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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Comparative Analysis Of Conformational Transition Pathways In Homologous Proteins, Dylan Sebastien Ogden
Comparative Analysis Of Conformational Transition Pathways In Homologous Proteins, Dylan Sebastien Ogden
Graduate Theses and Dissertations
Molecular dynamics (MD) simulations are routinely used to study the dynamics of proteins. However, conventional MD limited to the sampling of local conformational changes as the functionally important conformational transitions of proteins often extend beyond the timescales of the simulations employed, for example, membrane transport proteins. We have determined the combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of large-scale conformational changes in membrane proteins. The methodology is based on biased, nonequilibrium collective variable based simulations including nonequilibrium pulling, string method with swarms of trajectories, bias-exchange umbrella sampling, and rate estimation techniques. …
Spike Protein Structural Dynamics Of Sars-Cov-2 Coronaviruses Studied Using Molecular Dynamics, William Strickland
Spike Protein Structural Dynamics Of Sars-Cov-2 Coronaviruses Studied Using Molecular Dynamics, William Strickland
Biological Sciences Undergraduate Honors Theses
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has overwhelmingly impacted the global population, accounting for millions of confirmed infections and deaths over the last year. The virus’s influence on the health and safety of individuals, the economy, and daily life has been disruptive and devastating. While SARS-CoV-2 and SARS-CoV-1, two closely related members of the SARS coronaviruses, have shown the ability to cross the species barrier and infect humans, SARS-CoV-2 has predominantly been the virus responsible for the number of infections presently known. SARS-CoV-2 has also proven to be volatile, as many variants have …