{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T02:24:11Z","timestamp":1760235851593,"version":"build-2065373602"},"reference-count":72,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Many biological and biotechnological processes are controlled by protein\u2013protein and protein\u2013solvent interactions. In order to understand, predict, and optimize such processes, it is important to understand how solvents affect protein structure during protein\u2013solvent interactions. In this study, all-atom molecular dynamics are used to investigate the structural dynamics and energetic properties of a C-terminal domain of the Rift Valley Fever Virus L protein solvated in glycerol and aqueous glycerol solutions in different concentrations by molecular weight. The Generalized Amber Force Field is modified by including restrained electrostatic potential atomic charges for the glycerol molecules. The peptide is considered in detail by monitoring properties like the root-mean-squared deviation, root-mean-squared fluctuation, radius of gyration, hydrodynamic radius, end-to-end distance, solvent-accessible surface area, intra-potential energy, and solvent\u2013peptide interaction energies for hundreds of nanoseconds. Secondary structure analysis is also performed to examine the extent of conformational drift for the individual helices and sheets. We predict that the peptide helices and sheets are maintained only when the modeling strategy considers the solvent with lower glycerol concentration. We also find that the solvent-peptide becomes more cohesive with decreasing glycerol concentrations. The density and radial distribution function of glycerol solvent calculated when modeled with the modified atomic charges show a very good agreement with experimental results and other simulations at 298.15K.<\/jats:p>","DOI":"10.3390\/biom11101427","type":"journal-article","created":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T08:27:44Z","timestamp":1632904064000},"page":"1427","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2816-5726","authenticated-orcid":false,"given":"Gideon K.","family":"Gogovi","sequence":"first","affiliation":[{"name":"Department of Mathematics and Statistics, University of Houston\u2014Downtown, Houston, TX 77054, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3300-1961","authenticated-orcid":false,"given":"Swabir","family":"Silayi","sequence":"additional","affiliation":[{"name":"Office of Research Computing, George Mason University, Fairfax, VA 22030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5230-4610","authenticated-orcid":false,"given":"Amarda","family":"Shehu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, George Mason University, Fairfax, VA 22030, USA"},{"name":"Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA"},{"name":"School of Systems Biology, George Mason University, Fairfax, VA 22030, USA"},{"name":"Center for Advancing Human-Machine Partnerships, George Mason University, Fairfax, VA 22030, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.coviro.2012.02.017","article-title":"Breaking the chain: Rift Valley fever virus control via livestock vaccination","volume":"2","author":"Bird","year":"2012","journal-title":"Curr. 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