List of Chapters
Insights into Protein-Ligand Interactions: Thermodynamic Signatures
Author(s): Margarita Viniegra; Iris N Serratos*
Non-covalent interactions play a central role in biochemical processes, mainly in the recognition of charged molecules or ligands to biological molecules such as proteins. This molecular recognition is driven by thermodynamics, through characterizing the binding energetics: the increment of binding free energy change (ΔGb) and, therefore, equilibrium binding constant (Kb), binding enthalpy change (ΔHb), binding entropy change (ΔSb), and heat capacity change (ΔCp).
Unfolding and Targeting Thermodynamics of the Sarcin Ricin Loop and its DNA Analog
Author(s): Calliste Reiling; Luis A Marky*
The Sarcin Ricin Loop (SRL) is an important structure in rRNA involved in translation by interacting with elongation factors. However, SRL is susceptible to cleavage by the binding of toxic proteins, inhibiting translation. The aim of this work is to determine the thermodynamic contributions of a RNA/DNA targeting reaction relative to a DNA/DNA reaction and to determine if DNA oligonucleotides can be used to mimic the targeting of RNA structures. We used a thermodynamic approach to study both SRL (rSRL) and its DNA analog (dSRL) and have shown, based on enthalpic contributions, these two molecules are forming a similar secondary structure.
