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Protein Folding Dynamics

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Ebola VP40-Membrane
P2RX2 Channel
mCherry Fluorescent Protein




Prem P. Chapagain, PhD

Associate Professor
Department of Physics
Florida International University
11200 SW 8th St
CP 204
Miami, FL 33199
Ph: 305-348-6266
Fax: 305-348-6700
Email: chapagap@fiu.edu


Research Highlights:

The Theoretical Biophysics Group at FIU is involved in several research projects in the area of biological physics. My research has focused on biomolecular dynamics, which involves applying computational and statistical mechanical techniques to understand the dynamics and structural transitions of proteins and nucleic acids. Current major projects include theoretical and computational investigations of protein folding dynamics, protein aggregation and fibril formation in neurodegenerative diseases, photo-physical properties of fluorescent proteins, membrane interactions of viral proteins (Ebola, Marburg and Zika virus), and DNA structure and dynamics.

 In addition to the thermodynamics and statistical mechanics of protein folding and aggregation of model peptide systems, I am interested in investigating the dynamics and photophysical properties of fluorescent proteins using detailed all-atom molecular dynamics simulations. My research interests also include  broadly related fields of biological physics such as mathematical modeling of the dynamics of infectious diseases, self-organization and complexity.

Latest Selected Publications:

Pokhrel, R., Gerstman, B. S., Hutcheson, J. D., & Chapagain, P. P.* (2018). In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles. The Journal of Physical Chemistry B, 122, 3782-3789. Link

Sandhaus, S., Chapagain, P. P.*, & Tse-Dinh, Y. C.* (2018). Discovery of novel bacterial topoisomerase I inhibitors by use of in silico docking and in vitro assays. Scientific reports, 8, 1437. Link

Del Vecchio et al. (2018). A cationic, C-terminal patch and structural rearrangements in Ebola virus matrix VP40 protein control its interactions with phosphatidylserine. Journal of Biological Chemistry, doi: 10.1074/jbc.M117.816280. Link

Steckmann, T.; Bhandari, Y. R.; Chapagain, P. P.; Gerstman, B. S. (2017) Cooperative Structural Transitions in Amyloid-Like Aggregation. The Journal of chemical physics 146, 135103. Link

Mittal, R., et al. (2017). Zika Virus: An Emerging Global Health Threat. Frontiers in cellular and infection microbiology, 7, 486. Link

Gc, J. B.; Pokhrel, R.; Bhattarai, N.; Johnson, K. A.; Gerstman, B. S., Stahelin, R. V.; Chapagain, P. P., (2017). Graphene-Vp40 Interactions and Potential Disruption of the Ebola Virus Matrix Filaments. Biochemical and biophysical research communications, 493, 176-181. Link

Gc, J. B.; Gerstman, B. S.; Chapagain, P. P.* (2017). Membrane Association and Localization Dynamics of the Ebola Virus Matrix Protein Vp40. Biochimica et biophysica acta, 1859, 2012-2020. Link

Wijesinghe, K. J.; Urata, S.; Bhattarai, N.; Kooijman, E. E.; Gerstman, B. S.; Chapagain, P. P.; Li, S.; Stahelin, R. V. (2017), Detection of Lipid-Induced Structural Changes of the Marburg Virus Matrix Protein Vp40 Using Hydrogen/Deuterium Exchange-Mass Spectrometry. The Journal of biological chemistry  292, 6108-6122. Link

Bhattarai, N.; Gc, J. B.; Gerstman, B. S.; Stahelin, R. V.; Chapagain, P. P.* (2017). Plasma Membrane Association Facilitates Conformational Changes in the Marburg Virus Protein Vp40 Dimer. RSC advances  7, 22741-22748. Link

Mittal, R., et al. (2017). Indispensable Role of Ion Channels and Transporters in the Auditory System. Journal of cellular physiology, 232, 743-758. Link

More Articles:
List of publications on Google Scholar



January 2018 - Prem Chapagain