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Computational Models Exploring The Role Of Flexibility In Binding Tat Peptide To Tar Rna, Thanh Quoc Le
Computational Models Exploring The Role Of Flexibility In Binding Tat Peptide To Tar Rna, Thanh Quoc Le
Master's Theses
Viral-encoded regulatory proteins interacting with RNA target sequences control the gene expression of lentiviruses, notably the human immunodeficiency virus (HIV) and bovine immunodeficiency virus (BIV). The latter provides a simpler interaction model between the viral trans-activator protein (Tat) and trans-activation response RNA element (TAR), including Tat peptides binding to TAR RNA fragments. This model may offer insights into clinical approaches for treatment, initially through theoretical consideration of the role of peptide flexibility in binding as evidenced by literature-based binding assays and NMR. It has more recently been suggested that DNA-protein binding may also be enhanced by increases in conformational entropy. …
Biophysical Approaches For Studying Desolvation Energy In Dna:Dna Binding Systems, Caroline Rose Harmon
Biophysical Approaches For Studying Desolvation Energy In Dna:Dna Binding Systems, Caroline Rose Harmon
Master's Theses
Hydration spheres have unique water behavior compared to the disorder of the bulk water phase. These hydration spheres have been shown to be crucial for structural and conformational stability, yet their effect on binding association has been largely mistreated. For a one-to-one binding system, we propose to append the classical Gibbs-free energy equation as follows: ΔG^0=-RT ln(K_i )-[AB]ΔG_i^(H_2 O). Having a stronger grasp on how desolvation energy affects binding will ultimately aid studies from drug development and metabolism, to interpretation of structural models. To test our equation, we studied two small oligonucleotides that follow Watson-Crick base pairing using two different …