Protein Structure, Interactions, and Nucleic Acids

Dimensional Structure of Proteins: Intermolecular Forces

Ionic Bonds (Salt Bridges)

• Occur between a negatively charged carboxylic acid group ($-COO^-$) and a positively charged basic amino acid (e.g., an amino group that has acquired a proton, $-NH_3^+$). These are charge-charge interactions.
• While present, they are not necessarily the dominant stabilizing force compared to hydrogen bonds.
• Not all proteins will contain ionic bonds, or "salt bridges."

Hydrogen Bonds

• Considered the dominant stabilizing interaction in proteins.
• Form between a hydrogen atom that is part of a polar covalent bond (e.g., $-O-H$ or $-N-H$) and an electronegative atom (like oxygen or nitrogen) as an acceptor.
• Hydrogens not in polar covalent bonds (e.g., $-C-H$) cannot form hydrogen bonds.

Van der Waals Forces

• These forces become more predominant in regions of protein structure characterized by hydrophobic-hydrophobic interactions.

Hydrophobic Effect

• This is not a bond but a crucial organizing principle driven primarily by entropy.
• When hydrophobic molecules (e.g., oil) are placed in water, water molecules tend to form ordered