Chapagain, Prem Graduate Faculty
- Professor, Physics , College of Arts, Sciences & Education
Overview
overview
- Dr. Chapagain is a Professor in the Department of Physics at Florida International University, specializing in biological physics. His research focuses on the computational investigations of biomolecules and he has extensively published on various topics of biophysics including protein aggregation, exploring novel antimicrobial compounds against antibiotic-resistant pathogens, membrane interactions and dynamics of viral proteins of emerging viruses such as Ebola and Marburg viruses and more recently SARS-CoV-2. He has developed an excellent research infrastructure in computational biophysics at FIU with external funding from the NSF, NIH, DoD, and industry partners. He has been recognized by teaching and research awards, including the 2019 Faculty Excellence in Teaching Award. Dr. Chapagain has a highly successful record of teaching and mentoring both graduate and undergraduate students.
Publications
Patents issued
selected scholarly works & creative activities
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Article
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2025Lasso Peptide Syanodin I: Loop-Pulling Two-Step Thermal Unthreading Mechanism. Analytical Chemistry. 97:25111-25119.Full Text via DOI: 10.1021/acs.analchem.5c04118 Web of Science: 001603140700001
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2025Unscheduled m6A Deposition in RNA via m6ATP Incorporation by DNA Polymerases. International Journal of Molecular Sciences. 26.Full Text via DOI: 10.3390/ijms26199263 Web of Science: 001594839400001
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2025Variants of the Ebola virus matrix protein VP40 have differential effects on oligomerization and plasma membrane interactions. Journal of Biological Chemistry. 301.Full Text via DOI: 10.1016/j.jbc.2025.110489 Web of Science: 001565786500001
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2025Substituted Triazole-3,5-Diamine Compounds as Novel Human Topoisomerase III Beta Inhibitors. International Journal of Molecular Sciences. 26.Full Text via DOI: 10.3390/ijms26136193 Web of Science: 001526374400001
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2025Mapping the Interactions Among Class IIa Histone Deacetylases and Myocyte Enhancer Factor 2s. Journal of Chemical Information and Modeling. 65:6249-6260.Full Text via DOI: 10.1021/acs.jcim.5c00858 Web of Science: 001503521500001
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2025Design of a stapled peptide that binds to the Ebola virus matrix protein dimer interface. RSC Chemical Biology. 6:963-974.Full Text via DOI: 10.1039/d5cb00048c Web of Science: 001482673200001
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2025Interplay of hypoxia, immune dysregulation, and metabolic stress in pathophysiology of type 1 diabetes. Frontiers in Immunology. 16.Full Text via DOI: 10.3389/fimmu.2025.1599321 Web of Science: 001510512600001
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2025Tables Turned-Structural Mechanisms of Target-Induced miRNA Destabilization. Journal of Physical Chemistry B. 129:5166-5175.Full Text via DOI: 10.1021/acs.jpcb.5c01093 Web of Science: 001479256700001
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2025BPS2025 - Investigating class IIa HDACS interactions with MEF2A. Biophysical Journal. 124:157a-158a.Full Text via DOI: 10.1016/j.bpj.2024.11.864
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2025BPS2025 - Molecular dynamics simulations of the interplay of miRNA-target interactions. Biophysical Journal. 124:252a.Full Text via DOI: 10.1016/j.bpj.2024.11.1372
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2025BPS2025 - Molecular dynamics simulations of the lipid-II interactions and assembly of Nisin chains in bacterial membranes. Biophysical Journal. 124:69a.Full Text via DOI: 10.1016/j.bpj.2024.11.438
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2025BPS2025 - Molecular dynamics simulations of the lipid-II interactions and assembly of nisin chains in bacterial membranes. Biophysical Journal. 124:26a.Full Text via DOI: 10.1016/j.bpj.2024.11.203
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2025P-1346. Identification of aminoglycoside 6′-N-acetyltransferase type Ib small molecule inhibitors using mixture-based combinatorial libraries and structure-activity relationship studies. Open Forum Infectious Diseases. 12:ofae631.1523.Full Text via DOI: 10.1093/ofid/ofae631.1523
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2025Substrate binding of human and bacterial type IA topoisomerase: An experimentation with AlphaFold 3.0. Computational and Structural Biotechnology Journal. 27:1342-1349.Full Text via DOI: 10.1016/j.csbj.2025.03.041 Web of Science: 001461468000001
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2024Characterization of molecular interactions between HDAC7 and MEF2A. Journal of Biomolecular Structure and Dynamics.Full Text via DOI: 10.1080/07391102.2024.2437523 Web of Science: 001374865700001
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2024Binding of Peptides Containing D-Amino Acids to the Tsg101 Tumor Susceptibility Protein. ChemistrySelect. 9.Full Text via DOI: 10.1002/slct.202402860 Web of Science: 001328762500001
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2024Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation. Journal of Chemical Information and Modeling. 64:7977-7986.Full Text via DOI: 10.1021/acs.jcim.4c01050 Web of Science: 001330668000001
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2024Ebola Virus Matrix Protein VP40 Single Mutations G198R and G201R Significantly Enhance Plasma Membrane Localization. Journal of Physical Chemistry B. 128:11335-11344.Full Text via DOI: 10.1021/acs.jpcb.4c02700 Web of Science: 001324894400001
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2024Insights into the DNA and RNA Interactions of Human Topoisomerase III Beta Using Molecular Dynamics Simulations. Journal of Chemical Information and Modeling. 64:6062-6071.Full Text via DOI: 10.1021/acs.jcim.4c00472 Web of Science: 001272779800001
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2024Minor electrostatic changes robustly increase VP40 membrane binding, assembly, and budding of Ebola virus matrix protein derived virus-like particles. Journal of Biological Chemistry. 300.Full Text via DOI: 10.1016/j.jbc.2024.107213 Web of Science: 001345372000001
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2024Role of phosphatidic acid lipids on plasma membrane association of the Ebola virus matrix protein VP40. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids. 1869.Full Text via DOI: 10.1016/j.bbalip.2024.159464 Web of Science: 001188883500001
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2024Computational and experimental identification of keystone interactions in Ebola virus matrix protein VP40 dimer formation. Protein Science. 33.Full Text via DOI: 10.1002/pro.4978 Web of Science: 001198718500001
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2024PI(4,5)P2 binding sites in the Ebola virus matrix protein VP40 modulate assembly and budding. Journal of Lipid Research. 65.Full Text via DOI: 10.1016/j.jlr.2024.100512 Web of Science: 001199138100001
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2024PI(4,5)P2 binding sites in the Ebola virus matrix protein VP40 modulate assembly and budding. Journal of Lipid Research. 65.
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2023miRNA-211 maintains metabolic homeostasis in medulloblastoma through its target gene long-chain acyl-CoA synthetase 4. Acta Neuropathologica Communications. 11.Full Text via DOI: 10.1186/s40478-023-01684-w Web of Science: 001130118700002
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2023Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase. Journal of Biological Chemistry. 299.Full Text via DOI: 10.1016/j.jbc.2023.105439 Web of Science: 001165005500001
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2023Distinctive 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.Full Text via DOI: 10.3390/ijms241612586 Web of Science: 001056249900001
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2023Elucidating Residue-Level Determinants Affecting Dimerization of Ebola Virus Matrix Protein Using High-Throughput Site Saturation Mutagenesis and Biophysical Approaches. Journal of Physical Chemistry B. 127:6449-6461.Full Text via DOI: 10.1021/acs.jpcb.3c01759 Web of Science: 001027374700001
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2023The oncogenic circular RNA circ_63706 is a potential therapeutic target in sonic hedgehog-subtype childhood medulloblastomas. Acta Neuropathologica Communications. 11.Full Text via DOI: 10.1186/s40478-023-01521-0 Web of Science: 000948988700003
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2023Epitopedia: identifying molecular mimicry between pathogens and known immune epitopes. ImmunoInformatics. 9:100023.Full Text via DOI: 10.1016/j.immuno.2023.100023
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2023Exploring the dimer-dimer association of the ebolavirus matrix protein VP40 at the human plasma membrane. Biophysical Journal. 122.Full Text via DOI: 10.1016/j.bpj.2022.11.1194
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2023Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness. Journal of Physical Chemistry B. 127:52-61.Full Text via DOI: 10.1021/acs.jpcb.2c05584 Web of Science: 000906465500001
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2023RNA-guided DNA base damage repair via DNA polymerase-mediated nick translation. Nucleic Acids Research (NAR). 51:166-181.Full Text via DOI: 10.1093/nar/gkac1178 Web of Science: 000899689000001
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2023Molecular interactions between perlecan LG3 and the SARS-CoV-2 spike protein receptor binding domain. Protein Science. 33.Full Text via DOI: 10.1002/pro.4843 Web of Science: 001127314400001
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2023Responsiveness of the electrically stimulated cochlear nerve in patients with a missense variant in ACTG1: Preliminary Results.. Frontiers in audiology and otology. 1:1213323.Full Text via DOI: 10.3389/fauot.2023.1213323
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2022Potent Inhibition of Bacterial DNA Gyrase by Digallic Acid and Other Gallate Derivatives. ChemMedChem. 17.Full Text via DOI: 10.1002/cmdc.202200301 Web of Science: 000870041900001
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2022Molecular Modeling and Simulation of the Peptidoglycan Layer of Gram-Positive Bacteria Staphylococcus aureus. Journal of Chemical Information and Modeling. 62:4955-4962.Full Text via DOI: 10.1021/acs.jcim.2c00437 Web of Science: 000877041700001
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2022Immunoinformatic screening of Marburgvirus epitopes and computational investigations of epitope-allele complexes. International Immunopharmacology. 111.Full Text via DOI: 10.1016/j.intimp.2022.109109 Web of Science: 000862677800002
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2022Novel and Structurally Diversified Bacterial DNA Gyrase Inhibitors Discovered through a Fluorescence-Based High-Throughput Screening Assay. ACS Pharmacology and Translational Science. 5:932-944.Full Text via DOI: 10.1021/acsptsci.2c00113 Web of Science: 000878179400001
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2022Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience. 25.Full Text via DOI: 10.1016/j.isci.2022.104685 Web of Science: 000888517800002
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2022Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. Science Advances. 8.Full Text via DOI: 10.1126/sciadv.abn1440 Web of Science: 000828233900008
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2022Exploring the Conformational and Binding Dynamics of HMGA2•DNA Complexes Using Trapped Ion Mobility Spectrometry-Mass Spectrometry. Journal of the American Society for Mass Spectrometry.Full Text via DOI: 10.1021/jasms.2c00101 Web of Science: 000819457300001
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2022Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachment. Physical Chemistry, Chemical Physics - PCCP. 24:9123-9129.Full Text via DOI: 10.1039/d2cp00169a Web of Science: 000779732000001
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2022A 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. 63:2095-2103.Full Text via DOI: 10.1021/acs.jcim.2c01294 Web of Science: 000905347600001
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2022AT-hook peptides bind the major and minor groove of AT-rich DNA duplexes. Nucleic Acids Research (NAR). 50:2431-2439.Full Text via DOI: 10.1093/nar/gkac115 Web of Science: 000768143600001
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2022Detecting Individual Proteins and Their Surface Charge Variations in Solution by the Potentiometric Nanoimpact Method. ACS Sensors. 7:555-563.Full Text via DOI: 10.1021/acssensors.1c02385 Web of Science: 000746813600001
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2022Ebola virus protein VP40 binding to Sec24c for transport to the plasma membrane. Proteins: Structure, Function and Bioinformatics. 90:340-350.Full Text via DOI: 10.1002/prot.26221 Web of Science: 000692659700001
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2022Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides. Journal of Chemical Theory and Computation. 18:516-525.Full Text via DOI: 10.1021/acs.jctc.1c00666 Web of Science: 000730568600001
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2022Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repair. DNA Repair. 109.Full Text via DOI: 10.1016/j.dnarep.2021.103258 Web of Science: 000789227700003
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2021Mutation-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.Full Text via DOI: 10.1016/j.bbrc.2021.08.036 Web of Science: 000687461600001
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2021Inhibition of Aminoglycoside 6′-N-acetyltransferase Type Ib (AAC(6′)-Ib): Structure-Activity Relationship of Substituted Pyrrolidine Pentamine Derivatives as Inhibitors. Biomedicines. 9.Full Text via DOI: 10.3390/biomedicines9091218 Web of Science: 000699202200001
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2021Structural insights into the repair mechanism of AGT for methyl-induced DNA damage. Biological Chemistry. 402:1203-1211.Full Text via DOI: 10.1515/hsz-2021-0198 Web of Science: 000696239800004
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2021Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351. Journal of Physical Chemistry B. 125:7101-7107.Full Text via DOI: 10.1021/acs.jpcb.1c01626 Web of Science: 000672740600004
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2021Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop. Viruses. 13.Full Text via DOI: 10.3390/v13071375 Web of Science: 000677080900001
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2021The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 Infection. JACC: Basic to Translational Science. 6:1-8.Full Text via DOI: 10.1016/j.jacbts.2020.10.003 Web of Science: 000613908200001
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2020Identification of HMGA2 inhibitors by AlphaScreen-based ultra-high-throughput screening assays. Scientific Reports. 10.Full Text via DOI: 10.1038/s41598-020-75890-0 Web of Science: 000589618700022
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2020EF-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.Full Text via DOI: 10.1021/acschemneuro.0c00399 Web of Science: 000569269100010
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2020In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever. Scientific Reports. 10.Full Text via DOI: 10.1038/s41598-020-63640-1 Web of Science: 000534024000034
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2020Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development. ChemMedChem. 15:623-631.Full Text via DOI: 10.1002/cmdc.201900721 Web of Science: 000520292700001
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2020Mutation of Hydrophobic Residues in the C-Terminal Domain of the Marburg Virus Matrix Protein VP40 Disrupts Trafficking to the Plasma Membrane. Viruses. 12.Full Text via DOI: 10.3390/v12040482 Web of Science: 000539525300124
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2019Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. Journal of Physical Chemistry B. 123:9045-9053.Full Text via DOI: 10.1021/acs.jpcb.9b04674 Web of Science: 000493865200001
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2019Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140. Physical Chemistry, Chemical Physics - PCCP. 21:12530-12539.Full Text via DOI: 10.1039/c9cp01558b Web of Science: 000478994100046
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2019Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins. Methods in molecular biology (Clifton, N.J.). 1958:297-311.Full Text via DOI: 10.1007/978-1-4939-9161-7_15 Web of Science: 000706398300016
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2018Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24-Human Keap1 Complex. ACS Omega. 3:18639-18645.Full Text via DOI: 10.1021/acsomega.8b02386 Web of Science: 000458439900046
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2018Investigating molecular interactions between oxidized neuroglobin and cytochrome c. Scientific Reports. 8.Full Text via DOI: 10.1038/s41598-018-28836-6 Web of Science: 000438343600067
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2018A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss. Human Genetics. 137:437-446.Full Text via DOI: 10.1007/s00439-018-1895-y Web of Science: 000439463700002
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2018A cylindrical assembly model and dynamics of the Ebola virus VP40 structural matrix. Scientific Reports. 8.Full Text via DOI: 10.1038/s41598-018-28077-7 Web of Science: 000436398100001
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2018Amino acid 118 in the deafness causing (DFNA20/26) ACTG1 gene is a mutational hot spot. Gene Reports. 11:264-269.Full Text via DOI: 10.1016/j.genrep.2018.04.011 Web of Science: 000433193600041
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2018In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles. Journal of Physical Chemistry B. 122:3782-3789.Full Text via DOI: 10.1021/acs.jpcb.8b00169 Web of Science: 000430641900011
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2018ELMOD3, a novel causative gene, associated with human autosomal dominant nonsyndromic and progressive hearing loss. Human Genetics. 137:329-342.Full Text via DOI: 10.1007/s00439-018-1885-0 Web of Science: 000431534200005
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2018A 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.Full Text via DOI: 10.1074/jbc.M117.816280 Web of Science: 000426562800025
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2018Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Scientific Reports. 8.Full Text via DOI: 10.1038/s41598-018-19944-4 Web of Science: 000423045400010
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2017Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments. Biochemical and Biophysical Research Communications. 493:176-181.Full Text via DOI: 10.1016/j.bbrc.2017.09.052 Web of Science: 000413134200028
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2017Membrane association and localization dynamics of the Ebola virus matrix protein VP40. Biochimica et Biophysica Acta - Biomembranes. 1859:2012-2020.Full Text via DOI: 10.1016/j.bbamem.2017.07.007 Web of Science: 000411419000026
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2017Detection of lipid-induced structural changes of the Marburg virus matrix protein VP40 using hydrogen/deuterium exchange-mass spectrometry. Journal of Biological Chemistry. 292:6108-6122.Full Text via DOI: 10.1074/jbc.M116.758300 Web of Science: 000399538700009
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2017Cooperative structural transitions in amyloid-like aggregation. Journal of Chemical Physics. 146.Full Text via DOI: 10.1063/1.4979516 Web of Science: 000399073300052
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2017Plasma membrane association facilitates conformational changes in the Marburg virus protein VP40 dimer. RSC Advances. 7:22741-22748.Full Text via DOI: 10.1039/c7ra02940c Web of Science: 000400338000016
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2016The Ebola virus protein VP40 hexamer enhances the clustering of PI(4,5)P2 lipids in the plasma membrane. Physical Chemistry, Chemical Physics - PCCP. 18:28409-28417.Full Text via DOI: 10.1039/c6cp03776c Web of Science: 000386668200003
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2016Structures of the kinetically trapped i-motif DNA intermediates. Physical Chemistry, Chemical Physics - PCCP. 18:26691-26702.Full Text via DOI: 10.1039/c6cp04418b Web of Science: 000385175000037
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2016Characterization of molecular interactions between Escherichia coli RNA polymerase and topoisomerase I by molecular simulations. FEBS Letters. 590:2844-2851.Full Text via DOI: 10.1002/1873-3468.12321 Web of Science: 000384807500004
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2016Interdomain salt-bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization. Protein Science. 25:1648-1658.Full Text via DOI: 10.1002/pro.2969 Web of Science: 000383619100008
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2016Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675. Journal of Physical Chemistry Letters. 7:3046-3051.Full Text via DOI: 10.1021/acs.jpclett.6b01172 Web of Science: 000381236400029
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2016Cover Image, Volume 231, Number 8, August 2016. Journal of Cellular Physiology. 231:i-i.Full Text via DOI: 10.1002/jcp.25403
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2016Characterization of ATPase Activity of P2RX2 Cation Channel. Frontiers in Physiology. 7.Full Text via DOI: 10.3389/fphys.2016.00186 Web of Science: 000443553200001
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2016Direct observation of a 91 bp LacI-mediated, negatively supercoiled DNA loop by atomic force microscope. FEBS Letters. 590:613-618.Full Text via DOI: 10.1002/1873-3468.12094 Web of Science: 000371402700003
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2016DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli. Scientific Reports. 6.Full Text via DOI: 10.1038/srep19243 Web of Science: 000368157700001
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2015The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation. Journal of Physical Chemistry B. 119:12750-12759.Full Text via DOI: 10.1021/acs.jpcb.5b05681 Web of Science: 000362701900003
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2015Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator. Protein Science. 24:741-751.Full Text via DOI: 10.1002/pro.2646 Web of Science: 000353524700016
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2015Pairwise amino acid secondary structural propensities. Physical Review E. 91.Full Text via DOI: 10.1103/PhysRevE.91.042709 Web of Science: 000352850200007
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2015Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integrative Biology (United Kingdom). 7:263-273.Full Text via DOI: 10.1039/c4ib00251b Web of Science: 000349668600011
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2014Molecular Dynamics Investigations of the α-Helix to β-Barrel Conformational Transformation in the RfaH Transcription Factor. Journal of Physical Chemistry B. 118:5101-5108.Full Text via DOI: 10.1021/jp502193v Web of Science: 000336199100013
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2014Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants. Journal of Physical Chemistry B. 118:2940-2948.Full Text via DOI: 10.1021/jp412371y Web of Science: 000333381800016
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2013Exploring 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.Full Text via DOI: 10.1021/jp308366y Web of Science: 000315707900003
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2013Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation. Methods in molecular biology (Clifton, N.J.). 932:191-204.Full Text via DOI: 10.1007/978-1-62703-65-6_12
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2012Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins. Journal of Physical Chemistry B. 116:12426-12440.Full Text via DOI: 10.1021/jp3060944 Web of Science: 000309902400006
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2012Structural propensities and entropy effects in peptide helix-coil transitions. Physical Review E. 86.Full Text via DOI: 10.1103/PhysRevE.86.031915 Web of Science: 000308872700005
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2012Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization. Journal of Chemical Physics. 137.Full Text via DOI: 10.1063/1.4752247 Web of Science: 000309100400057
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2012Kinetics of peptide secondary structure conversion during amyloid β-protein fibrillogenesis. Journal of Theoretical Biology. 301:95-102.Full Text via DOI: 10.1016/j.jtbi.2012.02.012 Web of Science: 000303079500010
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2011Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectories. Physical Review E. 83.Full Text via DOI: 10.1103/PhysRevE.83.061905 Web of Science: 000291437200003
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2010Stabilization 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.Full Text via DOI: 10.1021/jp909872a Web of Science: 000273405000015
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2008The trigger sequence in the GCN4 leucine zipper: alpha-helical propensity and multistate dynamics of folding and dimerization. Journal of Chemical Physics. 129.Full Text via DOI: 10.1063/1.3006421 Web of Science: 000260777400053
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2008The effect of heterogeneous infectious period and contagiousness on the dynamics of Salmonella transmission in dairy cattle. Epidemiology and Infection. 136:1496-1510.Full Text via DOI: 10.1017/S0950268807000209 Web of Science: 000260750500008
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2008The importance of culling in Johne's disease control. Journal of Theoretical Biology. 254:135-146.Full Text via DOI: 10.1016/j.jtbi.2008.05.008 Web of Science: 000258938200015
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2008Simulation 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.Full Text via DOI: 10.1016/j.prevetmed.2007.09.006 Web of Science: 000254109000012
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2008A mathematical model of the dynamics of Salmonella Cerro infection in a US dairy herd. Epidemiology and Infection. 136:263-272.Full Text via DOI: 10.1017/S0950268807008400 Web of Science: 000259337000015
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2008Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper. Journal of Chemical Physics. 128.Full Text via DOI: 10.1063/1.2831513 Web of Science: 000252821200094
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2007Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide. Journal of Chemical Physics. 127.Full Text via DOI: 10.1063/1.2757172 Web of Science: 000248905300035
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2006Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model α-helical hairpin peptide. Biopolymers. 81:167-178.Full Text via DOI: 10.1002/bip.20388 Web of Science: 000235041200003
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2004Excluded volume entropic effects on protein unfolding times and intermediary stability. Journal of Chemical Physics. 120:2475-2481.Full Text via DOI: 10.1063/1.1637032 Web of Science: 000188498400046
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2003Finite size scaling of structural transitions in a simulated protein with secondary and tertiary structure. Journal of Chemical Physics. 119:1174-1180.Full Text via DOI: 10.1063/1.1579673 Web of Science: 000183842500058
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Lipid-specific oligomerization of the Marburg virus matrix protein VP40 is regulated by two distinct interfaces for virion assembly. Journal of Biological Chemistry. 296.Full Text via DOI: 10.1016/j.jbc.2021.100796 Web of Science: 000674717300016
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Conference
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2025Investigating class IIa HDACS interactions with MEF2A. Biophysical Journal. 157A-158A.Web of Science: 001547074100021
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2025Molecular dynamics simulations of the interplay of miRNA target interactions. Biophysical Journal.Web of Science: 001461404400166
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2025Molecular dynamics simulations of the lipid-II interactions and assembly of Nisin chains in bacterial membranes. Biophysical Journal.Web of Science: 001462255300291
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2025Molecular dynamics simulations of the lipid-II interactions and assembly of nisin chains in bacterial membranes. Biophysical Journal. 26A-26A.Web of Science: 001440845200002
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2025Molecular dynamics simulations of the lipid-II interactions and assembly of nisin chains in bacterial membranes. Biophysical Journal.Web of Science: 001462255300102
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2025Unravelling the interaction between perlecan LG3 and the SARS-CoV-2 spike protein. Biophysical Journal.Web of Science: 001462255300213
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2023Exploring the dimer-dimer association of the ebolavirus matrix protein VP40 at the human plasma membrane. Biophysical Journal. 196A-196A.Web of Science: 000989629701082
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2022Immunomodulatory LASI lncRNA Regulates Cigarette Smoke Exacerbated SARS-CoV-2 Infectivity in COPD Airway Epithelial Cells. American Journal of Respiratory and Critical Care Medicine.Web of Science: 000792480403149
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2020Calculating the Binding Free Energy Difference between Conformational Changes of AT-Rich DNA Sequences. Biophysical Journal. 218A-218A.Web of Science: 000513023201340
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2020Computational Study of the Molecular Details of Ebola Virus Matrix Protein VP40 and Human Sec24C Protein Interaction. Biophysical Journal. 506A-506A.Web of Science: 000513023203272
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2020Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide. Biophysical Journal. 586A-587A.Web of Science: 000513023203666
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2020Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling. Biophysical Journal. 305A-305A.Web of Science: 000513023202030
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2019Computational Study of Calcium Phosphate Mineralization in Extracellular Vesicles. Biophysical Journal. 572A-572A.Full Text via DOI: 10.1016/j.bpj.2018.11.3075 Web of Science: 000460779802874
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2019Dynamics of the Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament. Biophysical Journal. 472A-472A.Full Text via DOI: 10.1016/j.bpj.2018.11.2549 Web of Science: 000460779802370
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2019Molecular Basis of the Marburg Virus Protein VP24 Interactions with Human Keap1. Biophysical Journal. 182A-182A.Full Text via DOI: 10.1016/j.bpj.2018.11.1011 Web of Science: 000460779800901
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2019Molecular Dynamics Investigations of Enzyme Conformational Changes. Biophysical Journal. 186A-186A.Full Text via DOI: 10.1016/j.bpj.2018.11.1031 Web of Science: 000460779800921
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2018Conformational Changes in Marburg Virus VP40 upon Plasma Membrane Association. Biophysical Journal. 459A-459A.Web of Science: 000430563200066
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2018Covalent Complex Model of DNA Topoisomerase and DNA for Molecular Dynamics Simulation. Biophysical Journal. 340A-340A.Full Text via DOI: 10.1016/j.bpj.2017.11.1898 Web of Science: 000430450000197
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2017Plasma membrane localization dynamics of the filovirus matrix protein VP40. European Biophysics Journal. S211-S211.Web of Science: 000416406201256
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2017Exploring Molecular Interactions between Escherichia coli RNA Polymerase and Topoisomerase I by Molecular Simulations. Biophysical Journal. 287A-287A.Full Text via DOI: 10.1016/j.bpj.2016.11.1555 Web of Science: 000402375600419
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2017Pi(4,5)P-2 Clustering by the Ebola Virus Matrix Protein VP40. Biophysical Journal. 326A-326A.Full Text via DOI: 10.1016/j.bpj.2016.11.1765 Web of Science: 000402375600611
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2017Temperature Dependent Pair-Wise Amino Acid Structural Propensity in cc beta and Implications for alpha to beta Secondary Structural Conversion. Biophysical Journal. 191A-191A.Full Text via DOI: 10.1016/j.bpj.2016.11.1059 Web of Science: 000402328000944
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2016Interdomain Interactions and the Mechanism of Structural Transformation in RfaH. Biophysical Journal. 378A-378A.Full Text via DOI: 10.1016/j.bpj.2015.11.2040 Web of Science: 000375142200330
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2016On the Origin of the Extended Stoke's Shifts in Fluorescent Proteins. Biophysical Journal. 377A-378A.Full Text via DOI: 10.1016/j.bpj.2015.11.2039 Web of Science: 000375142200329
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2015Hydrogen Bond Flexibility and Water Dynamics in the Far Red Fluorescent Protein TagRFP675. Biophysical Journal. 469A-469A.Full Text via DOI: 10.1016/j.bpj.2014.11.2562 Web of Science: 000362849400778
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2014Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Protein Mplum. Biophysical Journal. 649A-649A.Full Text via DOI: 10.1016/j.bpj.2013.11.3592 Web of Science: 000337000403623
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Other Scholarly Work
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2025Inhibition of HMGA2 binding to AT-rich DNA by its negatively charged C-terminus ( vol 53, gkaf035, 2025). Nucleic Acids Research (NAR).Full Text via DOI: 10.1093/nar/gkaf193 Web of Science: 001439210700007
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2025The Role of Protonation in the PfMATE Transporter Protein Structural Transitions. Methods in molecular biology (Clifton, N.J.). 315-340.Full Text via DOI: 10.1007/978-1-0716-4213-9_16
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2024Identification of flexible hinge region residues in bacterial topoisomerase IA. Journal of Biological Chemistry. S657-S658.Full Text via DOI: 10.1016/j.jbc.2024.106904 Web of Science: 001326666902306
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2024Revealing the nucleic acid interactions of human topoisomerase 3 beta, a unique dualacting topoisomerase, and discovering its inhibitors. Journal of Biological Chemistry. S644-S644.Full Text via DOI: 10.1016/j.jbc.2024.106882 Web of Science: 001326666902284
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2024Computational studies of pressure-induced effects on DNA hairpin structures. Biophysical Journal. 495A-495A.Web of Science: 001194120702801
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2024Investigating the effects of CTD mutations as plasma membrane association of the Marburg virus protein VP40. Biophysical Journal. 448A-448A.Web of Science: 001194120702575
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2024Investigation of HDAC7-MEF2A interactions using molecular simulations. Biophysical Journal. 136A-136A.Web of Science: 001194120700648
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2023Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development (vol 15, pg 623, 2020). ChemMedChem.Full Text via DOI: 10.1002/cmdc.202100427 Web of Science: 000663166200001
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2022Alternating access switching in molecular dynamics simulations of PfMATE transporter. Biophysical Journal. 250A-251A.Web of Science: 000759523001484
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2022Changes in the receptor-binding interface may cause immune evasion by the SARS-CoV-2 delta variant b.1.617.2. Biophysical Journal. 44-44.Web of Science: 000759523000209
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2021Effects of G198R Mutation in the Ebola VP40 Matrix Protein: A Molecular Dynamics Study. Biophysical Journal. 303A-303A.Web of Science: 000629601401715
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2018Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets. Biophysical Journal. 218A-218A.Full Text via DOI: 10.1016/j.bpj.2017.11.1217 Web of Science: 000430439600337
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2015Pairwise amino acid secondary structural propensities (vol 91, 042709, 2015). Physical Review E.Full Text via DOI: 10.1103/PhysRevE.91.049902 Web of Science: 000353463600018
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2008Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper (vol 128, art no 045106, 2008). Journal of Chemical Physics.Full Text via DOI: 10.1063/1.2898870 Web of Science: 000254537200086
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Preprint
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2025Identification of novel human topoisomerase III beta inhibitors.Full Text via DOI: 10.1101/2025.03.18.642440
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2023PIsToN: Evaluating Protein Binding Interfaces with Transformer NetworksFull Text via DOI: 10.1101/2023.01.03.522623
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Review
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2025The Multifaceted Role of miR-211 in Health and Disease. Biomolecules.Full Text via DOI: 10.3390/biom15081109 Web of Science: 001557901200001
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2023Restoring susceptibility to aminoglycosides: identifying small molecule inhibitors of enzymatic inactivation. RSC Medicinal Chemistry. 1591-1602.Full Text via DOI: 10.1039/d3md00226h Web of Science: 001040556100001
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2023Multi-functional auto-fluorescent nanogels for theranostics. Journal of NeuroVirology. 252-257.Full Text via DOI: 10.1007/s13365-023-01138-y Web of Science: 000996995700001
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2018Genetic basis of hearing loss in Spanish, Hispanic and Latino populations. Gene. 297-305.Full Text via DOI: 10.1016/j.gene.2018.01.027 Web of Science: 000425576500037
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2017Zika Virus: An Emerging Global Health Threat. Frontiers in Cellular and Infection Microbiology.Full Text via DOI: 10.3389/fcimb.2017.00486 Web of Science: 000417474100001
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2017Indispensable Role of Ion Channels and Transporters in the Auditory System. Journal of Cellular Physiology. 743-758.Full Text via DOI: 10.1002/jcp.25631 Web of Science: 000393761400008
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2016Intricate Functions of Matrix Metalloproteinases in Physiological and Pathological Conditions. Journal of Cellular Physiology. 2599-2621.Full Text via DOI: 10.1002/jcp.25430 Web of Science: 000387040700006
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2016Molecular Structure and Regulation of P2X Receptors With a Special Emphasis on the Role of P2X2 in the Auditory System. Journal of Cellular Physiology. 1656-1670.Full Text via DOI: 10.1002/jcp.25274 Web of Science: 000375123600004
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2008Self-Organizing Dynamics in Protein Folding. Progress in Molecular Biology and Translational Science. 1-37.Full Text via DOI: 10.1016/S0079-6603(08)00401-7 Web of Science: 000263621700001
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Research
principal investigator on
- Therapeutic and diagnostic potential of urine-enriched molecular markers for high-risk prostate cancer in men awarded by Florida Department of Health 2024 - 2027
- Computational and Biophysical Analysis of the Filovirus Matrix Protein System awarded by National Institutes of Health 2021 - 2026
- The molecular function and the therapeutic potential of microRNA-211 in Group 3 medulloblastomas in children awarded by Johns Hopkins University 2022 - 2024
- Computer-aided design for improved lantibiotics awarded by General Medical Sciences 2021 - 2023
- Investigation of the role of phosphatidic acid metabolism in Filovirus budding awarded by National Institutes of Health 2020 - 2022
- Computational modeling of lantibiotics interactions with lipid II and membrane awarded by Oragenics Inc. 2019 - 2021
- Investigation of VP40 mutations found in previous outbreaks on the assembly and budding of filoviruses awarded by Allergy and Infectious Diseases 2017 - 2019
- Marburg Virus Prophylactic Medical Countermeasure awarded by U.S. Department of Defense 2018 - 2019
- Computational Investigations of Monomeric Variants of Red Flourescent Proteins awarded by General Medical Sciences 2011 - 2016
co-principal investigator on
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Grant
investigator on
- A Nanoanalytical Approach to Unraveling Differences Between Physiological and Pathological Mineralization (Year 3) awarded by Miami Heart Research Institute 2025 - 2026
- A Nanoanalytical Approach to Unraveling Differences Between Physiological and Pathological Mineralization awarded by Miami Heart Research Institute 2024 - 2025
- A Nanoanalytical Approach to Unraveling Differences Between Physiological and Pathological Mineralization awarded by Miami Heart Research Institute 2023 - 2024
Contact
full name
- Prem Chapagain
