PUBLICATIONS

    2026

  1. Santos-Fernandez, M., Jeanne Dit Fouque, K., Pita, S., Chapagain, P., Leng, F. and Fernandez-Lima, F., Mapping native peptide-peptide noncovalent interactions: Insights from trapped ion mobility spectrometry, electron- and UV-fragmentation, tandem mass spectrometry, and molecular dynamics. Journal of the American Society for Mass Spectrometry (2026). Journal Cover Link
  2. Stebliankin, V., Baral, P., Balbin, C., Nunez-Castilla, J., Sobhan, M., Cickovski, T., Mondal, A.M., Siltberg-Liberles, J., Chapagain, P., Mathee, K. and Narasimhan, G., EMoMiS: a pipeline for epitope-based molecular mimicry search in protein structures with applications to SARS-CoV-2. Computational and Structural Biotechnology Journal (2026). Link

    3. 2025

  3. Santos-Fernandez, M., Jeanne Dit Fouque, K., Karki, U., Blond, A., Zirah, S., Chapagain, P.P., Hegemann, J.D. and Fernandez-Lima, F., Lasso Peptide Syanodin I: Loop-Pulling Two-Step Thermal Unthreading Mechanism. Analytical Chemistry (2025). Journal Cover Link
  4. Mamun, Y., Aguado, A., Preza, A., Kadel, A., Mogallur, A., Gonzalez, B., De La Rosa, J., Diaz, D., Evdokimova, P., Karki, U. and Tse-Dinh, Y.C., Substrate binding of human and bacterial type IA topoisomerase: An experimentation with AlphaFold 3.0. Computational and Structural Biotechnology Journal 27, 1342-1349 (2025). Link
  5. Shirali, A., Stebliankin, V., Karki, U., Shi, J., Chapagain, P. and Narasimhan, G., A comprehensive survey of scoring functions for protein docking models. BMC Bioinformatics 26, 25 (2025). Link
  6. Saxena, R., Wright, M.M., Rathman, B.M., Karki, U., Chapagain, P.P., Del Valle, J.R. and Stahelin, R.V., Design of a stapled peptide that binds to the Ebola virus matrix protein dimer interface. RSC Chemical Biology 6, 963-974 (2025). Link
  7. Karki, U. and Chapagain, P., Tables Turned─ Structural Mechanisms of Target-Induced miRNA Destabilization. The Journal of Physical Chemistry B 129, 5166-5175 (2025). Journal Cover Link
  8. Qu, F., Fuente, J., Chapagain, P. and Liu, Y., Unscheduled m6A Deposition in RNA via m6ATP Incorporation by DNA Polymerases. International Journal of Molecular Sciences 26(19), 9263 (2025). Link
  9. Rayo Parra, J., Grand, Z., Gonzalez, G., Perera, R., Pandeya, D., Weiler, T. and Chapagain, P., The Multifaceted Role of miR-211 in Health and Disease. Biomolecules 15(8), 1109 (2025). Link
  10. Motsa, B.B., Bhowal, B., Narkhede, Y.B., Karki, U., Ramirez, V.T., Eger, S.W., Wiest, O., Chapagain, P.P. and Stahelin, R.V., Variants of the Ebola virus matrix protein VP40 have differential effects on oligomerization and plasma membrane interactions. Journal of Biological Chemistry 110489 (2025). Link
  11. Mamun, Y., Chadni, S.H., Rayala, R., Shafi, H., Ferdous, S., Pokhrel, R., Nefzi, A., Chapagain, P. and Tse-Dinh, Y.C., Substituted Triazole-3,5-Diamine Compounds as Novel Human Topoisomerase III Beta Inhibitors. International Journal of Molecular Sciences 26(13), 6193 (2025). Link
  12. Gautam, N., Wang, S., Üren, A., Chapagain, P.P., Adhikari, N.P. and Tiwari, P.B., Mapping the Interactions Among Class IIa Histone Deacetylases and Myocyte Enhancer Factor 2s. Journal of Chemical Information and Modeling 65(12), 6249 (2025). Link
  13. Mittal, R., Lemos, J.R., Chapagain, P. and Hirani, K., Interplay of hypoxia, immune dysregulation, and metabolic stress in pathophysiology of type 1 diabetes. Frontiers in Immunology 16, 1599321 (2025). Link
  14. Su, L., Deng, Z., Santos-Fernandez, M., Jeanne Dit Fouque, K., Chapagain, P.P., Chambers, J.W., Fernandez-Lima, F. and Leng, F., Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus. Nucleic Acids Research 53(3), gkaf035 (2025). Link

    15. 2024

  15. Cioffi, M.D., Sharma, T., Motsa, B.B., Bhattarai, N., Gerstman, B.S., Stahelin, R.V. and Chapagain, P.P., Ebola Virus Matrix Protein VP40 Single Mutations G198R and G201R Significantly Enhance Plasma Membrane Localization. The Journal of Physical Chemistry B 128(46), 11335-11344 (2024). Journal Cover Link
  16. Gautam, N., Chapagain, P.P., Adhikari, N.P. and Tiwari, P.B., Characterization of molecular interactions between HDAC7 and MEF2A. Journal of Biomolecular Structure and Dynamics (2024). Link
  17. Perez, H.A., Wang, Z., Gerstman, B.S., He, J. and Chapagain, P.P., Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation. Journal of Chemical Information and Modeling 64(20), 7977-7986 (2024). Link
  18. Mamun, Y., Tse-Dinh, Y.C. and Chapagain, P., Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 64(15), 6062-6071 (2024). Link
  19. Sklenicka, J., Tran, T., Ramirez, M.S., Donow, H.M., Magaña, A.J., LaVoi, T., Mamun, Y., Jimenez, V., Chapagain, P., Santos, R. and Pinilla, C., Structure-activity relationship of pyrrolidine pentamine derivatives as inhibitors of the Aminoglycoside 6′-N-Acetyltransferase type ib. Antibiotics 13(7), 672 (2024). Link
  20. 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., Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Science 33(5), e4978 (2024). Link
  21. Motsa, B.B., Sharma, T., Cioffi, M., Chapagain, P.P. and Stahelin, R.V., Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. Journal of Biological Chemistry (2024). Link
  22. 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). Journal Cover Link
  23. 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 159464 (2024). Link
  24. 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., The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. Human Genetics (2024). Link
  25. Perez, H., Chapagain, P.P. and Gerstman, B.S., Binding of Peptides Containing D-Amino Acids to the Tsg101 Tumor Susceptibility Protein. ChemistrySelect 9(38), e202402860 (2024). Link

    26. 2023

  26. Stebliankin, V., Shirali, A., Baral, P., Shi, J., Chapagain, P., Mathee, K. and Narasimhan, G., Evaluating protein binding interfaces with transformer networks. Nature Machine Intelligence 5, 1042-1053 (2023). Link
  27. Deng, Z., Chapagain, P. and Leng, F., Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase. Journal of Biological Chemistry 299, 102832 (2023). Link
  28. Magaña, A.J., Sklenicka, J., Pinilla, C., Giulianotti, M., Chapagain, P., Santos, R. and Tolmasky, M.E., Restoring susceptibility to aminoglycosides in MRSA. RSC Medicinal Chemistry (2023). Journal Cover Link
  29. 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. International Journal of Molecular Sciences 24, 12586 (2023). Link
  30. Tsegay, P.S., Hernandez, D., Qu, F., Olatunji, M., Mamun, Y., Chapagain, P. and Liu, Y., RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. Nucleic Acids Research 51(1), 166-181 (2023). Link
  31. Narkhede, Y.B., Bhardwaj, A., Motsa, B.B., Saxena, R., Sharma, T., Chapagain, 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
  32. 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 29, 252-257 (2023). Link
  33. Katsushima, K., Pokhrel, R., Mahmud, I., Yuan, M., Murad, R., Baral, P., Zhou, R., Chapagain, P., Garrett, T., Stapleton, S. and Jallo, G., The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas. Acta Neuropathologica Communications 11(1), 38 (2023). Link
  34. 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., Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes. ImmunoInformatics 9, 100023 (2023). Link
  35. Thapa, B., Adhikari, N.P., Tiwari, P.B. and Chapagain, P.P., 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 (2023). Link

    36. 2022

  36. 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 Pharmacology & Translational Science 5(10), 915 (2022). Journal Cover Link
  37. Pokhrel, R., Shakya, R., Baral, P. and Chapagain, P., Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. Journal of Chemical Information and Modeling 62, 2824 (2022). Journal Cover Link
  38. 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., 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), eabn1440 (2022). Journal Cover Link
  39. 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), 1415 (2022). Link
  40. Garabedian, A., Jeanne Dit Fouque, K., Chapagain, P.P., Leng, F. and Fernandez-Lima, F., AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes. Nucleic Acids Research 50(5), 2431-2439 (2022). Link
  41. Alfonso, E.E., Troche, R., Deng, Z., Annamalai, T., Chapagain, P., Tse-Dinh, Y.C. and Leng, F., Potent inhibition of bacterial DNA gyrase by digallic acid and other gallate derivatives. ChemMedChem (2022). Link
  42. 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
  43. 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
  44. Jeanne Dit Fouque, K., Sipe, S.N., Garabedian, A., Mejia, G., Su, L., Hossen, M.L., Chapagain, 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). Journal Cover Link
  45. 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 104685 (2022). Link
  46. Hossen, M.L., Baral, P., Sharma, T., Gerstman, B.S. 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 (2022). Link
  47. 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, 103258 (2022). Link
  48. 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 (2022). Link

    49. 2021

  49. Amiar, S., Husby, M.L., Wijesinghe, K.J., Angel, S., Bhattarai, N., Gerstman, B.S., Chapagain, P.P., Li, S. and Stahelin, R.V., Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. Journal of Biological Chemistry 296, 100489 (2021). Link
  50. Pokhrel, R., Bhattarai, N., Baral, P., Gerstman, B.S., Park, J.H., Handfield, M. and Chapagain, P.P., Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides. Journal of Chemical Theory and Computation 18, 516-525 (2021). Link
  51. Rocha, K., Magallon, J., Reeves, C., Phan, K., Vu, P., Oakley-Havens, C.L., Kwan, S., Ramirez, M.S., LaVoi, T., Donow, H., Chapagain, P., Santos, R., Pinilla, C., Giulianotti, M.A. and Tolmasky, M.E., 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
  52. Baral, P., Bhattarai, N., Hossen, M.L., Stebliankin, V., Gerstman, B.S., Narasimhan, G. and Chapagain, P.P., 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, 14-20 (2021). Link
  53. 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), 340-350 (2021). Link
  54. 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). Journal Cover Link
  55. Koirala, R.P., Pokhrel, R., Baral, P., Tiwari, P.B., Chapagain, P.P. and Adhikari, N.P., Structural insights into the repair mechanism of AGT for methyl-induced DNA damage. Biological Chemistry (2021). Link
  56. 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), 1375 (2021). Link
  57. 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). Link

    58. 2020

  58. 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 69, 864 (2020). Link
  59. 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 11, 2543-2548 (2020). Link
  60. 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
  61. 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
  62. 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). Link
  63. 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). Link
  64. Tiwari, P., Chapagain, P.P., Seddek, A., Annamalai, T., Üren, A. and Tse-Dinh, Y.C., Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem 15, 623-631 (2020). Link

    65. 2019 and Earlier

  65. 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). Link
  66. 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). Link
  67. Porter, J.E., Chapagain, P. and Fernandez-Lima, F., Single stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. Rapid Communications in Mass Spectrometry 33, 60-65 (2018). Link
  68. Pokhrel, R., Sompornpisut, P., Chapagain, P., Olson, B., et al., Domain rearrangement and denaturation in Ebola virus protein VP40. AIP Advances 8, 125129 (2018). Link
  69. Bhattarai, N., Gerstman, B.S. and Chapagain, P.P., Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24-Human Keap1 Complex. ACS Omega 3, 18639-18645 (2018). Link
  70. Butcher, D., Chapagain, P.P., Leng, F. and Fernandez-Lima, F., Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility Spectrometry. The Journal of Physical Chemistry B 122(27) (2018). Link
  71. Tiwari, P.B., Chapagain, P.P. and Üren, A., Investigating molecular interactions between oxidized neuroglobin and cytochrome c. Scientific Reports 8(1), 10557 (2018). Link
  72. Pokhrel, R., Gerstman, B.S., Hutcheson, J.D. and Chapagain, P.P., In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles. The Journal of Physical Chemistry B 122(14), 3782-3789 (2018). Link
  73. Sandhaus, S., Chapagain, P.P. and Tse-Dinh, Y.C., Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Scientific Reports 8(1), 1437 (2018). Link
  74. Del Vecchio, K., Frick, C.T., Gc, J.B., Oda, S., Gerstman, B.S., Saphire, E.O., Chapagain, P.P. and Stahelin, R.V., A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine. Journal of Biological Chemistry 293, 3335-3349 (2018). Link
  75. Pavadai, E., Gerstman, B.S. and Chapagain, P.P., A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix. Scientific Reports 8, 9776 (2018). Link
  76. Bhattarai, N., Gc, J.B., Gerstman, B.S., Stahelin, R.V. and Chapagain, P.P., Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer. RSC Advances 7, 22741-22748 (2017). Link
  77. Gc, J.B., Gerstman, B.S. and Chapagain, P.P., Membrane association and localization dynamics of the Ebola virus matrix protein VP40. Biochimica et Biophysica Acta (BBA) - Biomembranes 1859(10), 2012-2020 (2017). Link
  78. Wijesinghe, K.J., Urata, S., Bhattarai, N., Kooijman, E.E., Gerstman, B.S., Chapagain, P.P., Li, S. and Stahelin, R.V., Detection of Lipid Induced Structural Changes of the Marburg Virus Matrix Protein VP40 Using Hydrogen/Deuterium Exchange Mass Spectrometry. Journal of Biological Chemistry 292(9), 3335 (2017). Link
  79. Gc, J.B., Gerstman, B.S., Stahelin, R.V. and Chapagain, P.P., The Ebola virus Protein VP40 hexamer enhances the PIP(4,5)P2 clustering in the plasma membrane. Physical Chemistry Chemical Physics 18, 28409-28418 (2016). Journal Cover Link
  80. Gc, J.B., Johnson, K.A., Husby, M.L., Frick, C.T., Gerstman, B.S., Stahelin, R.V. and Chapagain, P.P., Interdomain salt-bridges in Ebola virus protein VP40 and their role in domain association and plasma membrane localization. Protein Science 25, 1648-1658 (2016). Link
  81. Tiwari, P.B., Chapagain, P.P., Banda, S., Darici, Y., Üren, A. and Tse-Dinh, Y.C., Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations. FEBS Letters 590, 2844-2851 (2016). Link
  82. Mittal, R., Aranke, M., Debs, L.H., Nguyen, D., Patel, A.P., Grati, M., Mittal, J., Yan, D., Chapagain, P., Eshraghi, A.A. and Liu, X.Z., Indispensable Role of Ion Channels and Transporters in the Auditory System. Journal of Cellular Physiology 232, 743-758 (2016). Journal Cover Link
  83. Mittal, R., Patel, A.P., Debs, L.H., Nguyen, D., Patel, K., Grati, M., Mittal, J., Yan, D., Chapagain, P. and Liu, X.Z., Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. Journal of Cellular Physiology 231, 2599-2621 (2016). Link
  84. Garabedian, A., Butcher, D., Lippens, J.L., Miksovska, J., Chapagain, P.P., Fabris, D., Ridgeway, M.E., Park, M.A. and Fernandez-Lima, F., Structures of the kinetically trapped i-motif DNA intermediates. Physical Chemistry Chemical Physics 18, 26691-26702 (2016). Link
  85. Fulcrand, G., Chapagain, P., Dunlap, D. and Leng, F., Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS Letters 590, 613-618 (2016). Link
  86. Fulcrand, G., Dages, S., Zhi, X., Chapagain, P., Gerstman, B., Dunlap, D. and Leng, F., DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. Scientific Reports 6, 19243 (2016). Link
  87. Gc, J.B., Gerstman, B.S. and Chapagain, P.P., The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation. Journal of Physical Chemistry B 119, 12750-12759 (2015). Link
  88. Pham, K., Dhulipala, G., Gonzalez, W.G., Gerstman, B., Regmi, C., Chapagain, P.P. and Miksovska, J., Ca2+ and Mg2+ modulate conformational dynamics and stability of Downstream Regulatory Element Antagonist Modulator. Protein Science 24, 741-750 (2015). Link
  89. Dean, K.M., Lubbeck, J.L., Davis, L.M., Regmi, C.K., Chapagain, P.P., Gerstman, B.S., Jimenez, R. and Palmer, A.E., Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integrative Biology 7, 263-273 (2015). Link
  90. Gc, J.B., Bhandari, Y.R., Gerstman, B.S. and Chapagain, P.P., 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). Link
  91. Konold, P., Regmi, C.K., Chapagain, P.P., Gerstman, B.S. and Jimenez, R., Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants. Journal of Physical Chemistry B 118, 2940-2949 (2014). Link
  92. Regmi, C.K., Bhandari, Y.R., Gerstman, B.S. and Chapagain, P.P., 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). Link
  93. Laurent, A.D., Mironov, V.A., Chapagain, P.P., Nemukhin, A.V. and Krylov, A.I., 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). Link
  94. Steckmann, T., Awan, Z., Gerstman, B. and Chapagain, P.P., Kinetics of peptide secondary structure conversion during Amyloid β-protein fibrillogenesis. Journal of Theoretical Biology 301, 95-101 (2012). Link
  95. Chapagain, P.P., Regmi, C. and Castillo, W., Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry. Journal of Chemical Physics 135, 235101 (2011). Journal Cover Link
  96. Chapagain, P.P., Gerstman, B., Bhandari, Y. and Rimal, D., Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories. Physical Review E 83, 061905 (2011). Link
  97. Liu, Y., Chapagain, P.P. and Gerstman, B.S., 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). Link
  98. Chapagain, P.P., Liu, Y. and Gerstman, B., 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). Link
  99. Lu, Z., Mitchell, R.M., Smith, R.L., Chapagain, P.P., Schukken, Y.H. and Grohn, Y.T., The importance of culling in Johne's disease. Journal of Theoretical Biology 254, 135-146 (2008). Link
  100. Liu, Y., Chapagain, P.P., Parra, J.L. and Gerstman, B.S., 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). Link
  101. Lanzas, C., Brien, S., Ivanek, R., Lo, Y., Chapagain, P.P., Ray, K.A., Ayscue, P., Warnick, L.D. and Gröhn, Y.T., The effect of heterogeneous infectious period and contagiousness on the dynamics of Salmonella transmission. Epidemiology and Infection 136, 1496-1510 (2008). Link
  102. Mitchell, R.M., Whitlock, R.H., Stehman, S.M., Benedictus, A., Chapagain, P.P., Grohn, Y.T. and Schukken, Y.H., Simulation modeling to evaluate the persistence of Mycobacterium avium subsp. paratuberculosis (MAP) on commercial dairy farms in the United States. Preventive Veterinary Medicine 83, 360-380 (2008). Link
  103. Chapagain, P.P., Van Kessel, J.S., Karns, J.S., Wolfang, D.R., Hovingh, E., Nelen, K.A., Schukken, Y.H. and Grohn, Y.T., A mathematical model of the dynamics of Salmonella Cerro infection in a US dairy herd. Epidemiology and Infection 136, 263-272 (2008). Link
  104. Chapagain, P.P., Parra, J.L., Gerstman, B.S. and Liu, Y., 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). Link
  105. Chapagain, P.P. and Gerstman, B.S., Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide. Biopolymers 81, 167-177 (2006). Link
  106. Gerstman, B.S. and Chapagain, P.P., Self-organization and the hydrophobic interaction in protein folding. Journal of Chemical Physics 123, 054902 (2005). Link
  107. Chapagain, P.P. and Gerstman, B.S., Excluded volume entropic effects on protein unfolding times and intermediary stability. Journal of Chemical Physics 120, 2475-2482 (2004). Link
  108. Chapagain, P.P. and Gerstman, B.S., Finite-size scaling of structural transitions in a simulated protein with secondary and tertiary structure. Journal of Chemical Physics 119, 1174-1183 (2003). Link

    109. PATENTS

    1. Vashist, A., Raymond, A.D., Chapagain, P., Nair, M.P. and Runowicz, C.D., Polyols and polyol-based hydrogels with anti-cancer activity. (2025). U.S. Patent Application 19/175,507. Link
    2. Vashist, A., Chapagain, P., Raymond, A.D., Chand, H. and Nair, M., Treatment and prevention of infections using vegetable oil-derived polyols. (2026). US Patent App. 19/323,352. Link

    REVIEW/BOOK CHAPTERS

    1. Gerstman, B.S., Chapagain, P.P., Gc, J.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). Link
    2. Gerstman, B.S. and Chapagain, P.P., Computational simulations of Protein Folding to Engineer Amino Acid Sequences to Encourage Desired Supersecondary Structure Formation. Methods in Molecular Biology 932, 191-204 (2013). Link
    3. Gerstman, B.S. and Chapagain, P.P., Self-Organizing Dynamics in Protein Folding. Progress in Nucleic Acid Research and Molecular Biology 84, 1-37 (2008). Link

    PROCEEDINGS & PREPRINTS

    1. Chapagain, P., Potential Role of Cellular Senescence on Coronavirus Infections. Preprints (2020). Link