Protein–Ligand Interactions: Induced Fit


Protein–ligand interactions include two major components: protein folding and binding mechanisms; and hinge bending conformational transitions.

Keywords: hydrophobic effect; hydrogen bond; shape complementarity; molecular recognition; receptor–ligand interactions

Figure 1.

Schematic illustration of the landscapes of protein–ligand interactions. The energy landscape of the protein–ligand complex is a fusion between two individual funnel‐like landscapes, corresponding to the protein and the ligand. In real protein–ligand associations, the energy landscapes for the protein, ligand and the protein–ligand complex will be much more rugged, depending upon the flexibility of the protein, the ligand and the protein–ligand complex.

Figure 2.

Ribbon diagram showing domain motion in adenylate kinase. Unbound adenylate kinase is shown in green. Adenylate kinase bound with the inhibitor Ap5A is shown in red.

Figure 3.

Ribbon diagram showing subunit motion in aspartate receptor. Only the ligand (aspartate) binding domains are shown. Unbound aspartate receptor is shown in green. Aspartate‐bound aspartate receptor is shown in red. The orientation of the subunits in aspartate receptor changes upon aspartate binding.



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Ma, Buyong, Kumar, Sandeep, Tsai, Chung‐Jung, Wolfson, Haim, Sinha, Neeti, and Nussinov, Ruth(May 2001) Protein–Ligand Interactions: Induced Fit. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1038/npg.els.0003140]