Protein–Ligand Interactions: General Description


Protein–ligand interactions are fundamental to almost all processes occuring in living organisms. Ligand‐mediated signal transmission via molecular complementarity is essential to all life processes; these chemical interactions comprise biological recognition at the molecular level. The evolution of protein function is dependent in part on the development of highly specific sites designed to bind small‐molecule ligands with affinities tuned to the needs of the cell. Cooperativity in ligand binding is critically important to the regulation of competing biological functions. Regulation of cellular processes via cooperative protein–ligand interactions occurs through molecular mechanisms involving protein conformational transitions among low‐ and high‐affinity states. Consequently, ligand‐binding interactions are used to switch proteins among states of different function. Examples ranging from dioxygen transport to gene expression are presented. The structures of protein–ligand complexes at atomic resolution make possible the design of small‐molecule drugs for the treatment of disease.

Key Concepts:

  • Molecular recognition via protein–ligand interactions is of fundamental importance to most processes occurring within living organisms.

  • Transmission of signals via molecular complementarity is essential to all life processes.

  • The evolution of protein function includes the development of highly specific sites for the binding of ligands with affinities tailored to meet the needs of biological function.

  • Cooperativity in ligand binding plays an important role in the regulation of biological function.

  • Cooperativity in ligand binding is linked to conformational change in the protein.

  • Well‐defined mathematical expressions based on the stoichiometry of the binding equilibrium provide a means for quantifying ligand‐binding interactions.

  • The equilibrium constants of ligand–macromolecule interactions provide a thermodynamic measure of the strength of the interaction.

  • The atomic resolution structures of ligand complexes provide a chemical basis for understanding protein–ligand interactions and these structures are often used as the basis for the design of small‐molecule drugs for the treatment of disease.

Keywords: cooperativity; ligand; dissociation constant; biological recognition; specificity; drugs; signal transmission; binding; bonding forces

Figure 1.

(a) Theoretical ligand‐binding isotherms for (i) noncooperative, (ii) positive cooperative and (iii) mixed negative and positive cooperative systems. (b) Experimentally measured ligand‐binding isotherm curves for an allosteric protein (i) in the absence of effectors (primarily the R state) and (ii) in the presence of a negative effector and (iii) a system showing mixed positive and negative cooperativity.

Figure 5.

Structure–function relationships in the binding of dioxygen to haemoglobin. (a) Stick representation inside the transparent van der Waals surface of the haem group (protophorphin X) with bound Fe(II) (cpk colouring scheme). (b) Backbone representation of the haemoglobin tetramer viewed along the pseudo‐twofold symmetry axis with haem groups shown as space‐filling balls; α chains, magenta; β‐chains, yellow). (c) Details of the binding site for the allosteric effector, IHP to the central cavity. Hb subunits are shown as ribbons, IHP is shown in a stick representation (C pale blue, O red phosphorus orange) and positively charged side‐chain residues (Lys and His), which form charge–charge interactions with IHP, are also shown in stick representations (C yellow, N blue, O red). Dashed yellow lines indicate H‐bonds between side chains and IHP (C light blue, O red, P orange). (d and e) Details of the conformational change due to dioxygen binding to the haem iron. The haem groups (wire frame) are viewed from the edge, and portions of the protein have been cut away to display the haem and its interactions with the protein. The distal His residue, His92 and His63 are shown as sticks inside their van der Waals surfaces (transparent). The haem iron (orange ball) and dioxygen (red balls) are also shown. His63 forms an H‐bond to one O of dioxygen. The movement of the iron into the plane of the haem when dioxygen binds displace the distal His by ∼0.04 nm. Images prepared with PyMOL 1.1r1 using PDB codes 2DN1 and 2DN2.

Figure 6.

Conformational events and bonding interactions that accompany the binding of a transition‐state analogue, phosphoglycohydroxamic acid (PGH), to triosephosphate isomerase. (a) Stereo view (side‐by‐side, wall‐eye) of the open conformation (magenta cartoon) of the enzyme superimposed on the closed enzyme–PGH complex (green cartoon) showing the loop region that folds down over bound substrate (open loop, red; closed loop, yellow). Loop residues 171–174 and active‐site residues in the open (ligand‐free) and closed (ligand‐bound) structures are depicted in red and yellow, respectively. Bound PGH is shown as a stick structure (C yellow, O red, N blue, P orange). The 1‐nitrogen and the carbonyl O of PGH are H‐bonded to site residues Glu165 and Lys13, respectively; the PGH hydroxyl is H‐bonded to His95. The dashed line between the 1‐N of PGH and Glu165 of the open structure is too long (0.44‐nm) for an H‐bonding interaction. Protein images prepared with PyMOL 1.1r1 using PDB codes 1YPI and 7TIM.

Figure 7.

The complex of the HIV protease with the cyclic urea amide inhibitor, SD146. (a) Cartoon ribbon representations of the open (pale blue) and SD146‐stabilised closed (yellow) conformations of the HIV protease viewed along the twofold symmetry axis with the active‐site Asp25A and Asp25* side chains represented in sticks. SD146 bound to the closed conformation is shown in sticks within its transparent van der Waals surface (cpk colours). (b) View of the H‐bonding interactions between bound SD146 and the active site. SD146 interacts with at least 31 protein residues, including 14 H‐bonds (dashed lines) and 177 van der Waals contacts (not shown). SD146 (cpk colouring) and H‐bonding residues from the protein (C yellow, O red, N blue) are shown in sticks and the protein is shown in cartoon ribbon (yellow). Images prepared with PyMOL 1.1r1 using PDB codes 1BWB and 1HSI.

Figure 8.

(a) Schematic antibody subunit structure with disulfide crosslinks. (b) Ribbon diagram depicting the complex between lysozyme (magenta) and the Fab fragment of an antibody viewed at the binding site. The heavy chain is shown in green and the light chain in light blue. The amino acid residues at the antibody–antigen interface are shown as sticks surrounded by their van der Waals surfaces. Protein image prepared with PyMOL 1.1r1 using PDB code 1FDL.

Figure 9.

(a) Structure of the trpR–trpO complex with l‐Trp. A monomeric unit of the dimeric trpR is shown as a cartoon ribbon diagram (yellow) with l‐Trp shown in sticks (cpk colours). The trpO DNA is shown as a space‐filling structure (magenta, blue‐green). Two water molecules involved in recognition of the operator by the repressor are shown as grey balls. (b) Cut away view showing the l‐Trp interactions. l‐Trp is shown in sticks (cpk colours), the trpR dimer is shown as yellow and orange cartoon ribbons with site residues in sticks. DNA is shown as sticks (C light blue, O red, N blue, P orange). The H‐bonding interaction between the phosphoryl oxygen of the trpO DNA and the indole ring NH of l‐Trp is shown by the yellow dashed line. The l‐Trp indole ring is inserted into a cavity formed by the side chains of two Arg residues that make coulombic charge–charge interactions with phosphoryl groups of the DNA. Protein images prepared with PyMOL 1.1r1 using PDB code 1TRR.

Figure 2.

Figure 3.

Figure 4.


Further Reading

Changeux JP and Edelstein SJ (2005) Allosteric mechanisms of signal transduction. Science 308: 1424–1428.

Dunn MF (2005) Zinc‐ligand interactions modulate assembly and stability of the insulin hexamer – a review. Biometals 18: 295–303.

Fischmann TO, Bentley GA, Bhat TN et al. (1991) Crystallographic refinement of the three dimensional structure of the Fab d1.3‐lysozyme complex at 2.5 Å resolution. Journal of Biological Chemistry 266: 12915–12920.

Hurlburt BK and Yanofsky C (1992) Trp repressor/trp operator interaction. Equilibrium and kinetic analysis of complex formation and stability. Journal of Biological Chemistry 267: 16783–16789.

Koshland DE, Nemethy G and Filmer D (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5: 365–385.

Kyte J (1995) Structure in Protein Chemistry, chaps. 5 and 6. New York: Garland.

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Nelson DL and Cox MM (2008) Lehninger Principles of Biochemistry, 5th edn, especially chaps. 5 and 6. New York: WH Freeman.

Pauling L (1948) Chemical achievement and hope for the future. American Scientist 36: 51.

Perutz MF (1989) Mechanisms of cooperativity and allosteric regulation in proteins. Quarterly Review of Biophysics 22: 139–236.

Pompliano DL, Peyman A and Knowles JR (1990) Stabilization of a reaction intermediate as a catalytic device: definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry 29: 3186–3194.

Seydoux F, Malhotra OP and Bernhard SA (1974) Half‐site reactivity. CRC Critical Reviews in Biochemistry 2: 227–257.

Siegler PB (1992) The molecular mechanism of trp repression. In: McKnight SL and Yamamoto KR (eds) Transcriptional Regulation, vol. 1, pp. 475–499. Cold Spring Harbor: Cold Spring Harbor Laboratory Press.

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Dunn, Michael F(Apr 2010) Protein–Ligand Interactions: General Description. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001340.pub2]