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.
research interests
- Dr. Chapagain specializes 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, exploration of novel antimicrobial compounds against antibiotic-resistant pathogens, membrane interactions, and dynamics and function of various proteins of emerging viruses such as Ebolavirus and Marburgvirus, and more recently SARS-CoV-2. He has developed an excellent research infrastructure in computational biophysics at FIU with external funding from the National Science Foundation, National Institutes of Health, Department of Defense and industry partners.
Scholarly & Creative Works
selected publications
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Article
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2022Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerizationFull Text via DOI: 10.1126/sciadv.abn1440 Web of Science: 000828233900008
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2022Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human ProteinsFull Text via DOI: 10.3390/v14071415 Web of Science: 000831881500001
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2022Effects of sidechain isomerism on polymer-based non-covalent protein deliveryFull Text via DOI: 10.1039/d2cc02343a Web of Science: 000820390400001
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2022Significance of the RBD mutations in the SARS-CoV-2 omicron: from spike opening to antibody escape and cell attachmentFull Text via DOI: 10.1039/d2cp00169a Web of Science: 000779732000001
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2022AT-hook peptides bind the major and minor groove of AT-rich DNA duplexesFull 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 MethodFull Text via DOI: 10.1021/acssensors.1c02385 Web of Science: 000746813600001
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2022Incorporation of 5',8-cyclo-2'deoxyadenosines by DNA repair polymerases via base excision repairFull Text via DOI: 10.1016/j.dnarep.2021.103258 Web of Science: 000789227700003
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2021Lipid II Binding and Transmembrane Properties of Various Antimicrobial LanthipeptidesFull Text via DOI: 10.1021/acs.jctc.1c00666 Web of Science: 000730568600001
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2021Ebola virus protein VP40 binding to Sec24c for transport to the plasma membraneFull Text via DOI: 10.1002/prot.26221 Web of Science: 000692659700001
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2021Structural insights into the repair mechanism of AGT for methyl-induced DNA damageFull 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.1.351Full Text via DOI: 10.1021/acs.jpcb.1c01626 Web of Science: 000672740600004
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2021The Integrin Binding Peptide, ATN-161, as a Novel Therapy for SARS-CoV-2 InfectionFull Text via DOI: 10.1016/j.jacbts.2020.10.003 Web of Science: 000613908200001
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2020Livestock Movement in Gaurisankhar Valley, Dolakha, NepalFull Text via DOI: 10.3126/tgb.v7i0.34263
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2020From present to future development pathways in fragile mountain landscapesFull Text via DOI: 10.1016/j.envsci.2020.09.016 Web of Science: 000591437100009
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2020Identification of HMGA2 inhibitors by AlphaScreen-based ultra-high-throughput screening assaysFull Text via DOI: 10.1038/s41598-020-75890-0 Web of Science: 000589618700022
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2020Building climate change resilience by using a versatile toolkit for local governments and communities in rural HimalayaFull Text via DOI: 10.1016/j.envres.2020.109636 Web of Science: 000564662200020
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2020In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic feverFull 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 DevelopmentFull Text via DOI: 10.1002/cmdc.201900721 Web of Science: 000520292700001
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2020Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2Full Text via DOI: 10.1099/jmm.0.001203 Web of Science: 000546951100013
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2019Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix FilamentFull Text via DOI: 10.1021/acs.jpcb.9b04674 Web of Science: 000493865200001
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2019Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formationFull Text via DOI: 10.1002/rcm.8367 Web of Science: 000516887600008
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2019Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140Full Text via DOI: 10.1039/c9cp01558b Web of Science: 000478994100046
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2019Membrane pore formation and ion selectivity of the Ebola virus delta peptideFull Text via DOI: 10.1039/c8cp07323f Web of Science: 000461722800020
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2019Multi-sited Himalayan households and the misleading rural-urban dichotomyFull Text via DOI: 10.1111/area.12450 Web of Science: 000457926700019
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2019Molecular Dynamics Simulations of Conformational Conversions in Transformer ProteinsFull Text via DOI: 10.1007/978-1-4939-9161-7_15 Web of Science: 000706398300016
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2018Domain rearrangement and denaturation in Ebola virus protein VP40Full Text via DOI: 10.1063/1.5063474 Web of Science: 000454615100058
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2018Role of K-Loop Cysteine Residues in the Marburg Virus Protein VP24-Human Keap1 ComplexFull Text via DOI: 10.1021/acsomega.8b02386 Web of Science: 000458439900046
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2018Differentiating Parallel and Antiparallel DNA Duplexes in the Gas Phase Using Trapped Ion Mobility SpectrometryFull Text via DOI: 10.1021/acs.jpcb.7b12544 Web of Science: 000439002900001
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2018Investigating molecular interactions between oxidized neuroglobin and cytochrome cFull 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 lossFull 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 matrixFull 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 spotFull 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 VesiclesFull 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 lossFull Text via DOI: 10.1007/s00439-018-1885-0 Web of Science: 000431534200005
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2018Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assaysFull 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 filamentsFull 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 VP40Full Text via DOI: 10.1016/j.bbamem.2017.07.007 Web of Science: 000411419000026
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2017Cooperative structural transitions in amyloid-like aggregationFull 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 dimerFull 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)P-2 lipids in the plasma membraneFull Text via DOI: 10.1039/c6cp03776c Web of Science: 000386668200003
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2016Structures of the kinetically trapped i-motif DNA intermediatesFull 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 simulationsFull 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 localizationFull 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 TagRFP675Full Text via DOI: 10.1021/acs.jpclett.6b01172 Web of Science: 000381236400029
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2016Characterization of ATPase Activity of P2RX2 Cation ChannelFull 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 microscopeFull 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 coliFull 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 TransformationFull 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 modulatorFull Text via DOI: 10.1002/pro.2646 Web of Science: 000353524700016
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2015Pairwise amino acid secondary structural propensitiesFull 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 photobleachingFull Text via DOI: 10.1039/c4ib00251b Web of Science: 000349668600011
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2014Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription FactorFull Text via DOI: 10.1021/jp502193v Web of Science: 000336199100013
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2014Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum VariantsFull 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 SimulationsFull Text via DOI: 10.1021/jp308366y Web of Science: 000315707900003
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2012Structural propensities and entropy effects in peptide helix-coil transitionsFull 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 dimerizationFull Text via DOI: 10.1063/1.4752247 Web of Science: 000309100400057
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2012Kinetics of peptide secondary structure conversion during amyloid beta-protein fibrillogenesisFull Text via DOI: 10.1016/j.jtbi.2012.02.012 Web of Science: 000303079500010
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2011Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherryFull Text via DOI: 10.1063/1.3660197 Web of Science: 000298539900045
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2011Free-energy landscapes and thermodynamic parameters of complex molecules from nonequilibrium simulation trajectoriesFull 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 DimerFull 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 dimerizationFull 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 cattleFull Text via DOI: 10.1017/S0950268807000209 Web of Science: 000260750500008
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2008The importance of culling in Johne's disease controlFull Text via DOI: 10.1016/j.jtbi.2008.05.008 Web of Science: 000258938200015
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2008A mathematical model of the dynamics of Salmonella Cerro infection in a US dairy herdFull 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 zipperFull 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 peptideFull 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 alpha-helical hairpin peptideFull Text via DOI: 10.1002/bip.20388 Web of Science: 000235041200003
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2005Self-organization in protein folding and the hydrophobic interactionFull Text via DOI: 10.1063/1.1990110 Web of Science: 000231168700071
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2004Excluded volume entropic effects on protein unfolding times and intermediary stabilityFull 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 structureFull Text via DOI: 10.1063/1.1579673 Web of Science: 000183842500058
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Conference
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2020
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2020
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2020Ion Selective Pentameric Pore Formation by Ebola Virus Delta Peptide. 586A-587A.Web of Science: 000513023203666
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2020Lassa Virus Epitope-Allele Complexes Identified through Computational Modeling. 305A-305A.Web of Science: 000513023202030
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2019Computational Investigations of a Complex Formation between Neuroglobin and Cytochrome C Ferric Heme Proteins. 433A-433A.Full Text via DOI: 10.1016/j.bpj.2018.11.2333 Web of Science: 000460779802174
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2019Computational Study of Calcium Phosphate Mineralization in Extracellular Vesicles. 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. 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. 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. 186A-186A.Full Text via DOI: 10.1016/j.bpj.2018.11.1031 Web of Science: 000460779800921
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2019Temperature Dependence of the Protein-Chromophore Hydrogen Bond Dynamics in the Far-Red Fluorescent Proteins mNeptune1, mNeptune2.5 and mCardinal2. 475A-475A.Full Text via DOI: 10.1016/j.bpj.2018.11.2564 Web of Science: 000460779802385
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2018A Cylindrical Assembly Model and Dynamics of the Ebola Virus VP40. 64A-64A.Web of Science: 000429315800331
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2018Conformational Changes in Marburg Virus VP40 upon Plasma Membrane Association. 459A-459A.Web of Science: 000430563200066
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2018Covalent Complex Model of DNA Topoisomerase and DNA for Molecular Dynamics Simulation. 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. S211-S211.Web of Science: 000416406201256
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2017Temperature Dependent Pair-Wise Amino Acid Structural Propensity in cc beta and Implications for alpha to beta Secondary Structural Conversion. 191A-191A.Full Text via DOI: 10.1016/j.bpj.2016.11.1059 Web of Science: 000402328000944
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2017Exploring Molecular Interactions between Escherichia coli RNA Polymerase and Topoisomerase I by Molecular Simulations. 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. 326A-326A.Full Text via DOI: 10.1016/j.bpj.2016.11.1765 Web of Science: 000402375600611
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2016Interdomain Interactions and the Mechanism of Structural Transformation in RfaH. 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. 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. 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. 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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2022Alternating access switching in molecular dynamics simulations of PfMATE transporter. 250A-251A.Web of Science: 000759523001484
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2021Covalent Complex of DNA and Bacterial Topoisomerase: Implications in Antibacterial Drug Development (vol 15, pg 623, 2020)Full Text via DOI: 10.1002/cmdc.202100427 Web of Science: 000663166200001
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2021Effects of G198R Mutation in the Ebola VP40 Matrix Protein: A Molecular Dynamics Study. 303A-303A.Web of Science: 000629601401715
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2018Potential Disruption of Ebola Virus Matrix by Graphene Nano-Sheets. 218A-218A.Full Text via DOI: 10.1016/j.bpj.2017.11.1217 Web of Science: 000430439600337
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Preprint
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2020Potential Role of Cellular Senescence on Coronavirus InfectionsFull Text via DOI: 10.20944/preprints202004.0532.v1
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Review
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2018Genetic basis of hearing loss in Spanish, Hispanic and Latino populations. 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 ThreatFull 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. 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. 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 P2X(2) in the Auditory System. 1656-1670.Full Text via DOI: 10.1002/jcp.25274 Web of Science: 000375123600004
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2008Self-Organizing Dynamics in Protein Folding. 1-37.Full Text via DOI: 10.1016/S0079-6603(08)00401-7 Web of Science: 000263621700001
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Works By Students
chaired theses and dissertations
- GC, Jeevan, Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins 2017
- Steckmann, Timothy Michael, Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins 2016
- Regmi, Chola K, Structural Flexibility and Oxygen Diffusion Pathways in Monomeric Fluorescent Proteins 2014
- Bhandari, Yuba R, Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins 2013
Research
principal investigator on
- Computational and Biophysical Analysis of the Filovirus Matrix Protein System awarded by National Institutes of Health 2021 - 2026
- Investigation of the role of phosphatidic acid metabolism in Filovirus budding awarded by National Institutes of Health 2020 - 2022
- Computer-aided design for improved lantibiotics awarded by Oragenics Inc. 2020 - 2021
- 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
Contact
full name
- Prem Chapagain
Identifiers
ORCID iD
- https://orcid.org/0000-0002-0999-4975 (confirmed)
- https://orcid.org/0000-0001-7316-8769 (confirmed)
visualizations
publication subject areas
- Biochemistry & Molecular Biology
- Biophysics
- Cell Biology
- Chemistry
- Genetics & Heredity
- Immunology
- Infectious Diseases
- Life Sciences & Biomedicine - Other Topics
- Materials Science
- Mathematical & Computational Biology
- Microbiology
- Physics
- Physiology
- Public, Environmental & Occupational Health
- Science & Technology - Other Topics
- Veterinary Sciences