.M. and Byrareddy, S.N., Immunomodulatory LncRNA on Antisense Strand of ICAM-1 Augments SARS-CoV-2 Infection-associated Airway Mucoinflammatory Phenotype. iScience, p.104685 (2022). Link

  25. Nunez-Castilla, J., Stebliankin, V., Baral, P., Balbin, C.A., Sobhan, M., Cickovski, T., Mondal, A.M., Narasimhan, G., Chapagain, P., Mathee, K. and Siltberg-Liberles, J., Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. Viruses, 14(7), p.1415 (2022). Link

  26. Garabedian, A., Jeanne Dit Fouque, K., Chapagain, P. Leng, F., Fernandez-Lima, F., AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes. Nucleic Acids Research, 50, 2431-2439 (2022). Link

  27. Hossen, M.L., Baral, P., Sharma, T., Gerstman, B. and Chapagain, P.*, Significance of the RBD mutations in the SARS-CoV-2 Omicron: From spike opening to antibody escape and cell attachment. Physical Chemistry Chemical Physics, 24(16), pp.9123-9129 (2022). Link

  28. Jeanne Dit Fouque, K., Sipe, S.N., Garabedian, A., Mejia, G., Su, L., Hossen, M.L., Chapagain, P.P., Leng, F., Brodbelt, J.S. and Fernandez-Lima, F., Exploring the Conformational and Binding Dynamics of HMGA2· DNA Complexes Using Trapped Ion Mobility Spectrometry–Mass Spectrometry. Journal of the American Society for Mass Spectrometry 33, 1103-1112 (2022). [ Featured on the journal cover ]. Link

  29. Pandey, P., Bhattarai, N., Su, L., Wang, X., Leng, F., Gerstman, B., Chapagain, P.P. and He, J., Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact Method. ACS sensors.5;7(2):555-563 (2022). PubMed

  30. Tsegay, P.S., Hernandez, D., Brache, C., Chatgilialoglu, C., Krokidis, M.G., Chapagain, P. and Liu, Y., Incorporation of 5’, 8-cyclo-2’deoxyadenosines by DNA repair polymerases via base excision repair. DNA repair, 109, p.103258 (2022).PubMed

  31. Bhattarai, N., Pavadai, E., Pokhrel, R., Baral, P., Hossen, M.L., Stahelin, R.V., Chapagain, P.P. and Gerstman, B.S., Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane. Proteins: Structure, Function, and Bioinformatics, 90(2), pp.340-350 (2022). PubMed

    32. 2021

    )
  32. Pokhrel, Rudramani, et al. "Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides. Journal of Chemical Theory and Computation 18.1, 516-525 (2021). Link

  33. Rocha, K., Magallon, J., Reeves, C., et al., Inhibition of Aminoglycoside 6’-N-Acetyltransferase Type Ib [Aac (6′)-Ib]: Structure-Activity Relationship of Substituted Pyrrolidine Pentamine Derivatives as Inhibitors Biomedicines 9(9), 1218 (2021). Link

  34. Baral, P., Bhattarai, N., Hossen, M.L., Stebliankin, V., Gerstman, B.S., Narasimhan, G. and Chapagain, P.P.*, 2021. Mutation-induced changes in the receptor-binding interface of the SARS-CoV-2 Delta variant B. 1.617. 2 and implications for immune evasion. Biochemical and Biophysical Research Communications 574, 14-19 (2021). PubMed

  35. Bhattarai, N., Baral, P., Gerstman, B.S. and Chapagain, P.P.*, Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B. 1.1.7 and B.1.351. The Journal of Physical Chemistry B 125, 7101-7107 (2021). [ Featured on the journal cover ]. PubMed

  36. Koirala, R. P., Pokhrel, R., Baral, P., Tiwari, P. B., Chapagain, P. P.*, & Adhikari, N. P., Structural insights into the repair mechanism of AGT for methyl-induced DNA damage. Biological Chemistry (2021). PubMed

  37. Johnson, K.A., Bhattarai, N., Budicini, M.R., LaBonia, C.M., Baker, S.C.B., Gerstman, B.S., Chapagain, P.P. and Stahelin, R.V., Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop. Viruses, 13(7), p.1375 (2021). PubMed

  38. Beddingfield, B.J., Iwanaga, N., Chapagain, P.P., Zheng, W., Roy, C.J., Hu, T.Y., Kolls, J.K. and Bix, G.J., The integrin binding peptide, ATN-161, as a novel therapy for SARS-CoV-2 infection. JACC: Basic to Translational Science, 6, 1-8 (2021). PubMed

    39. 2020

  39. Su, L., Bryan, N., Battista, S., Freitas, J., Garabedian, A., et al., Identification of HMGA2 inhibitors by AlphaScreen-based ultra-high-throughput screening assays. Scientific Reports, 10, 1-14 (2020). Link

  40. Azam, S., Bhattarai, N., Riveron, A., Rodriguez, S., Chapagain, P.P. and Miksovska, J., EF-hands in Neuronal Calcium Sensor Downstream Regulatory Element Antagonist Modulator Demonstrate Submillimolar Affinity for Li+: a new prospect for Li+ therapy. ACS chemical neuroscience, https://doi.org/10.1021/acschemneuro.0c00399 (2020).PubMed

  41. Pokhrel, R., Chapagain, P. and Siltberg-Liberles, J.; Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2. Journal of Medical Microbiology, 001203 (2020). PubMed

  42. Prabin, B., Elumalai, P., Gerstman, B.S. and Chapagain, P.P.*, In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever. Scientific Reports 10(1) (2020). Link

  43. Johnson, K.A., Pokhrel, R., Budicini, M.R., Gerstman, B.S., Chapagain, P.P. and Stahelin, R.V. A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation. Pathogens, 9(5), 402 (2020).PubMed

  44. Wijesinghe, K.J., McVeigh, L., Husby, M.L., Bhattarai, N., Ma, J., Gerstman, B.S., Chapagain, P.P. and Stahelin, R.V., Mutation of Hydrophobic Residues in the C-Terminal Domain of the Marburg Virus Matrix Protein VP40 Disrupts Trafficking to the Plasma Membrane. Viruses, 12, 482 (2020).PubMed

  45. P Tiwari, PP Chapagain, A Seddek, T Annamalai, A Üren and YC Tse-Dinh, Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 15, 623–631 (2020).PubMed

    46. 2019

  46. Pavadai, E., Bhattarai, N., Baral, P., Stahelin, R.V., Chapagain, P.P*. and Gerstman, B.S., Conformational Flexibility of the Protein–Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. The Journal of Physical Chemistry B, 123(43), 9045-9053 (2019).Google Scholar

  47. Pokhrel, R., Bhattarai, N., Baral, P., Gerstman, B.S., Park, J.H., Handfield, M. and Chapagain, P.P.*. Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140. Physical Chemistry Chemical Physics, 21 12530-12539 (2019).Google Scholar

  48. R Pokhrel, B. Gerstman, and P Chapagain*, “Membrane pore formation and ion selectivity of the Ebola virus delta peptide” Physical Chemistry Chemical Physics 21, 5578-85 (2019).Google Scholar

    49. 2018

  49. JE Porter, P Chapagain, F Fernandez‐Lima, “Single stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation” Rapid Communications in Mass Spectrometry 33, 60-65 (2018).Google Scholar

  50. R Pokhrel, P Sompornpisut, P Chapagain, B Olson et al., “Domain rearrangement and denaturation in Ebola virus protein VP40” AIP Advances, 8, 125129 (2018).Google Scholar

  51. N Bhattarai, BS Gerstman, PP Chapagain*, “Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24–Human Keap1 Complex” ACS Omega 3, 18639–18645 (2018).Google Scholar

  52. D Butcher, PP Chapagain, F Leng, F Fernandez-Lima, “Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry” The Journal of Physical Chemistry B 122 (27) (2018).Google Scholar

  53. PB Tiwari, PP Chapagain, A Üren, “Investigating molecular interactions between oxidized neuroglobin and cytochrome c” Scientific reports 8 (1), 10557 (2018).Google Scholar

  54. L Wang, Y Feng, D Yan, L Qin, M Grati, et al. “A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss” Human genetics, 137 (2018). Google Scholar

  55. W Li, J Sun, J Ling, J Li, C He, Y Liu et al. “ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss” Human genetics, 137 (2018). Google Scholar

  56. R Mittal, AP Patel, D Nguyen, DR Pan et al, “Genetic basis of hearing loss in Spanish, Hispanic and Latino populations”, Gene 647, 297-305 (2018).

  57. R Pokhrel, BS Gerstman, JD Hutcheson, PP Chapagain*, “In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles” The Journal of Physical Chemistry B 122 (14), 3782-3789 (2018).

  58. S Sandhaus, PP Chapagain*, YC Tse-Dinh*, “Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays” Scientific reports 8 (1), 1437 (2018).

  59. Kathryn Del Vecchio, Cary T Frick, Jeevan B Gc, Shun-ichiro Oda, Bernard S Gerstman, Erica Ollmann Saphire, Prem P Chapagain, Robert V Stahelin “A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine” Journal of Biological Chemistry, doi: 10.1074/jbc.M117.816280 (2018).

  60. Pavadai E, Gerstman BS, Chapagain PP* “A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix” Scientific reports. 8, 9776 (2018).

    2017

  61. Bhattarai N, GC JB, Gerstman BS, Stahelin RV and Chapagain PP* “Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer” RSC Adv. 7, 22741-2274826702 (2017).

  62. R Mittal, D Nguyen, LH Debs, AP Patel et al. “Zika virus: An emerging global health threat” Frontiers in cellular and infection microbiology 7, 486 (2017).

  63. GC JB, Gerstman BS, and Chapagain PP* “Membrane association and localization dynamics of the Ebola virus matrix protein VP40” Biochimica et Biophysica Acta (BBA) Biomembranes 10, 2012-2020 (2017).

  64. KJ Wijesinghe, S Urata, N Bhattarai, EE. Kooijman, BS. Gerstman, PP Chapagain, S Li and RV Stahelin “Detection of Lipid Induced Structural Changes of the Marburg Virus Matrix Protein VP40 Using Hydrogen/Deuterium Exchange Mass Spectrometry” Journal of Biological Chemistry doi: 10.1074/jbc.M116.758300 (2017).

    2016

  65. Jeevan B. GC, Bernard S. Gerstman, Robert V. Stahelin, and Prem P. Chapagain* “The Ebola virus Protein VP40 hexamer enhances the PIP(4,5)P2 clustering in the plasma membrane” Physical Chemistry Chemical Physics 18, 28409 (2016). [ Featured on the journal cover ].

  66. Jeevan B. GC, Kathleen A. Johnson, M.L. Husby, Cary T. Frick, Bernard S. Gerstman, Robert V. Stahelin, and Prem P. Chapagain* “Interdomain salt-bridges in Ebola virus protein VP40 and their role in domain association and plasma membrane localization” Protein Science 25, 1648-58 (2016).

  67. Purushottam B. Tiwari, Prem P. Chapagain, Srikanth Banda, Yesim Darici, Aykut Üren, Yuk-Ching Tse-Dinh “Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations” FEBS Letters 590, 2844–2851 (2016).

  68. Rahul Mittal, Mayank Aranke, Luca H. Debs, Desiree Nguyen, Amit P. Patel, M'hamed Grati, Jeenu Mittal, Denise Yan, Prem Chapagain, Adrien A. Eshraghi, Xue Zhong Liu, “Indispensable Role of Ion Channels and Transporters in the Auditory System” Journal of Cellular Physiology 232, 743–758 (2016). [ Featured on the journal cover ].

  69. Rahul Mittal, Amit P. Patel, Luca H. Debs, Desiree Nguyen, Kunal Patel, M'hamed Grati, Jeenu Mittal, Denise Yan, Prem Chapagain, Xue Zhong Liu, “Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions” Journal of Cellular Physiology 231, 2599–2621 (2016).

  70. Alyssa Garabedian, David Butcher, Jennifer L. Lippens, Jaroslava Miksovska, Prem P. Chapagain, Daniele Fabris, Mark E. Ridgeway, Melvin A. Park and Francisco Fernandez-Lima, “Structures of the kinetically trapped i-motif DNA intermediates” Physical Chemistry Chemical Physics 18, 26691-26702 (2016).

  71. Rahul Mittal, M’hamed Grati, Miloslav Sedlacek, Fenghua Yuan, Qing Chang, Denise Yan, Xi Lin, Bechara Kachar, Amjad Farooq, Prem Chapagain, Yanbin Zhang, Xue Zhong Liu “Characterization of ATPase activity of P2X2 cation channel” Frontiers in Physiology (2016).

  72. Geraldine Fulcrand, Prem Chapagain, David Dunlap, and Fenfei Leng “Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope” FEBS Letters 590, 613-8 (2016).

  73. Geraldine Fulcrand, Samantha Dages, Xiaoduo Zhi, Prem Chapagain, Bernard Gerstman, David Dunlap, and Fenfei Leng “DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli” Scientific Reports 6, 19243 (2016).

    2015
  74. Rahul Mittal, Brandon Chan, M'hamed Grati, Jeenu Mittal, Kunal Patel, Luca H. Debs, Amit P. Patel, Denise Yan, Prem Chapagain, and Xue Zhong Liu “Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System” Journal of Cellular Physiology 9999, 1–15 (2015).

  75. Jeevan B. GC, Bernard S. Gerstman, and Prem P. Chapagain*, “The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation” Journal of Physical Chemistry B 119, 12750 (2015).

  76. Khoa Pham, Gangadhar Dhulipala, Walter G. Gonzalez, Bernard Gerstman, Chola Regmi, Prem P. Chapagain, and Jaroslava Miksovska “Ca2+ and Mg2+ modulate conformational dynamics and stability of Downstream Regulatory Element Antagonist Modulator” Protein Science, 24, 741 (2015).

  77. Kevin M. Dean, Jennifer L. Lubbeck, Lloyd M. Davis, Chola K. Regmi, Prem P. Chapagain, Bernard S. Gerstman, Ralph Jimenez, and Amy E. Palmer “Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching” Integrative Biology, 7, 263 (2015).

    2014 and older
  78. Jeevan B. GC, Yuba R. Bhandari, Bernard S. Gerstman, and Prem P. Chapagain* “Molecular Dynamics Investigations of the α-Helix to β-Barrel Conformational Transformation in the RfaH Transcription Factor” Journal of Physical Chemistry B 118, 5101–5108 (2014).

  79. Patrick Konold, Chola K. Regmi, Prem P. Chapagain, Bernard S. Gerstman, and Ralph Jimenez “Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants” Journal of Physical Chemistry B 118, 2940 (2014).

  80. Chola K. Regmi, Yuba R. Bhandari, Bernard S. Gerstman, and Prem P. Chapagain* "Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations" Journal of Physical Chemistry B 117, 2247-2253 (2013).

  81. Adele D. Laurent, Vladimir A. Mironov, Prem P. Chapagain, Alexandar V. Nemukhin, and Anna I. Krylov, "Exploring Structural and optical properties of fluorescent proteins by squeezing: Modeling high-pressure effects on the mStraberry and mCherry red fluorescent proteins" Journal of Physical Chemistry B 116, 12426-12440 (2012).

  82. Timothy Steckmann, Zubair Awan, Bernard Gerstman and Prem P. Chapagain*, “Kinetics of peptide secondary structure sonversion during Amyloid β-protein fibrillogenesis” Journal of Theoretical Biology 301, 95-101 (2012). [Featured as the Model of the Month by the European Bioinformatics Institute, part of the European Molecular Biology Laboratory EMBL-EBI, October 2015].

  83. Prem P. Chapagain*, Chola Regmi and William Castillo, “Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry” Journal of Chemical Physics 135, 235101 (2011). [ Featured on the journal cover ]]; also featured in the Virtual Journal of Biological Physics Research].

  84. Prem P. Chapagain*, Bernard Gerstman, Yuba Bhandari, and Dipak Rimal, “Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories”, Physical Review E 83, 061905 (2011).

  85. Yanxin Liu, Prem P. Chapagain, and Bernard S. Gerstman, Stabilization of Native and Non-native Structures by Salt Bridges in a Lattice Model of the GCN4 Leucine Dimer". Journal of Physical Chemistry B 114, 796-803 (2010).

  86. Prem P. Chapagain, Yanxin Liu, and Bernard Gerstman, “The trigger sequence in the leucine zipper: α-helical propensity dependence of folding and dimerization of GCN4-p1 leucine zipper” Journal of Chemical Physics 129, 175103 (2008).

  87. Zhou Lu, Rebecca M. Mitchell, Rebecca L. Smith, Prem P. Chapagain, Ynte H. Schukken and Yrjo T. Grohn, “The importance of culling in Johne’s disease” Journal of Theoretical Biology 254, 135-146 (2008).

  88. Yanxin Liu, Prem P. Chapagain, Jose L. Parra, and Bernard S. Gerstman, “Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 leucine zipper” Journal of Chemical Physics 128, 045106 (2008). (Featured in the Virtual Journal of Biological Physics Research).

  89. C. Lanzas, S. Brien, R. Ivanek, Y. Lo, P. P. Chapagain, K.A. Ray, P. Ayscue, L.D, Warnick and Y.T. Gröhn. “The effect of heterogeneous infectious period and contagiousness on the dynamics of Salmonella transmission” Epidemiology and Infection 136, 1496-1510 (2008).

  90. R. M Mitchell, R. H. Whitlock, S. M. Stehman, A. Benedictus, P. P. Chapagain, Y. T. Grohn, and Y. H. Schukken, “Simulation modeling to evaluate the persistence of Mycobacterium avium subsp. paratuberculosis (MAP) on commercial dairy farms in the United States” Prev. Vet. Med. 83, 360-380 (2008).

  91. P. P. Chapagain, J. S. Van Kessel, J. S. Karns, D. R. Wolfang, E. Hovingh, K. A. Nelen, Y. H. Schukken, and Yrjo T. Grohn, “A mathematical model of the dynamics of Salmonella Cerro infection in a US dairy herd” Epidemioloy and Infection 136, 263 (2008).

  92. Prem P. Chapagain, Jose L. Parra, Bernard S. Gerstman and Yanxin Liu, “Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide” Journal of Chemical Physics 127, 075103 (2007). (Featured in the Virtual Journal of Biological Physics Research).

  93. Prem P. Chapagain and Bernard S. Gerstman, “Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide” Biopolymers 81, 167 (2006).

  94. Bernard S. Gerstman and Prem P. Chapagain, “Self-organization and the hydrophobic interaction in protein folding” Journal of Chemical Physics 123, 054902 (2005). (Featured in the Virtual Journal of Biological Physics Research).

  95. Prem P. Chapagain and Bernard S. Gerstman, “Excluded volume entropic effects on protein unfolding times and intermediary stability”, Journal of Chemical Physics 120, 2475 (2004). (Featured in the Virtual Journal of Biological Physics Research).

  96. Prem P. Chapagain and Bernard S. Gerstman, "Finite size scaling of structural transitions in a simulated protein with secondary and tertiary structure", Journal of Chemical Physics 119, 1174 (2003). (Featured in Virtual Journal of Biological Physics Research).

    Review/Book Chapters:

  97. Gerstman, B.S., Chapagain, P.P., Jeevan, G.C. and Steckmann, T., Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins. In Protein Supersecondary Structures (pp. 297-311). Humana Press, New York, NY (2019).

  98. Bernard S. Gerstman and Prem P. Chapagain, "Computational simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation", Methods in Mol. Biol. 932, 191-204 (2013).

  99. Bernard S. Gerstman and Prem P. Chapagain, “Self-Organizing Dynamics in Protein Folding”, Progress in Nucleic Acid Research and Molecular Biology, 84, 1-37 (2008).

    Proceedings and preprints:
  100. Chapagain, Prem. "Potential Role of Cellular Senescence on Coronavirus Infections." DOI: https://www.preprints.org/manuscript/202004.0532/v1 (2020).

  101. P. P. Chapagain, RM. Mitchell, SM Stehman, YH Schukken, YT Grohn “Characteristics of a mathematical model of Mycobacterium avium subsp. paratuberculosis (MAP) transmission” Proceedings of the 11th International Symposium on Veterinary Epidemiology and Economics, 2006


Email: chapagap@fiu.edu