Molecular binding

Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other.

In some cases, the associations can be quite strong—for example, the protein streptavidin and the vitamin biotin have a dissociation constant (reflecting the ratio between bound and free biotin) on the order of 10¹⁴—and so the reactions are effectively irreversible. The result of molecular binding is sometimes the formation of a molecular complex in which the attractive forces holding the components together are generally non-covalent, and thus are normally energetically weaker than covalent bonds.

Molecular binding occurs in biological complexes (e.g., between pairs or sets of proteins, or between a protein and a small molecule ligand it binds) and also in abiologic chemical systems, e.g. as in cases of coordination polymers and coordination networks such as metal-organic frameworks.

Types

Molecular binding can be classified into the following types:^[1]

• non-covalent – no chemical bonds are formed between the two interacting molecules hence the association is fully reversible
• reversible covalent – a chemical bond is formed, however the free energy difference separating the noncovalently-bonded reactants from bonded product is near equilibrium and the activation barrier is relatively low such that the reverse reaction which cleaves the chemical bond easily occurs
• irreversible covalent – a chemical bond is formed in which the product is thermodynamically much more stable than the reactants such that the reverse reaction does not take place.

Bound molecules are sometimes called a "molecular complex" - the term generally refers to non-covalent associations.^[2] Non-covalent interactions can effectively become irreversible; for example, tight binding inhibitors of enzymes can have kinetics that closely resemble irreversible covalent inhibitors. Among the tightest known protein–protein complexes is that between the enzyme angiogenin and ribonuclease inhibitor; the dissociation constant for the human proteins is 5x10⁻¹⁶ mol/L.^[3][4] Another biological example is the binding protein streptavidin, which has extraordinarily high affinity for biotin (vitamin B7/H, dissociation constant, K_d ≈10⁻¹⁴ mol/L).^[5] In such cases, if the reaction conditions change (e.g., the protein moves into an environment where biotin concentrations are very low, or pH or ionic conditions are altered), the reverse reaction can be promoted. For example, the biotin-streptavidin interaction can be broken by incubating the complex in water at 70 °C, without damaging either molecule.^[6] An example of change in local concentration causing dissociation can be found in the Bohr effect, which describes the dissociation of ligands from hemoglobin in the lung versus peripheral tissues).^[5]

Some protein–protein interactions result in covalent bonding,^[7] and some pharmaceuticals are irreversible antagonists that may or may not be covalently bound.^[8] Drug discovery has been through periods when drug candidates that bind covalently to their targets are attractive and then are avoided; the success of bortezomib made boron-based covalently binding candidates more attractive in the late 2000s.^[9][10]

Driving force

In order for the complex to be stable, the free energy of complex by definition must be lower than the solvent separated molecules. The binding may be primarily entropy-driven (release of ordered solvent molecules around the isolated molecule that results in a net increase of entropy of the system). When the solvent is water, this is known as the hydrophobic effect. Alternatively the binding may be enthalpy-driven where non-covalent attractive forces such as electrostatic attraction, hydrogen bonding, and van der Waals / London dispersion forces are primarily responsible for the formation of a stable complex.^[11] Complexes that have a strong entropy contribution to formation tend to have weak enthalpy contributions. Conversely complexes that have strong enthalpy component tend to have a weak entropy component. This phenomenon is known as enthalpy-entropy compensation.^[12]

Measurement

The association constant (K_I) also known as the binding constant (K_A) between the components of complex is the ratio of the concentration of the complex divided by the product of the concentrations of the isolated components at equilibrium:

$A+B \rightleftharpoons AB:\log K_{I} =\log \left(\frac{[AB]}{[A][B]} \right)=pK_I$

Examples

Molecules that can participate in molecular binding include proteins, nucleic acids, carbohydrates, lipids, and small organic molecules such as drugs. Hence the types of complexes that form as a result of molecular binding include:

• protein–protein^[13]
• protein–DNA^[14]
• protein–hormone
• protein–drug^[15]

Proteins that form stable complexes with other molecules are often referred to as receptors while their binding partners are called ligands.^[16]

See also

• Receptor (biochemistry)
• Supramolecular chemistry

References

1. Smith AJ, Zhang X, Leach AG, Houk KN (Jan 2009). "Beyond picomolar affinities: quantitative aspects of noncovalent and covalent binding of drugs to proteins". Journal of Medicinal Chemistry 52 (2): 225–33. doi:10.1021/jm800498e. PMC 2646787. PMID 19053779.
2. "Definition of a molecular complex". Compendium of Chemical Terminology: Gold Book. International Union of Pure and Applied Chemistry. 2012-08-19. A molecular entity formed by loose association involving two or more component molecular entities (ionic or uncharged), or the corresponding chemical species. The bonding between the components is normally weaker than in a covalent bond. The term has also been used with a variety of shades of meaning in different contexts: it is therefore best avoided when a more explicit alternative is applicable. In inorganic chemistry the term 'coordination entity' is recommended instead of 'complex'.
3. Papageorgiou AC, Shapiro R, Acharya KR (Sep 1997). "Molecular recognition of human angiogenin by placental ribonuclease inhibitor--an X-ray crystallographic study at 2.0 A resolution". The EMBO Journal 16 (17): 5162–77. doi:10.1093/emboj/16.17.5162. PMC 1170149. PMID 9311977.
4. Dickson KA, Haigis MC, Raines RT (2005). "Ribonuclease inhibitor: structure and function". Progress in Nucleic Acid Research and Molecular Biology 80: 349–374. doi:10.1016/S0079-6603(05)80009-1. PMC 2811166. PMID 16164979.
5. Green NM (1975). "Avidin". Advances in Protein Chemistry 29: 85–133. doi:10.1016/s0065-3233(08)60411-8. PMID 237414.
6. Holmberg A, Blomstergren A, Nord O, Lukacs M, Lundeberg J, Uhlén M (Feb 2005). "The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures". Electrophoresis 26 (3): 501–510. doi:10.1002/elps.200410070. PMID 15690449.
7. Westermarck J, Ivaska J, Corthals GL (Jul 2013). "Identification of protein interactions involved in cellular signaling". Molecular & Cellular Proteomics 12 (7): 1752–63. doi:10.1074/mcp.R113.027771. PMC 3708163. PMID 23481661.
8. Rang HP, Ritter JM (2007). Rang and Dale's pharmacology (6th ed.). Philadelphia, PA: Churchill Livingstone/Elsevier. p. 19. ISBN 0-443-06911-5.
9. Hunter P (Feb 2009). "Not boring at all. Boron is the new carbon in the quest for novel drug candidates". EMBO Reports 10 (2): 125–8. doi:10.1038/embor.2009.2. PMID 19182828.
10. London N, Miller RM, Krishnan S, Uchida K, Irwin JJ, Eidam O, Gibold L, Cimermančič P, Bonnet R, Shoichet BK, Taunton J (Dec 2014). "Covalent docking of large libraries for the discovery of chemical probes". Nature Chemical Biology 10 (12): 1066–72. doi:10.1038/nchembio.1666. PMID 25344815.
11. Miyamoto S, Kollman PA (Sep 1993). "What determines the strength of noncovalent association of ligands to proteins in aqueous solution?". Proceedings of the National Academy of Sciences of the United States of America 90 (18): 8402–6. doi:10.1073/pnas.90.18.8402. PMC 47364. PMID 8378312.
12. Cooper A (Oct 1999). "Thermodynamic analysis of biomolecular interactions". Current Opinion in Chemical Biology 3 (5): 557–63. doi:10.1016/S1367-5931(99)00008-3. PMID 10508661.
13. Fu H (2004). Protein–protein interactions: methods and applications. Totowa, NJ: Humana Press. ISBN 1-58829-120-0.
14. Seitz H (2007). Analytics of Protein–DNA Interactions (Advances in Biochemical Engineering / Biotechnology). Berlin: Springer. ISBN 3-540-48147-8.
15. Folkers G, Böhm HJ, Schneider G, Mannhold R, Kubinyi H (2003). Protein–ligand interactions from molecular recognition to drug design. Weinheim: Wiley-VCH. ISBN 3-527-30521-1.
16. Klotz IM (1997). Ligand-receptor energetics: a guide for the perplexed. Chichester: John Wiley & Sons. ISBN 0-471-17626-5.