Final answer:
Interactions that contribute to intrinsic binding in molecular biology include hydrogen bonding, van der Waals forces, and ionic interactions, with influences from conformational changes and protein-ligand docking studies that determine binding affinity and specificity.
Step-by-step explanation:
The question is about the interactions that contribute to the intrinsic binding of molecules, particularly within the context of molecular biology or biochemistry. Such interactions include noncovalent bonding mechanisms like hydrogen bonding, van der Waals forces, and ionic interactions. For instance, binding sites on proteins for RNA or ligands, as described by quantitative binding constants (Kp and Kô), suggest that the strength of the interaction correlates to the number of bonds formed and the degree of interaction. Proteins with multiple interaction sites generally show stronger binding affinities, illustrated by more negative values of ΔGbind. Conformational changes in molecules can affect the binding properties and interactions with other molecules, leading to biological functions such as ligand-receptor activation and formation of compound structures like dimers. Moreover, protein-ligand docking studies can reveal specific interactions at the active site, aiding the understanding of competitive inhibitor binding, the role of nucleobases in binding, and the changes in accessible surface area upon ligand binding.