Molecular Recognition

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Crystal structure of two isophthalic acid molecules Isophthalic acid molecules which are bound to a host molecule via hydrogen bonds (shown in dotted lines) .

The term molecule recognition or molecular recognition denotes a non- covalent interaction between two or more molecules that is specific for precisely this combination of molecules. In this interaction there is often a larger host molecule that interacts with a guest molecule. Molecular recognition is based on the lock and key principle .

Types of interactions

There are a variety of interactions that play a role in molecule recognition. These include hydrogen bonds , Van de Waals interactions , complex formation reactions , hydrophobicity effects , pi complexes , halogen bonds or electrostatic interactions . In addition to these direct interactions, solvent effects can also play a decisive role.

Static or dynamic

Above: Static recognition between a guest molecule and a single host binding site. Bottom: In dynamic recognition, the binding of the first guest molecule leads to a conformational change at another binding site, which influences the binding constant there (positive in this case)

Molecule recognition can be divided into static molecule recognition and dynamic molecule recognition . Static molecule recognition is a 1: 1 connection between a host molecule and a guest molecule to form a host-guest complex.

In dynamic molecule recognition, the binding of a first guest molecule to a first binding site leads to a change in a second binding site. In positive allosteric systems, the bond of the first guest strengthens the bond of the second, in negative it is weakened. Dynamic molecule recognition can improve the ability to differentiate between competing target molecules. Dynamic molecule recognition is also being studied for use in chemical sensors and molecular machines.

Complexity of Molecular Recognition

A study carried out in 2011 on the molecular simulation of molecule recognition processes showed that even for small molecules such as carbohydrates, the recognition process cannot be predicted, although the strengths of all hydrogen bonds were known.

Occurrence

Biological systems

Crystal structure of a short peptide L-Lys-D-Ala-D-Ala (a precursor for bacterial cell walls), which is bound to the antibiotic vancomycin by means of hydrogen bonds .

Molecular recognition plays a very important role in biological systems. For example in receptor - ligand , antigen - antibody , DNA-protein and enzyme - substrate interactions. An important example of molecule recognition is provided by the antibiotic vancomycin , which selectively binds to peptides with terminal D-alanyl-D- alanine in bacterial cells by means of five hydrogen bonds . The connection with the vancomycin makes the peptides useless for the construction of the cell wall.

Supramolecular Systems

In the meantime it has been shown that artificial supramolecular systems can be constructed in such a way that they have molecular recognition. One of the earliest examples of such systems are crown ethers , which only bind to certain cations.

Web links

  • Molecular Recognition. (Special issue on Molecular Recognition of the International Journal of Molecular Sciences; English)

Individual evidence

  1. ↑ Christopher Bielawski, Yuan-Shek Chen, Peng Zhang, Peggy-Jean Perst, Jeffrey S. Moore: A modular approach to constructing multi-site receptors for isophthalic acid . (Free full text) In: Chemical Communications . No. 12, 1998, pp. 1313-4. doi : 10.1039 / a707262g .
  2. ^ Samuel H. Gellman: Introduction: Molecular Recognition . In: Chemical Reviews . 97, No. 5, 1997, pp. 1231-1232. doi : 10.1021 / cr970328j . PMID 11851448 .
  3. ^ I Cosic: Macromolecular bioactivity: is it resonant interaction between macromolecules? —Theory and applications . In: IEEE transactions on bio-medical engineering . 41, No. 12, 1994, pp. 1101-14. doi : 10.1109 / 10.335859 . PMID 7851912 .
  4. ↑ Riccardo Baron, Piotr Setny, J. Andrew McCammon: Water in Cavity ligand recognition . In: Journal of the American Chemical Society . 132, No. 34, 2010, pp. 12091-12097. doi : 10.1021 / ja1050082 . PMID 20695475 . PMC 2933114 (free full text).
  5. ^ Riccardo Baron, J. Andrew McCammon: Molecular Recognition and Ligand Binding . In: Annual Review in Physical Chemistry . 64, 2013, pp. 151-175. doi : 10.1146 / annurev-physchem-040412-110047 . PMID 23473376 .
  6. ↑ Seiji Shinkai, Masato Ikeda, Atsushi Sugasaki, Masayuki Takeuchi: Positive allosteric systems designed on dynamic supramolecular scaffolds: toward switching and amplification of guest affinity and selectivity . In: Accounts of chemical research . 34, No. 6, 2001, pp. 494-503. doi : 10.1021 / ar000177y . PMID 11412086 .
  7. ^ Jörg Grunenberg: Complexity in molecular recognition . In: Physical Chemistry Chemical Physics . tape 13 , no. 21 , May 18, 2011, p. 10136-10146 , doi : 10.1039 / C1CP20097F .
  8. ↑ James R. Knox, RF Pratt: Different modes of vancomycin and D-alanyl-D-alanine peptidase binding to cell wall peptide and a possible role for the vancomycin resistance protein . (Free full text) In: Antimicrobial agents and chemotherapy . 34, No. 7, July 1990, pp. 1342-7. doi : 10.1128 / AAC.34.7.1342 . PMID 2386365 . PMC 175978 (free full text).