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Full-Text Articles in Other Biochemistry, Biophysics, and Structural Biology
Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez
Electronic Theses and Dissertations
Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …
The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen
The Role Of Conformational Changes In Viral And Bacterial Protein Functions, Md Lokman Hossen
FIU Electronic Theses and Dissertations
Proteins do versatile work in cells. They require a cascade of structural changes to perform different tasks like binding to the other neighboring biomolecules, transporting small chemicals, activating a chemical reaction, etc. The structural conformations of proteins can be critical in changing their working ability. In this dissertation, I investigated the role of conformational changes of viral protein, e.g., spike and envelope protein of SARS-CoV-2, and bacterial protein, e.g., multidrug transporter and toxic extrusion protein- PfMATE from Pyrococcus furiosus. Also, I performed molecular docking-based drug screening targeting the E protein to suggest a set of drugs that can be repurposed …