The term molecular recognition refers to the specific interaction between two or more

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...

s through

noncovalent bonding In chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. Th ...

such as

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

ing, metal coordination, hydrophobic forces,

van der Waals force In molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and th ...

s, π-π interactions,

halogen bond A halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. Like a hydrogen ...

ing, or

resonant interaction In nonlinear systems, a resonant interaction is the interaction of three or more waves, usually but not always of small amplitude. Resonant interactions occur when a simple set of criteria coupling wave-vectors and the dispersion equation are met ...

effects. In addition to these ''direct'' interactions, solvents can play a dominant ''indirect'' role in driving molecular recognition in solution. The host and guest involved in molecular recognition exhibit molecular complementarity. Exceptions are molecular containers, including e.g.

nanotubes file:Chiraltube.png, A scanning tunneling microscopy image of a single-walled carbon nanotube file:Kohlenstoffnanoroehre Animation.gif, Rotating single-walled zigzag carbon nanotube A carbon nanotube (CNT) is a tube made of carbon with diameters ...

, in which portals essentially control selectivity.

Biological systems

Molecular recognition plays an important role in biological systems and is observed in between receptor-ligand,

antigen In immunology, an antigen (Ag) is a molecule or molecular structure or any foreign particulate matter or a pollen grain that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response. ...

antibody An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

, DNA-

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

sugar Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose, fructose, and galactose. Compound sugars, also called disaccharides or double ...

- lectin,

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...

, etc. An important example of molecular recognition is the

antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention of ...

vancomycin Vancomycin is a glycopeptide antibiotic medication used to treat a number of bacterial infections. It is recommended intravenously as a treatment for complicated skin infections, bloodstream infections, endocarditis, bone and joint infections, ...

that selectively binds with the

peptides Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A p ...

with terminal D-alanyl-D-alanine in bacterial cells through five hydrogen bonds. The vancomycin is lethal to the bacteria since once it has bound to these particular peptides they are unable to be used to construct the bacteria's

cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mech ...

Synthetic molecular recognition

Recent work suggests that molecular recognition elements can be synthetically produced at the nano-scale, circumventing the need for naturally occurring molecular recognition elements for the development of sensing tools for small molecules. Bio-mimetic polymers such as molecular imprinted polymers and peptoids can be used to recognize larger biological targets such as proteins and the conjugation of polymers to synthetic fluorescent nanomaterials can generate synthetic macromolecular structures that serve as synthetic antibodies for optical protein recognition and detection.

Supramolecular systems

Chemists have demonstrated that many artificial

supramolecular Supramolecular chemistry refers to the branch of chemistry concerning chemical systems composed of a discrete number of molecules. The strength of the forces responsible for spatial organization of the system range from weak intermolecular forces ...

systems can be designed that exhibit molecular recognition. One of the earliest examples of such a system are

crown ethers In organic chemistry, crown ethers are cyclic chemical compounds that consist of a ring containing several ether groups (). The most common crown ethers are cyclic oligomers of ethylene oxide, the repeating unit being ethyleneoxy, i.e., . Impo ...

which are capable of selectively binding specific cations. However, a number of artificial systems have since been established.

Static vs. dynamic

Molecular recognition can be subdivided into ''static molecular recognition'' and ''dynamic molecular recognition''. Static molecular recognition is likened to the interaction between a key and a keyhole; it is a 1:1 type complexation reaction between a host molecule and a guest molecule to form a host–guest complex. To achieve advanced static molecular recognition, it is necessary to make recognition sites that are specific for guest molecules. In the case of dynamic molecular recognition the binding of the first guest to the first binding site of a host affects the association constant of a second guest with a second binding site. leading to cooperativity of binding. In the case of positive allosteric systems the binding of the first guest increases the association constant of the second guest. While for negative allosteric systems the binding of the first guest decreases the association constant with the second. The dynamic nature of this type of molecular recognition is particularly important since it provides a mechanism to regulate binding in biological systems. Dynamic molecular recognition may enhance the ability to discriminate between several competing targets via the

conformational proofreading Conformational proofreading or conformational selection is a general mechanism of molecular recognition systems in which introducing a structural mismatch between a molecular recognizer and its target, or an energetic barrier, enhances the recogn ...

mechanism. Dynamic molecular recognition is also being studied for application in highly functional

chemical sensors A sensor is a device that produces an output signal for the purpose of sensing a physical phenomenon. In the broadest definition, a sensor is a device, module, machine, or subsystem that detects events or changes in its environment and sends ...

and molecular devices.

Complexity

A recent study based on molecular simulations and compliance constants describes molecular recognition as a phenomenon of organisation. 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. However, as Mobley et al. 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. Entropies are rarely observable in single bound structures (static snapshot).

Intragenic complementation

Jehle pointed out that, when immersed in a liquid and intermingled with other molecules, charge fluctuation forces favor the association of identical molecules as nearest neighbors. In accord with this principle, the multiple copies of a polypeptide encoded by a

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

often undergo molecular recognition with each other to form an ordered multi-polypeptide protein structure. When such a protein is formed from polypeptides produced by two different

mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It ...

allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chro ...

s of a particular gene, the protein composed of a mixture of polypeptides may exhibit greater functional activity than the multi-polypeptide protein formed by each of the mutants alone. In such a case, the phenomenon is referred to as

intragenic complementation Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dep ...

. Intragenic complementation (also called inter-allelic complementation) has been demonstrated in many different genes in a variety of organisms. Crick and Orgel Crick FH, Orgel LE. The theory of inter-allelic complementation. J Mol Biol. 1964 Jan;8:161-5. doi: 10.1016/s0022-2836(64)80156-x. PMID 14149958 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.”

References

External links

* http://www.mdpi.org/ijms/sections/molecular-recognition.htm Special Issue on Molecular Recognition in the Int. J. Mol. Sci. {{DEFAULTSORT:Molecular Recognition Supramolecular chemistry