Molecular recognition

[15] Molecular recognition plays an important role in biological systems and is observed in between receptor-ligand,[16][17] antigen-antibody, DNA-protein, sugar-lectin, RNA-ribosome, etc.

An important example of molecular recognition is the antibiotic vancomycin that selectively binds with the peptides with terminal D-alanyl-D-alanine in bacterial cells through five hydrogen bonds.

Even for small molecules like carbohydrates, the recognition process can not be predicted or designed even assuming that each individual hydrogen bond's strength is exactly known.

[26] However, as Mobley et al.[27] concluded, the accurate prediction of the molecular recognition events needs to go beyond the static snapshot of a single frame between the guest and the host.

Entropies are key contributors to binding thermodynamics and need to be accounted for in order to predict more accurately the recognition process.

In accord with this principle, the multiple copies of a polypeptide encoded by a gene often undergo molecular recognition with each other to form an ordered multi-polypeptide protein structure.

[31] Crick and Orgel[32] analyzed of the results of such studies and came to the conclusion that intragenic complementation, in general, arises from the interaction of differently defective polypeptide monomers when they form an ordered aggregate they called a “multimer.”

Crystal structure of a short peptide L-Lys-D-Ala-D-Ala (bacterial cell wall precursor) bound to the antibiotic vancomycin through hydrogen bonds [ 1 ]
Crystal structure of two isophthalic acids bound to a host molecule through hydrogen bonds [ 2 ]
Static recognition between a single guest and a single host binding site. In dynamic recognition binding the first guest at the first binding site induces a conformation change that affects the association constant of the second guest at the second binding site. In this case it is positive allosteric system.
A ribosome is a biological machine that utilizes protein dynamics on nanoscales to translate RNA into proteins