Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein
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Center for Simulation and Modeling, George Mason University, 4400 University Drive, MSN 6A12, Fairfax, VA 22030, USA
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Department of Computational and Data Sciences, George Mason University, 4400 University Drive, MSN 6A12, Fairfax, VA 22030, USA
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School of Systems Biology, George Mason University, 10900 University Blvd., MSN 5B3, Manassas, VA 20110, USA
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National Center for Biodefense and Infectious Diseases, George Mason University, 10650 Pyramid Place, MS 1J5, Manassas, VA 20110, USA
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Department of Computer Science, George Mason University, 4400 University Drive, MSN 4A5, Fairfax, VA 22030, USA
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Department of Bioengineering, George Mason University, 4400 University Drive, MSN 1J7, Fairfax, VA 22030, USA
*
Authors to whom correspondence should be addressed.
Academic Editors: Filip Jagodzinski, Brian Y. Chen and Francisco Torrens
Molecules 2019, 24(9), 1768; https://doi.org/10.3390/molecules24091768
Received: 11 March 2019
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Revised: 13 April 2019
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Accepted: 3 May 2019
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Published: 7 May 2019
(This article belongs to the Special Issue Selected Papers from the 11th Computational Structural Bioinformatics Workshop (CSBW-2018))
A tertiary structure governs, to a great extent, the biological activity of a protein in the living cell and is consequently a central focus of numerous studies aiming to shed light on cellular processes central to human health. Here, we aim to elucidate the structure of the Rift Valley fever virus (RVFV) L protein using a combination of in silico techniques. Due to its large size and multiple domains, elucidation of the tertiary structure of the L protein has so far challenged both dry and wet laboratories. In this work, we leverage complementary perspectives and tools from the computational-molecular-biology and bioinformatics domains for constructing, refining, and evaluating several atomistic structural models of the L protein that are physically realistic. All computed models have very flexible termini of about 200 amino acids each, and a high proportion of helical regions. Properties such as potential energy, radius of gyration, hydrodynamics radius, flexibility coefficient, and solvent-accessible surface are reported. Structural characterization of the L protein enables our laboratories to better understand viral replication and transcription via further studies of L protein-mediated protein–protein interactions. While results presented a focus on the RVFV L protein, the following workflow is a more general modeling protocol for discovering the tertiary structure of multidomain proteins consisting of thousands of amino acids.
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Keywords:
Rift Valley fever virus; multidomain protein; tertiary structure; computational structure determination
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MDPI and ACS Style
Gogovi, G.K.; Almsned, F.; Bracci, N.; Kehn-Hall, K.; Shehu, A.; Blaisten-Barojas, E. Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein. Molecules 2019, 24, 1768. https://doi.org/10.3390/molecules24091768
AMA Style
Gogovi GK, Almsned F, Bracci N, Kehn-Hall K, Shehu A, Blaisten-Barojas E. Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein. Molecules. 2019; 24(9):1768. https://doi.org/10.3390/molecules24091768
Chicago/Turabian StyleGogovi, Gideon K., Fahad Almsned, Nicole Bracci, Kylene Kehn-Hall, Amarda Shehu, and Estela Blaisten-Barojas. 2019. "Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein" Molecules 24, no. 9: 1768. https://doi.org/10.3390/molecules24091768
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