Determinants of ligand-binding specificity on proteins Which factor primarily dictates the specificity of a ligand-binding site on a protein?

Introduction / Context:
Protein–ligand recognition underlies enzyme catalysis, receptor signaling, and drug action. Specificity emerges from the three-dimensional microenvironment of the binding pocket.

Given Data / Assumptions:

• We consider a folded protein with a defined binding cleft.
• Physiological ionic strength and pH are assumed.

Concept / Approach:
Specificity is governed by complementary shape, charge distribution, hydrogen-bond donors and acceptors, hydrophobic patches, and flexibility of residues forming the pocket. These properties are encoded by the amino acid side chains that line the binding site and their precise arrangement in three dimensions.

Step-by-Step Solution:
Identify pocket chemistry: residues contribute electrostatics, polarity, and sterics.Consider induced fit or conformational selection that refines complementarity.Conclude that residues lining the pocket dominate specificity.

Verification / Alternative check:
Mutagenesis of pocket residues typically alters affinity and specificity, confirming their primary role. Structural studies show side chain complementarity with ligands.

Why Other Options Are Wrong:
Absence of competitors does not create specificity; waters modulate binding but are not the principal determinant; opposite chirality usually prevents binding rather than confers specificity; ionic strength can modulate affinity but does not dictate specific recognition.

Common Pitfalls:
Overlooking the role of backbone conformation and dynamics that position side chains for recognition.

Final Answer:
The amino acid residues lining the binding site.