Total chemical synthesis of crambin

Crambin is a small (46 amino acids) protein isolated from the seeds of the plant Crambe abyssinica. Crambin has been extensively used as a model protein for the development of advanced crystallography and NMR techniques and for computational folding studies. We set out to establish synthetic access to crambin. Initially, we synthesized the 46 amino acid polypeptide by native chemical ligation of two distinct sets of peptide segments (15 + 31 and 31 + 15 residues). The synthetic polypeptide chain folded in good yield to give native crambin containing three disulfide bonds. The chemically synthesized crambin was characterized by LC-MS and by 2D-NMR. However, the 31-residue peptide segments were difficult to purify, and this caused an overall low yield for the synthesis. To overcome this problem, we synthesized crambin by the native chemical ligation of three segments (15 + 16 + 15 residues). Total synthesis using the ligation of three segments gave more than a 10-fold increase in yield and a protein product of exceptionally high purity. This work demonstrates the efficacy of chemical protein synthesis by the native chemical ligation of three segments and establishes efficient synthetic access to the important model protein crambin for experimental studies of protein folding and stability.     

Chemical Synthesis of Proteins with Non‐Strategically Placed Cysteines Using Selenazolidine and Selective Deselenization

Although native chemical ligation has enabled the synthesis of hundreds of proteins, not all proteins are accessible through typical ligation conditions. The challenging protein, 125‐residue human phosphohistidine phosphatase 1 (PHPT1), has three cysteines near the C‐terminus, which are not strategically placed for ligation. Herein, we report the first sequential native chemical ligation/deselenization reaction. PHPT1 was prepared from three unprotected peptide segments using two ligation reactions at cysteine and alanine junctions. Selenazolidine was utilized as a masked precursor for N‐terminal selenocysteine in the middle segment, and, following ligation, deselenization provided the native alanine residue. This approach was used to synthesize both the wild‐type PHPT1 and an analogue in which the active‐site histidine was substituted with the unnatural and isosteric amino acid β‐thienyl‐l ‐alanine. The activity of both proteins was studied and compared, providing insights into the enzyme active site.     

蛋白质的化学全合成

含有非天然氨基酸的蛋白质（如翻译后修饰蛋白质、修饰有探针分子的蛋白质等）是化学生物学中重要的生理活性分子。这些分子难以通过生物表达来获取，而必须使用化学方法来合成。半胱氨酸肽片段连接方法是目前应用于蛋白质化学全合成中的一种重要方法，该方法能够在温和的水溶液中高效地实现肽片段的连接，从而生成天然或者非天然的蛋白质。本文系统地综述了半胱氨酸肽片段连接方法的基本原理，详细讨论了近年来人们对该方法的一些重要改进。最后又介绍了该方法在几类重要的蛋白质分子合成中的代表性应用。     

Semi-Synthesis and Analysis of Chemically Modified Zif268 Zinc-Finger Domains

Total synthesis of proteins can be challenging despite assembling techniques, such as native chemical ligation (NCL) and expressed protein ligation (EPL). Especially, the combination of recombinant protein expression and chemically addressable solid-phase peptide synthesis (SPPS) is well suited for the redesign of native protein structures. Incorporation of analytical probes and artificial amino acids into full-length natural protein domains, such as the sequence-specific DNA binding zinc-finger motifs, are of interest combining selective DNA recognition and artificial function. The semi-synthesis of the natural 90 amino acid long sequence of the zinc-finger domain of Zif268 is described including various chemically modified constructs. Our approach offers the possibility to exchange any amino acid within the third zinc finger. The realized modifications of the natural sequence include point mutations, attachment of a fluorophore, and the exchange of amino acids at different positions in the zinc finger by artificial amino acids to create additional metal binding sites. The individual constructs were analyzed by circular dichroism (CD) spectroscopy with respect to the integrity of the zinc-finger fold and DNA binding.     

Self-assembled templates for polypeptide synthesis

The chemical synthesis of polypeptide chains >50 amino acids with prescribed sequences is challenging. In one approach, native chemical ligation (NCL), short, unprotected peptides are connected through peptide bonds to render proteins in water. Here we combine chemical ligation with peptide self-assembly to deliver extremely long polypeptide chains with stipulated, repeated sequences. We use a self-assembling fiber (SAF) system to form structures tens of micrometers long. In these assemblies, tens of thousands of peptides align with their N- and C-termini abutting. This arrangement facilitates chemical ligation without the usual requirement for a catalytic cysteine residue at the reactive N-terminus. We introduced peptides with C-terminal thioester moieties into the SAFs. Subsequent ligation and disassembly of the noncovalent components produced extended chains > or =10 microm long and estimated at > or =3 MDa in mass. These extremely long molecules were characterized by a combination of biophysical, hydrodynamic, and microscopic measurements.     

Solid-phase synthesis of peptide and glycopeptide thioesters through side-chain-anchoring strategies

An efficient new strategy for the synthesis of peptide and glycopeptide thioesters is described. The method relies on the side-chain immobilization of a variety of Fmoc-amino acids, protected at their C-termini, on solid supports. Once anchored, peptides were constructed using solid-phase peptide synthesis according to the Fmoc protocol. After unmasking the C-terminal carboxylate, either thiols or amino acid thioesters were coupled to afford, after cleavage, peptide and glycopeptide thioesters in high yields. Using this method a significant proportion of the proteinogenic amino acids could be incorporated as C-terminal amino acid residues, therefore providing access to a large number of potential targets that can serve as acyl donors in subsequent ligation reactions. The utility of this methodology was exemplified in the synthesis of a 28 amino acid glycopeptide thioester, which was further elaborated to an N-terminal fragment of the glycoprotein erythropoietin (EPO) by native chemical ligation.     

Chemical synthesis of a glycoprotein having an intact human complex-type sialyloligosaccharide under the Boc and Fmoc synthetic strategies

The chemical synthesis of complex glycoproteins is an ongoing challenge in protein chemistry. We have examined the synthesis of a single glycoform of monocyte chemotactic protein-3 (MCP-3), a CC-chemokine that consists of 76 amino acids and one N-glycosylation site. A three-segment native chemical ligation strategy was employed using unprotected peptides and glycopeptide. Importantly, the synthesis required the development of methods for the generation of sialylglycopeptide-alphathioesters. For the sialylglycopeptide-alphathioester segment, we examined and successfully implemented approaches using Fmoc-SPPS and Boc-SPPS. To avoid use of hydrogen fluoride, the Boc approach utilized minimal side chain protection and direct thiolysis of the resin bound peptide. Using these strategies, we successfully synthesized a glycoprotein having an intact and homogeneous complex-type sialyloligosaccharide.     

N-to-C sequential ligation using peptidyl N,N-bis(2-mercaptoethyl)amide building blocks

A novel N- to C-terminus sequential chemical ligation approach has been developed for protein synthesis. Key to this strategy is the relative stability of the N,N-bis(2-mercaptoethyl)amide (BMEA) to the conventional conditions of native chemical ligation. We have also found a new thiol additive for the BMEA-mediated ligation reaction. The usefulness of this approach was demonstrated in the syntheses of a medium-sized peptide and ubiquitin.     

Recent developments in peptide ligation independent of amino acid side-chain functional group

Chemical synthesis of peptides and proteins has evolved into an indispensable tool for chemical biology. Peptide ligation is a straightforward technique for joining two short peptide fragments together via a native peptide bond to afford a larger natural peptide or protein. However, the junction sites are limited to several specific amino acids because most peptide ligations involve participation of the side-chain functional groups of the junction-site amino acids. To overcome such intrinsic limitations, “general” peptide ligations which do not rely on the side-chain functional group have been developed. This review summarized the recent developments in peptide ligations that are independent of side-chain functional group of ligation-junction-site amino acid.     

9-Fluorenylmethoxycarbonyl-based solid-phase synthesis of peptide α-thioesters

Peptide thioesters play a key role in convergent protein synthesis strategies such as native chemical ligation, traceless Staudinger ligation, and Ag(+) -mediated thioester ligation. The Boc-based solid-phase synthesis provides a very reliable access to peptide thioesters. However, the acid lability of many peptide modifications and the requirements of most parallel peptide synthesizers call for the milder Fmoc-based solid-phase synthesis. The Fmoc-based synthesis of peptide thioesters is more cumbersome and typically proceeds with lower yields than the synthesis of peptide acids and peptide amides. The success of native chemical ligation and related technologies has sparked intensive research effort devoted to the development of new methods. The recent progress in this rapidly expanding field is reviewed.     

Peptide dithiodiethanol esters for in situ generation of thioesters for use in native ligation

A new approach is described for the general Fmoc-based solid-phase synthesis of C-terminal peptide (thio)esters. One hydroxy group of 2,2-dithiodiethanol (used in large excess) was anchored on trityl resin, and the remaining hydroxy group was loaded with the first amino acid. Standard chain elongation and TFA-based peptide release yielded peptide C-terminal dithiodiethanol esters in good purities. Under standard conditions of native chemical ligation (excess thiol, neutral pH), the dithiodiethanol function is presumably reduced and rearranged (or equilibrated) to the thioester via a 5-membered intermediate. The resulting thioesters are shown to undergo native chemical ligation with N-terminal cysteine peptides. Notably, hydrolysis of the reduced ester is a major competing reaction, especially in the presence of 6 M guanidinium chloride, which is often required for solubilization of large peptide fragments.     

Chemical synthesis of a cyclotide via intramolecular cyclization of peptide O-esters

Cyclotides constitute a fascinating family of circular proteins containing ca.30 amino acid residues.They have a unique cyclic cysteine knot topology and exhibit remarkable thermal,chemical and enzymatic stabilities.These characteristics enable them to have a range of biological activities and promising pharmaceutical and agricultural applications.Here,we present a practical strategy for the chemical synthesis of cyclotides through the intramolecular ligation of fully unprotected peptide O-esters.This strategy involves the mild Fmoc solid-phase peptide synthesis of the peptide O-ester backbone,the head-to-tail cyclization of the cyclotide backbone by native chemical ligation,and the oxidative refolding to yield the natural knot protein.The simplicity and high efficiency of the strategy can be employed in the synthesis of artificial cyclotides for pharmaceutical applications.     

Synthesis of l‐ and d‐Ubiquitin by One‐Pot Ligation and Metal‐Free Desulfurization

Native chemical ligation combined with desulfurization has become a powerful strategy for the chemical synthesis of proteins. Here we describe the use of a new thiol additive, methyl thioglycolate, to accomplish one‐pot native chemical ligation and metal‐free desulfurization for chemical protein synthesis. This one‐pot strategy was used to prepare ubiquitin from two or three peptide segments. Circular dichroism spectroscopy and racemic protein X‐ray crystallography confirmed the correct folding of ubiquitin. Our results demonstrate that proteins synthesized chemically by streamlined 9‐fluorenylmethoxycarbonyl (Fmoc) solid‐phase peptide synthesis coupled with a one‐pot ligation–desulfurization strategy can supply useful molecules with sufficient purity for crystallographic studies.     

Native chemical ligation of hydrolysis-resistant 3'-peptidyl-tRNA mimics

Hydrolysis-resistant 3'-peptidyl-RNA conjugates that mimic tRNA termini represent a remarkable synthetic challenge, particularly if they contain amino acids with complex side-chain functionalities, such as arginines. Here we demonstrate a novel approach that combines solid-phase synthesis and bioconjugation to obtain these derivatives with high efficiency and purity. The key step is native chemical ligation of 3'-cysteinyl-RNA fragments to highly soluble peptide thioesters. The so-prepared 3'-peptidyl-RNA conjugates relate to resistance peptides that can render the ribosome resistant to macrolide antibiotics by a yet unknown ribosomal translation mechanism.     

Extending synthetic access to proteins with a removable acyl transfer auxiliary

A chemo- and regioselective auxiliary-mediated peptide ligation has been developed that is effective under nonidealized conditions for the synthesis of proteins. This general amide bond ligation utilizes a removable auxiliary that is analogous to the role of cysteine in native chemical ligation, combining chemoselective thioester exchange with efficient regioselective intramolecular acyl transfer. Acid lability and improved ligation efficiency were introduced into the 2-mercaptobenzyl auxiliary by increasing the electron density of the aromatic ring. The 62 amino acid SH3 domain from alpha-spectrin was synthesized using the auxiliary-mediated ligation at a Lys-Gly sequence. The auxiliary was removed with TFA and scavengers from the ligated product. This methodology enables unprotected peptides to be coupled at noncysteine ligation sites expanding the scope of protein synthesis and semisynthesis.     

Long‐Range Chemical Ligation from N→N Acyl Migrations in Tryptophan Peptides via Cyclic Transition States of 10‐ to 18‐Members

Chemical ligations to form native peptides from N→N acyl migrations in Trp‐containing peptides via 10‐ to 18‐membered cyclic transition states are described. In this study, a statistical, predictive model that uses an extensive synthetic and computational approach to rationalize the chemical ligation is reported. N→N acyl migrations that form longer native peptides without the use of Cys/Ser/Tyr residues or an auxiliary group at the ligation site were achieved. The feasibility of these traceless chemical ligations is supported by the N?C bond distance in N‐acyl isopeptides. The intramolecular nature of the chemical ligations is justified by using competitive experiments and theoretical calculations.     

Synthetic procedure for N-fmoc amino acyl-N-sulfanylethylaniline linker as crypto-Peptide thioester precursor with application to native chemical ligation

N-Sulfanylethylanilide (SEAlide) peptides 1, obtainable using Fmoc-based solid-phase peptide synthesis (Fmoc SPPS), function as crypto-thioesters in native chemical ligation (NCL), yielding a wide variety of peptides/proteins. Their acylating potential with N-terminal cysteinyl peptides 2 can be tuned by the presence or absence of phosphate salts, leading to one-pot/multifragment ligation, operating under kinetically controlled conditions. SEAlide peptides have already been shown to be promising for use in protein synthesis; however, a widely applicable method for the synthesis of N-Fmoc amino acyl-N-sulfanylethylaniline linkers 4, required for the preparation of SEAlide peptides, is unavailable. The present study addresses the development of efficient condensation protocols of 20 naturally occurring amino acid derivatives to the N-sulfanylethylaniline linker 5. N-Fmoc amino acyl aniline linkers 4 of practical use in NCL chemistry, except in the case of the proline- or aspartic acid-containing linker, were successfully synthesized by coupling of POCl(3)- or SOCl(2)-activated Fmoc amino acid derivatives with sodium anilide species 6, without accompanying racemization and loss of side-chain protection. Furthermore, SEAlide peptides 7 possessing various C-terminal amino acids (Gly, His, Phe, Ala, Asn, Ser, Glu, and Val) were shown to be of practical use in NCL chemistry.     

Protein synthesis by solid-phase chemical ligation using a safety catch linker

The native chemical ligation reaction has been used extensively for the synthesis of the large polypeptides that correspond to folded proteins and domains. The efficiency of the synthesis of the target protein is highly dependent on the number of peptide segments in the synthesis. Assembly of proteins from multiple components requires repeated purification and lyophilization steps that give rise to considerable handling losses. In principle, performing the ligation reactions on a solid support would eliminate these inefficient steps and increase the yield of the protein assembly. A new strategy is described for the assembly of large polypeptides on a solid support that utilizes a highly stable safety catch acid-labile linker. This amide generating linker is compatible with a wide range of N-terminal protecting groups and ligation chemistries. The utility of the methodology is demonstrated by a three-segment synthesis of vMIP I, a chemokine that contains all 20 natural amino acids and has two disulfide bonds. The crude polypeptide product was recovered quantitatively from the solid support and purified in 20%-recovered yield. This strategy should facilitate the synthesis of large polypeptides and should find useful applications in the assembly of protein libraries.     

Peptide o‐Aminoanilides as Crypto‐Thioesters for Protein Chemical Synthesis

Fully unprotected peptide o‐aminoanilides can be efficiently activated by NaNO₂ in aqueous solution to furnish peptide thioesters for use in native chemical ligation. This finding enables the convergent synthesis of proteins from readily synthesizable peptide o‐aminoanilides as a new type of crypto‐thioesters. The practicality of this approach is shown by the synthesis of histone H2B from five peptide segments. Purification or solubilization tags, which are sometimes needed to improve the efficiency of protein chemical synthesis, can be incorporated into the o‐aminoanilide moiety, as demonstrated in the preparation of the cyclic protein lactocyclicin Q.     

Chemical Synthesis of Proteins Containing 300 Amino Acids

Chemical synthesis of proteins containing up to 300 amino acids may cover 30%-50% of all the proteins encountered in biomedical studies and may provide an alternate approach to the usually used recombinant expression technology, vastly expanding the chemical space of the latter. In the present review article, we tried to survey the recent progresses made for more rapid synthesis of increasingly long peptides and more efficient ligation of multiple peptide segments. The developments of seminal methods by many research groups have greatly contributed to the recent breakthroughs in the successful total synthesis of a number of functionally important proteins, such as oligoubiquitins, bacterial GroEL/ES chaperones, and mirror-image DNA polymerases. Through these studies, a potential bottleneck has also been recognized for the chemical synthesis of large proteins, namely, how to ensure that each peptide segment from a large protein avoids unfavorable aggregation when dissolved in aqueous solution. Many new methods, such as removable backbone modification(RBM) strategy have been developed to overcome this bottleneck, while more studies need to be carried out to develop more effective and less costly methods that ultimately, may lead to fully automatable chemical synthesis of customized proteins of 300 amino acids bearing any artificial designs.