Native Chemical Ligation (NCL) is an important extension of the

chemical ligation Chemical ligation is a set of techniques used for creating long peptide or protein chains. It is the second step of a convergent approach. First, smaller peptides containing 30-50 amino acids are prepared by conventional chemical peptide synt ...

concept for constructing a larger

polypeptide 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 ...

chain by the covalent condensation of two or more unprotected peptides segments. Native chemical ligation is the most effective method for synthesizing native or modified proteins of typical size (''i.e.'',

proteins 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 ...

< ~300 AA).

Reaction

In native chemical ligation, the ionized

thiol In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl gro ...

group of an

N-terminal The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...

cysteine Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, sometime ...

residue of an unprotected peptide attacks the

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...

thioester In organic chemistry, thioesters are organosulfur compounds with the functional group . They are analogous to carboxylate esters () with the sulfur in the thioester playing the role of the linking oxygen in the carboxylate ester, as implied by t ...

of a second unprotected peptide, in an aqueous buffer at pH 7.0 and room temperature. This transthioesterification step is reversible in the presence of an aryl thiol catalyst, rendering the reaction both chemoselective and regioselective, and leads to formation of a thioester-linked intermediate. The intermediate rapidly and spontaneously rearranges by an intramolecular ''S,N- acyl shift'' that results in the formation of a native amide ('

peptide 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 ...

') bond at the ligation site (scheme 1). Remarks : *Thiol additives : The initial transthioesterification step of the native chemical ligation reaction is catalyzed by thiol additives. The most effective and commonly used thiol catalyst is 4-mercaptophenylacetic acid (MPAA), (ref). *

Regioselectivity In chemistry, regioselectivity is the preference of chemical bonding or breaking in one direction over all other possible directions. It can often apply to which of many possible positions a reagent will affect, such as which proton a strong base ...

: The key feature of native chemical ligation of unprotected peptides is the reversibility of the first step, the thiol(ate)–thioester exchange reaction. Native chemical ligation is exquisitely regioselective because that thiol(ate)–thioester exchange step is freely reversible in the presence of an added arylthiol catalyst. The high yields of final ligation product obtained, even in the presence of internal Cys residues in either/both segments, is the result of the irreversibility of the second (S-to-N acyl shift) amide-forming step under the reaction conditions used. *

Chemoselectivity Chemoselectivity is the preferential outcome of a chemical reaction over a set of possible alternative reactions. In another definition, chemoselectivity refers to the selective reactivity of one functional group in the presence of others; often ...

of NCL : No side-products are formed from reaction with the other functional groups present in either peptide segment (e.g. Asp, Glu side chain carboxylic acids; Lys epsilon amino group; Tyr phenolic hydroxyl; Ser, Thr hydroxyls, etc.).

Historical context

In 1992, Stephen Kent and Martina Schnölzer at

The Scripps Research Institute Scripps Research, previously known as The Scripps Research Institute (TSRI), is a nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California, the institu ...

developed the "Chemical Ligation" concept, the first practical method to covalently condense unprotected peptide segments; the key feature of chemical ligation is formation of an unnatural bond at the ligation site. Just two years later in 1994, Philip Dawson, Tom Muir and Stephen Kent reported "Native Chemical Ligation", an extension of the chemical ligation concept to the formation of a native amide ('peptide') bond after initial nucleophilic condensation formed a thioester-linked condensation product designed to spontaneously rearrange to the native amide bond at the ligation site. Theodor Wieland and coworkers had reported the S-to-N acyl shift as early as 1953, when the reaction of

valine Valine (symbol Val or V) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α- carboxylic acid group (which is in the deprotonat ...

-thioester and

amino acid in aqueous buffer was shown to yield the dipeptide valine-cysteine. The reaction proceeded through the intermediacy of a thioester containing the sulfur of the cysteine residue. However, Wieland's work did NOT lead to the development of the native chemical ligation reaction. Rather, the study of amino acid thioester reactions led Wieland and others to develop the 'active ester' method for the synthesis of protected peptide segments by conventional chemical methods carried out in organic solvents.

Features

Native chemical ligation forms the basis of modern chemical protein synthesis, and has been used to prepare numerous proteins and enzymes by total chemical synthesis. The payoff in the native chemical ligation method is that coupling long peptides by this technique is typically near quantitative and provides synthetic access to large peptides and proteins otherwise impossible to make, due to their large size, decoration by post-translational modification, and containing non-coded amino acid or other chemical building blocks. Native chemical ligation is inherently 'Green' in its atom economy and its use of benign solvents. It involves the reaction of an unprotected peptide thioester with a second, unprotected peptide that has an N-terminal cysteine residue. It is carried out in aqueous solution at neutral pH, usually in 6 M guanidine.hydrochloride, in the presence of an arylthiol catalyst and typically gives near-quantitative yields of the desired ligation product. Peptide-thioesters can be directly prepared by Boc chemistry SPPS; however, thioester-containing peptides are not stable to treatment with a nucleophilic base, thus preventing direct synthesis of peptide thioesters by Fmoc chemistry SPPS. Fmoc chemistry solid phase peptide synthesis techniques for generating peptide-thioesters are based on the synthesis of peptide hydrazides that are converted to peptide thioesters post-synthetically. Polypeptide C-terminal thioesters can also be produced ''in situ'', using so-called ''N,S''-acyl shift systems. ''Bis''(2-sulfanylethyl)amido group, also called SEA group, belongs to this family. Polypeptide C-terminal ''bis''(2-sulfanylethyl)amides (SEA peptide segments) react with Cys peptide to give a native peptide bond as in NCL. This reaction, which is called

SEA Native Peptide Ligation Protein chemical synthesis by native peptide ligation of unprotected peptide segments is an interesting complement and potential alternative to the use of living systems for producing proteins. The synthesis of proteins requires efficient native p ...

, is a useful variant of native chemical ligation. In making peptide segments that contain an N-terminal cysteine residue, exposure to ketones should be avoided since these may cap the N-terminal cysteine. Do not use protecting groups that release

aldehyde In organic chemistry, an aldehyde () is an organic compound containing a functional group with the structure . The functional group itself (without the "R" side chain) can be referred to as an aldehyde but can also be classified as a formyl grou ...

s or

ketones In organic chemistry, a ketone is a functional group with the structure R–C(=O)–R', where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group –C(=O)– (which contains a carbon-oxygen double bon ...

. For the same reason, the use of

acetone Acetone (2-propanone or dimethyl ketone), is an organic compound with the formula . It is the simplest and smallest ketone (). It is a colorless, highly volatile and flammable liquid with a characteristic pungent odour. Acetone is miscib ...

should be avoided, particularly in washing glassware used for

lyophilization Freeze drying, also known as lyophilization or cryodesiccation, is a low temperature dehydration process that involves freezing the product and lowering pressure, removing the ice by sublimation. This is in contrast to dehydration by most conve ...

. A feature of the native chemical ligation technique is that the product polypeptide chain contains cysteine at the site of ligation. The cysteine at the ligation site can be desulfurized to

alanine Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side c ...

, thus extending the range of possible ligation sites to include alanine residues. Other beta-thiol containing amino acids can used for native chemical ligation, followed by desulfurization. Alternatively, thiol-containing ligation auxiliaries can be used that mimic an N-terminal cysteine for the ligation reaction, but which can be removed after synthesis. The use of thiol-containing auxiliaries may not be as effective as ligation at a Cys residue. Native chemical ligation can also be performed with an N-terminal selenocysteine residue. Polypeptide C-terminal thioesters produced by recombinant DNA techniques can be reacted with an N-terminal Cys containing polypeptide by the same native ligation chemistry to provide very large semi-synthetic proteins. Native chemical ligation of this kind using a recombinant polypeptide segment is known as Expressed Protein Ligation. Similarly, a recombinant protein containing an N-terminal Cys can be reacted with a synthetic polypeptide

. Thus, native chemical ligation can be used to introduce chemically synthesized segments into recombinant proteins, regardless of size.

Reaction

Historical context

Features

See also

References

Further reading