Biological and Chemical Physics Commons^™

In Silico Identification Of Vaccine Candidates Against Viral Infections, Prabin Baral

FIU Electronic Theses and Dissertations

There are many viral diseases without effective treatments or vaccines. These viruses can cause catastrophic epidemics such as the Lassa, Ebola, and Marburg viruses. Similarly, the recent coronavirus pandemic is of great concern as new variants are continuously emerging with decreased susceptibility to antibodies and vaccines that were developed for earlier strains. A critical step in the immune system’s fight against viruses involves an immunological protein molecule binding to a viral protein molecule. I investigate the atomic and molecular details of binding site recognition and binding interactions and dynamics for three important viruses.

Antigens are molecules, such as viral proteins, …

Rate Kinetics And Molecular Dynamics Of The Structural Transitions In Amyloidogenic Proteins, Timothy Michael Steckmann

FIU Electronic Theses and Dissertations

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer’s, Creutzfeld-Jacob, diabetes, Parkinson’s and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous α-helix or random-coil structure. The α-helices convert their structure to β-strands that aggregate into β-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis …