Protein splicing and related forms of protein autoprocessing

Cyclization of the intrinsically disordered α1S dihydropyridine receptor II-III loop enhances secondary structure and in vitro function

A key component of excitation contraction (EC) coupling in skeletal muscle is the cytoplasmic linker (II-III loop) between the second and third transmembrane repeats of the α(1S) subunit of the dihydropyridine receptor (DHPR). The II-III loop has been previously examined in vitro using a linear II-III loop with unrestrained N- and C-terminal ends. To better reproduce the loop structure in its native environment (tethered to the DHPR transmembrane domains), we have joined the N and C termini using intein-mediated technology. Circular dichroism and NMR spectroscopy revealed a structural shift in the cyclized loop toward a protein with increased α-helical and β-strand structure in a region of the loop implicated in its in vitro function and also in a critical region for EC coupling. The affinity of binding of the II-III loop binding to the SPRY2 domain of the skeletal ryanodine receptor (RyR1) increased 4-fold, and its ability to activate RyR1 channels in lipid bilayers was enhanced 3-fold by cyclization. These functional changes were predicted consequences of the structural enhancement. We suggest that tethering the N and C termini stabilized secondary structural elements in the DHPR II-III loop and may reflect structural and dynamic characteristics of the loop that are inherent in EC coupling.

Structure of catalytically competent intein caught in a redox trap with functional and evolutionary implications

Inteins self-splice from precursor polypeptides to reconstitute functional proteins. Here we describe inteins as redox-responsive switches in bacteria. Regulation was achieved by engineering a disulfide bond between the intein’s catalytic cysteine and the flanking polypeptide. This interaction was validated by an X-ray structure, which includes a transient splice junction. A natural analogue of the designed system was identified in Pyrococcus abysii, suggesting an unprecedented form of adaptive, post-translational regulation.

Construction of a bacterial assay for estrogen detection based on an estrogen-sensitive intein

Escherichia coli strain DIER was constructed for estrogen detection by inserting an estrogen-sensitive intein (VMA(ER) intein) into the specific site of the constitutively expressed chromosomal lacZ gene. This VMA(ER) intein was generated by replacing the endonuclease region of the Saccharomyces cerevisiae VMA intein with the estrogen binding region of the human estrogen receptor α (hERα). When there were estrogens or analogs, the splicing of the VMA(ER) intein was induced to produce the mature LacZ protein, which was detected through a β-galactosidase colorimetric assay. Eight typical chemicals (17-β-estradiol, bisphenol A, chrysene, 6-OH-chrysene, benz[a]anthracene, pyrene, progesterone, and testosterone) were detected using this DIER strain, and the whole detection procedure was accomplished in 2 h. Their 50% effective concentrations (EC(50)), relative estrogenic activities, and estradiol equivalency factors were calculated and were quite consistent with those detected with the yeast estrogen screening (YES) system. Furthermore, the estrogenic activities of the synthetic musk samples extracted from the wastewater and waste sludge of a sewage treatment plant of Shanghai (China) were detected, and their results were comparable to those obtained from the YES system and gas chromatography-mass spectrometry (GC-MS). In conclusion, the DIER bioassay could fill a niche for the efficient, rapid, high-throughput screening of estrogenic compounds and has potential for the remote, near-real-time monitoring of environmental estrogens.

Energy matters: mitochondrial proteomics for biomedicine

This review compiles results of medical relevance from mitochondrial proteomics, grouped either according to the type of disease - genetic or degenerative - or to the involved mechanism - oxidative stress or apoptosis. The findings are commented in the light of our current understanding of uniformity/variability in cell responses to different stimuli. Specificities in the conceptual and technical approaches to human mitochondrial proteomics are also outlined.

Mutational analysis of splicing activities of ribonucleotide reductase α subunit protein from lytic bacteriophage P1201

A CP1201 RIR1 intein is found in the ribonucleotide reductase alpha subunit (RNR α subunit) protein of lytic bacteriophage P1201 from Corynebacterium glutamicum NCHU 87078. This intein can be over-expressed and spliced in Escherichia coli NovaBlue cells. Mutations of C539, the N-terminal residue of the C-extein in the CP1201 RIR1 protein, led to the changes of pattern and level of protein-splicing activities. A G392S variant was found to be a temperature-sensitive protein with complete splicing activity at 17 and 28°C but not at 37°C or higher. We also found that the cleavage at the CP1201 RIR1 intein C-terminus of the double mutant G392S/C539G was blocked, but other cleavage activities could be efficiently performed at 17°C. G392S/C539G variant possessed the properties of low-temperature-induced cleavage at the intein N-terminus.

Extending the scope of site-specific cysteine bioconjugation by appending a prelabeled cysteine tag to proteins using protein trans-splicing

Incorporating synthetic probes site-specifically into proteins is of central interest in several areas of biotechnology and protein chemistry. Bioconjugation techniques provide a simple and effective means of chemically modifying a protein. In particular, covalent chemical modifications of cysteine residues belong to one of the most important reactions due to the unique reactivity of its thiol moiety and the relatively low abundance of this amino acid in proteins. However, such types of modifications cannot be performed in a regioselective fashion when one or more additional cysteines are present. To address this limitation, we have developed an approach where a short cysteine-containing tag (Cys-Tag) fused to one part of a split intein and modified at its sulfhydryl group can be used to label proteins by trans-splicing with a protein of interest (POI) fused to the other half of the split intein. In this way, it is possible to selectively label a protein containing multiple cysteines. The artificially split Mycobacterium xenopi GyrA intein and the Synechocystis sp. DnaB intein were highly suitable for this purpose and were successfully used for the labeling of several proteins. This approach enables a simple route for labeling proteins by site-specific cysteine bioconjugation with any one of several commercially available cysteine-modifying probes.

Chemical biology of prion protein: tools to bridge the in vitro/vivo interface

Research on prion protein (PrP) and pathogenic prion has been very intensive because of its importance as model system for neurodegenerative diseases. One important aspect of this research has been the application of chemical biology tools. In this review we describe new developments like native chemical ligation (NCL) and expressed protein ligation (EPL) for the synthesis and semisynthesis of proteins in general and PrP in particular. These techniques allow the synthesis of designed tailor made analogs which can be used in conjunction with modern biophysical methods like fluorescence spectroscopy, solid state Nuclear Magnetic Resonance (ssNMR), and Electron Paramagnetic Resonance (EPR). Another aspect of prion research is concerned with the interaction of PrP with small organic molecules and metals. The results are critically reviewed and put into perspective of their implication for PrP function.

Spontaneous proton transfer to a conserved intein residue determines on-pathway protein splicing

The discovery of inteins, which are protein-splicing elements, has stimulated interest for various applications in chemical biology, bioseparations, drug delivery, and sensor development. However, for inteins to effectively contribute to these applications, an increased mechanistic understanding of cleavage and splicing reactions is required. While the multistep chemical reaction that leads to splicing is often explored and utilized, it is not clear how the intein navigates through the reaction space. The sequence of reaction steps must progress in concert in order to yield efficient splicing while minimizing off-pathway cleavage reactions. In this study, we demonstrate that formation of a previously identified branched intermediate is the critical step for determining splicing over cleavage products. By combining experimental assays and quantum mechanical simulations, we identify the electrostatic interactions that are important to the dynamics of the reaction steps. We illustrate, via an animated simulation trajectory, a proton transfer from the first C-terminal extein residue to a conserved aspartate, which synchronizes the multistep enzymatic reaction that is key to splicing. This work provides new insights into the complex interplay between critical active-site residues in the protein splicing mechanism, thereby facilitating biotechnological application while shedding light on multistep enzyme activity.

Canonical protein splicing of a class 1 intein that has a class 3 noncanonical sequence motif

A Thermobifida fusca intein has two characteristics of class 3 inteins: a noncontiguous covariant Trp-Cys-Thr triplet and a Ser flanking its C terminus. However, it has Cys at position one, characteristic of class 1 inteins. Splicing does not require the internal Cys, which may instead coordinate the active site. Therefore, the intein is class 1.

Use of protein trans-splicing to produce active and segmentally (2)H, (15)N labeled mannuronan C5-epimerase AlgE4

Alginate epimerases are large multidomain proteins capable of epimerising C5 on beta-D-mannuronic acid (M) turning it into alpha-L-guluronic acid (G) in a polymeric alginate. Azotobacter vinelandii secretes a family of seven epimerases, each of which is capable of producing alginates with characteristic G distribution patterns. All seven epimerases consist of two types of modules, denoted A and R, in varying numbers. Attempts to study these enzymes with solution-state NMR are hampered by their size-the smallest epimerase, AlgE4, consisting of one A- and one R-module, is 58 kDa, resulting in heavy signal overlap impairing the interpretation of NMR spectra. Thus we obtained segmentally (2)H, (15)N labeled AlgE4 isotopomeres (A-[(2)H, (15)N]-R and [(2)H, (15)N]-A-R) by protein trans-splicing using the naturally split intein of Nostoc punctiforme. The NMR spectra of native AlgE4 and the ligated versions coincide well proving the conservation of protein structure. The activity of the ligated AlgE4 was verified by two different enzyme activity assays, demonstrating that ligated AlgE4 displays the same catalytic activity as wild-type AlgE4.

Mechanism of protein splicing of the Pyrococcus abyssi lon protease intein

Protein splicing is a post-translational process by which an intervening polypeptide, the intein, excises itself from the flanking polypeptides, the exteins, coupled to ligation of the exteins. The lon protease of Pyrococcus abyssi (Pab) is interrupted by an intein. When over-expressed as a fusion protein in Escherichia coli, the Pab lon protease intein can promote efficient protein splicing. Mutations that block individual steps of splicing generally do not lead to unproductive side reactions, suggesting that the intein tightly coordinates the splicing process. The intein can splice, although it has Lys in place of the highly conserved penultimate His, and mutants of the intein in the C-terminal region lead to the accumulation of stable branched-ester intermediate.

Biological applications of protein splicing

Protein splicing is a naturally occurring process in which a protein editor, called an intein, performs a molecular disappearing act by cutting itself out of a host protein in a traceless manner. In the two decades since its discovery, protein splicing has been harnessed for the development of several protein-engineering methods. Collectively, these technologies help bridge the fields of chemistry and biology, allowing hitherto impossible manipulations of protein covalent structure. These tools and their application are the subject of this Primer.

Synthetic strategies for studying embryonic development

Developmental biology has evolved from a descriptive science to one based on genetic principles and molecular mechanisms. Although molecular biology and genetic technologies have been the primary drivers of this transformation, synthetic strategies have been increasingly utilized to interrogate the mechanisms of embryonic patterning with spatial and temporal precision. In this review, we survey how chemical tools and engineered proteins have been used to perturb developmental processes at the DNA, RNA, protein, and cellular levels. We discuss the design principles, experimental capabilities, and limitations of each method, as well as future challenges for the chemical and developmental biology communities.

Selective peptide bond hydrolysis of cysteine peptides in the presence of Ni(II) ions

Recently, we described a sequence-specific R1-(Ser/Thr) peptide bond hydrolysis reaction in peptides of a general sequence R1-(Ser/Thr)-Xaa-His-Zaa-R, which occurs in the presence of Ni(II) ions [A. Krężel, E. Kopera, A. M. Protas, A. Wysłouch-Cieszyńska, J. Poznański, W. Bal, J. Am. Chem. Soc. 132 (2010) 3355-3366]. In this study we explored the possibility of substituting the Ser/Thr and the His residues, necessary for the reaction to occur according to the Ni(II)-assisted acyl shift reaction mechanism, with Cys residues. We tested this concept by synthesizing three homologous peptides: R1-Ser-Arg-Cys-Trp-R2, R1-Cys-Arg-His-Trp-R2, and R1-Cys-Arg-Cys-Trp-R2, and the R1-Ser-Arg-His-Trp-R2 peptide as comparator (R1 and R2 were CH3CO-Gly-Ala and Lys-Phe-Leu-NH2, respectively). We studied their hydrolysis in the presence of Ni(II) ions, under anaerobic conditions and in the presence of TCEP as a thiol group antioxidant. We measured hydrolysis rates using HPLC and identified products of reaction using electrospray mass spectrometry. Potentiometry and UV-vis spectroscopy were used to assess Ni(II) complexation. We demonstrated that Ni(II) is not compatible with the Cys substitution of the Ser/Thr acyl acceptor residue, but the substitution of the Ni(II) binding His residue with a Cys yields a peptide susceptible to Ni(II)-related hydrolysis. The relatively high activity of the R1-Ser-Arg-Cys-Trp-R2 peptide at pH 7.0 suggests that this peptide and its Cys-containing analogs might be useful in practical applications of Ni(II)-dependent peptide bond hydrolysis.

Crystallographic snapshot of glycosylasparaginase precursor poised for autoprocessing

Glycosylasparaginase belongs to a family of N-terminal nucleophile hydrolases that autoproteolytically generate their mature enzymes from single-chain protein precursors. Previously, based on a precursor structure paused at pre-autoproteolysis stage by a reversible inhibitor (glycine), we proposed a mechanism of intramolecular autoproteolysis. A key structural feature, a highly strained conformation at the scissile peptide bond, had been identified and was hypothesized to be critical for driving autoproteolysis through an N-O acyl shift. To examine this "twist-and-break" hypothesis, we report here a 1. 9-Å-resolution structure of an autoproteolysis-active precursor (a T152C mutant) that is free of inhibitor or ligand and is poised to undergo autoproteolysis. The current crystallographic study has provided direct evidence for the natural conformation of the glycosylasparaginase autocatalytic site without influence from any inhibitor or ligand. This finding has confirmed our previous proposal that conformational strain is an intrinsic feature of an active precursor.

Autoproteolysis of the SEA module of rMuc3 C-terminal domain modulates its functional composition

rMuc3 is a typical transmembrane mucin and contains a 174 amino acid domain called an SEA module in its C-terminal domain which is cleaved in eukaryotic cells. However, the mechanism by which the rMuc3 SEA module is proteolyzed and its biological significance has to be elucidated. In this study, we showed that the rMuc3 C-terminal domain was cleaved at LSKGSIVV motif within SEA module in prokaryotic cells, the time-dependence of the cleavage was found in the purified rMuc3 C-terminal domain carrying a mutated LSKASIVV motif expressed in bacteria. Thus, the cleavage of rMuc3 SEA module depended on autoproteolysis. The autoproteolysis of the SEA module of rMuc3 C-terminal domain played a critical role in the migration and invasion of the LoVo human colon cancer cells with rMuc3 C-terminal domain in vitro. The rMuc3 C-terminal domain induced a significant activation of HER/ErbB2 phosphorylated form (py1248) in LoVo cells. Inhibition of the phosphorylation by gefitinib (ZD1839) did attenuate migration and invasion of LoVo cells with rMuc3 C-terminal domain. Thus, rMuc3 C-terminal domain undergoes autoproteolysis at its SEA module, which maintains its availability for the potentiation of the signaling process that is modulated by HER/ErbB2 phosphorylation to promote the migration and invasion of LoVo cells.

Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme

Penicillium chrysogenum Acyl coenzyme A:isopenicillin N acyltransferase (AT) performs the last step in the biosynthesis of hydrophobic penicillins, exchanging the hydrophilic side chain of a precursor for various hydrophobic side chains. Like other N-terminal nucleophile hydrolases AT is produced as an inactive precursor that matures upon posttranslational cleavage. The structure of a Cys103Ala precursor mutant shows that maturation is autoproteolytic, initiated by Cys103 cleaving its preceding peptide bond. The crystal structure of the mature enzyme shows that after autoproteolysis residues 92-102 fold outwards, exposing a buried pocket. This pocket is structurally and chemically flexible and can accommodate substrates of different size and polarity. Modeling of a substrate-bound state indicates the residues important for catalysis. Comparison of the proposed autoproteolytic and substrate hydrolysis mechanisms shows that in both events the same catalytic residues are used, but that they perform different roles in catalysis.

Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein

A novel strategy to modulate the assembly and trans-splicing activity of the Ssp DnaE split-intein was achieved by introducing two photolabile protecting groups onto the backbone of the C-intein polypeptide. This modification was not only able to efficiently block the trans-splicing activity, but also reduce significantly the binding affinity constant between the C- and N-intein fragments. The original activity of the wild-type split intein could be fully recovered by brief exposure to UV light.

Inteins, valuable genetic elements in molecular biology and biotechnology

Inteins are internal protein elements that self-excise from their host protein and catalyze ligation of the flanking sequences (exteins) with a peptide bond. They are found in organisms in all three domains of life, and in viral proteins. Intein excision is a posttranslational process that does not require auxiliary enzymes or cofactors. This self-excision process is called protein splicing, by analogy to the splicing of RNA introns from pre-mRNA. Protein splicing involves only four intramolecular reactions, and a small number of key catalytic residues in the intein and exteins. Protein-splicing can also occur in trans. In this case, the intein is separated into N- and C-terminal domains, which are synthesized as separate components, each joined to an extein. The intein domains reassemble and link the joined exteins into a single functional protein. Understanding the cis- and trans-protein splicing mechanisms led to the development of intein-mediated protein-engineering applications, such as protein purification, ligation, cyclization, and selenoprotein production. This review summarizes the catalytic activities and structures of inteins, and focuses on the advantages of some recent intein applications in molecular biology and biotechnology.

Backbone dynamics and global effects of an activating mutation in minimized Mtu RecA inteins

Inteins mediate protein splicing, which has found many applications in biotechnology and protein engineering. A single valine-to-leucine mutation (V67L) can globally enhance splicing and related cleavage reactions in minimized Mycobacterium tuberculosis RecA inteins. However, V67L mutation causes little change in crystal structures. To test whether protein dynamics contribute to activity enhancement in the V67L mutation, we have studied the conformations and dynamics of the minimized and engineered intein DeltaDeltaIhh-V67CM and a single V67L mutant, DeltaDeltaIhh-L67CM, by solution NMR. Chemical shift perturbations established that the V67L mutation causes global changes, including changes at the N-terminus and C-terminus of the intein, which are active sites for protein splicing. The single V67L mutation significantly slows hydrogen-exchange rates globally, indicating a shift to more stable conformations and reduction in ensemble distribution. Whereas the V67L mutation causes little change for motions on the picosecond-to-nanosecond timescale, motions on the microsecond-to-millisecond timescale affect a region involving the conserved F-block histidine and C-terminal asparagine, which are residues important for C-terminal cleavage. The V67L mutation is proposed to activate splicing by reducing the ensemble distribution of the intein structure and by modifying the active sites.

Branched intermediate formation stimulates peptide bond cleavage in protein splicing

Protein splicing is a posttranslational modification in which an intein domain excises itself out of a host protein. Here, we investigate how the steps in the splicing process are coordinated so as to maximize the production of the final splice products and minimize the generation of undesired cleavage products. Our approach has been to prepare a branched intermediate (and analogs thereof) of the Mxe GyrA intein using protein semi-synthesis. Kinetic analysis of these molecules indicates that the high fidelity of this protein splicing reaction results from the penultimate step in the process (intein-succinimide formation) being rate-limiting. NMR experiments indicate that formation of the branched intermediate affects the local structure around the amide bond cleaved during succinimide formation. We propose that this structural change reflects a re-organization of the catalytic apparatus to accelerate succinimide formation at the C-terminal splice junction.

Segmental isotopic labeling of multi-domain and fusion proteins by protein trans-splicing in vivo and in vitro

Segmental isotopic labeling is a powerful labeling technique for reducing nuclear magnetic resonance (NMR) signal overlap, which is associated with larger proteins by incorporating stable isotopes into only one region of a protein for NMR detections. Segmental isotopic labeling can not only reduce complexities of NMR spectra but also retain possibilities to carry out sequential resonance assignments by triple-resonance NMR experiments. We described in vivo (i.e., in Escherichia coli) and in vitro protocols for segmental isotopic labeling of multi-domain and fusion proteins via protein trans-splicing (PTS) using split DnaE intein without any refolding steps or alpha-thioester modification. The advantage of PTS approach is that it can be carried out in vivo by time-delayed dual-expression system with two controllable promoters. A segmentally isotope-labeled protein can be expressed in Escherichia coli within 1 d once required vectors are constructed. The total preparation time of a segmentally labeled sample can be as short as 7-13 d depending on the protocol used.

Controllable protein cleavages through intein fragment complementation

Intein-based protein cleavages, if carried out in a controllable way, can be useful tools of recombinant protein purification, ligation, and cyclization. However, existing methods using contiguous inteins were often complicated by spontaneous cleavages, which could severely reduce the yield of the desired protein product. Here we demonstrate a new method of controllable cleavages without any spontaneous cleavage, using an artificial S1 split-intein consisting of an 11-aa N-intein (I(N)) and a 144-aa C-intein (I(C)). In a C-cleavage design, the I(C) sequence was embedded in a recombinant precursor protein, and the small I(N) was used as a synthetic peptide to trigger a cleavage at the C-terminus of I(C). In an N-cleavage design, the short I(N) sequence was embedded in a recombinant precursor protein, and the separately produced I(C) protein was used to catalyze a cleavage at the N-terminus of I(N). These N- and C-cleavages showed >95% efficiency, and both successfully avoided any spontaneous cleavage during expression and purification of the precursor proteins. The N-cleavage design also revealed an unexpected and interesting structural flexibility of the I(C) protein. These findings significantly expand the effectiveness of intein-based protein cleavages, and they also reveal important insights of intein structural flexibility and fragment complementation.

Sexual mating of Botrytis cinerea illustrates PRP8 intein HEG activity

Strains of Botrytis cinerea are polymorphic for the presence of an intein in the Prp8 gene (intein +/-). The intein encodes a homing endonuclease (HEG). During meiosis in an intein +/- heterozygote, the homing endonuclease initiates intein 'homing' by inducing gene conversion. In such meioses, the homing endonuclease triggers gene conversion of the intein together with its flanking sequences into the empty allele. The efficiency of gene conversion of the intein was found to be 100%. The extent of flanking sequence affected by the gene conversion varied in different meioses. A survey of the inteins and flanking sequences of a group B. cinerea isolates indicates that there are two distinct variants of the intein both of which have active HEGs. The survey also suggests that the intein has been actively homing during the evolution of the species and that the PRP8 intein may have entered the species by horizontal transfer.

GPR56 interacts with extracellular matrix and regulates cancer progression

GPR56 is a relatively recent addition to the adhesion-GPCR family. Genetic and biochemical studies uncovered its roles in cancer and development and established its function as an adhesion receptor to mediate the interactions between cells and extracellular matrix. Despite of much progress on understanding its biological implications, the mechanism of its function remains elusive. It has not been firmly established whether GPR56 signals directly through G proteins and what its upstream stimuli and downstream effectors are to execute its various biological effects. This chapter will give an overview of the primary structures of the Gpr56 gene and its encoded protein and attempt to point out open questions in this research area, with an emphasis on its roles in cancer and signal transduction.

Erl1, a novel era-like GTPase from Magnaporthe oryzae, is required for full root virulence and is conserved in the mutualistic symbiont Glomus intraradices

Comparative analyses of genome sequences from several plant-infecting fungi have shown conservation and expansion of protein families with plant disease-related functions. Here, we show that this hypothesis can be extended to mutualistic symbiotic fungi. We have identified a gene encoding an Era (Escherichia coli Ras)-like GTPase in the rice blast fungus Magnaporthe oryzae and found that it is orthologous to the mature amino terminal part of the Gin1 protein from the arbuscular mycorrhizal (AM) fungus Glomus intraradices. M. oryzae Erl1 is required for full root virulence. Appressoria formation was not severely affected in Deltaerl1 strains, but invasive hyphae grew slower than in the wild type. Root browning defect of Deltaerl1 strains could be complemented by the AM gene under the control of the ERL1 promoter. Erl1 and Gin-N localized to the nucleus when carboxy-terminally labeled with green fluorescent protein (GFP). However, amino-terminal GFP-tagged versions of the proteins expressed in Aspergillus nidulans were shown to localize in the cytoplasm and to cause polarity defects. These data suggest that Erl1 and Gin-N are orthologs and might be involved in the control of hyphal growth in planta. This is the first characterization of an Era-like GTPase in filamentous fungi.

Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins

In the last 15 years substantial advances have been made to place isotope labels in native and glycosylated proteins for NMR studies and structure determination. Key developments include segmental isotope labeling using Native Chemical Ligation, Expressed Protein Ligation and Protein Trans-Splicing. These advances are pushing the size limit of NMR spectroscopy further making larger proteins accessible for this technique. It is just emerging that segmental isotope labeling can be used to define inter-domain interactions in NMR structure determination. Labeling of post-translational modified proteins like glycoproteins remains difficult but some promising developments were recently achieved. Key achievements are segmental and site-specific labeling schemes that improve resonance assignment and structure determination of the glycan moiety. We adjusted the focus of this perspective article to concentrate on the NMR applications based on recent developments rather than on labeling methods themselves to illustrate the considerable potential for biomolecular NMR.

Unnatural amino acids: better than the real things?

Considerable effort has been dedicated to the development of technology for the site-specific incorporation of unnatural amino acids into proteins, with nonsense codon suppression and expressed protein ligation emerging as two of the most promising methods. Recent research advances in which these methods have been applied to study protein function and mechanism are briefly highlighted, and the potential of the methods for efficient, widespread future use in vitro and in vivo is critically evaluated.

S-Adenosylmethionine decarboxylase

S-Adenosylmethionine decarboxylase is a key enzyme for the synthesis of polyamines in mammals, plants and many other species that use aminopropyltransferases for this pathway. It catalyses the formation of S-adenosyl-1-(methylthio)-3-propylamine (decarboxylated S-adenosylmethionine), which is used as the aminopropyl donor. This is the sole function of decarboxylated S-adenosylmethionine. Its content is therefore kept very low and is regulated by variation in the activity of S-adenosylmethionine decarboxylase according to the need for polyamine synthesis. All S-adenosylmethionine decarboxylases have a covalently bound pyruvate prosthetic group, which is essential for the decarboxylation reaction, and have similar structures, although they differ with respect to activation by cations, primary sequence and subunit composition. The present chapter describes these features, the mechanisms for autocatalytic generation of the pyruvate from a proenzyme precursor and for the decarboxylation reaction, and the available inhibitors of this enzyme, which have uses as anticancer and anti-trypanosomal agents. The intricate mechanisms for regulation of mammalian S-adenosylmethionine decarboxylase activity and content are also described.

Selection and structure of hyperactive inteins: peripheral changes relayed to the catalytic center

Inteins are phylogenetically diverse self-splicing proteins that are of great functional, evolutionary, biotechnological, and medical interest. To address the relationship between intein structure and function, particularly with respect to regulating the splicing reaction, and to groom inteins for application, we developed a phage display system to extend current in vivo selection for enhanced intein function to selection in vitro. We thereby isolated inteins that can function under excursions in temperature, pH, and denaturing environment. Remarkably, most mutations mapped to the surface of the intein, remote from the active site. We chose two mutants with enhanced splicing activity for crystallography, one of which was also subjected to NMR analysis. These studies define a "ripple effect", whereby mutations in peripheral non-catalytic residues can cause subtle allosteric changes in the active-site environment in a way that facilitates intein activity. Altered salt-bridge formation and chemical shift changes of the mutant inteins provide a molecular rationale for their phenotypes. These fundamental insights will advance the utility of inteins in chemical biology, biotechnology, and medicine.

Protein splicing of the three Pyrococcus abyssi ribonucleotide reductase inteins

An intein is a polypeptide that interrupts the functional domains of a protein, called the exteins. The intein can facilitate its own excision from the exteins, concomitant with the ligation of the exteins, in a process called protein splicing. The alpha subunit of the ribonucleotide reductase of the extreme thermophile Pyrococcus abyssi is interrupted by three inteins in separate insertion sites. Each intein can facilitate protein splicing when over-expressed in Escherichia coli, with affinity domains serving as the exteins. The influence of the N-terminal flanking residue on the efficiency of splicing is specific to each intein. Each intein has a different downstream nucleophilic residue, and cannot tolerate substitution to a residue of lesser or equal nucleophilicity. The influence of the conserved penultimate His also differs between the inteins.

Traceless protein splicing utilizing evolved split inteins

Split inteins are parasitic genetic elements frequently found inserted into reading frames of essential proteins. Their association and excision restore host protein function through a protein self-splicing reaction. They have gained an increasingly important role in the chemical modification of proteins to create cyclical, segmentally labeled, and fluorescently tagged proteins. Ideally, inteins would seamlessly splice polypeptides together with no remnant sequences and at high efficiency. Here, we describe experiments that identify the branched intermediate, a transient step in the overall splicing reaction, as a key determinant of the splicing efficiency at different splice-site junctions. To alter intein specificity, we developed a cell-based selection scheme to evolve split inteins that splice with high efficiency at different splice junctions and at higher temperatures. Mutations within these evolved inteins occur at sites distant from the active site. We present a hypothesis that a network of conserved coevolving amino acids in inteins mediates these long-range effects.

Modulation of intein activity by its neighboring extein substrates

Inteins comprise a large family of phylogenetically widespread self-splicing protein catalysts that colonize diverse host proteins. The evolutionary and functional relationship between the intein and the split-host protein, the exteins, is largely unknown. To probe an association, we developed an in vivo and in vitro intein assay based on FRET. The FRET assay reports cleavage of the intein from its N-terminal extein. Applying this assay to randomized extein libraries, we show that the nature of the extein substrate bordering the intein can profoundly influence intein activity. Residues proximal to the intein-splicing junction in both N- and C-terminal exteins can accelerate the N-terminal cleavage rate by >4-fold or attenuate cleavage by 1,000-fold, both resulting in compromised self-splicing efficiency. The existence and the magnitude of extein effects require consideration for maximizing the utility of inteins in biotechnological applications, and they predict biases in intein integration sites in nature.

Modeling protein splicing: reaction pathway for C-terminal splice and intein scission

Protein splicing is a post-translational process where a biologically inactive protein is activated after the release of a so-called intein domain. In spite of the importance of this type of process, the specific molecular mechanism for the catalysis is still uncertain. In this work, we present a computational study of one of the key steps in protein splicing: the release of the intein due to the cyclization of an asparagine, the last amino acid of the intein. Density functional theory (DFT) calculations using the B3LYP functional in conjunction with the polarizable continuum model (PCM) were used to study the main stationary points along various possible reaction pathways. The results are compared with other DFT functionals and the MP2 ab initio method. In the first part of this work, the Asn-Thr dipeptide is analyzed with the aim of determining the specific requirements for the activation of the intrinsically slow Asn cyclization. The results show that the nucleophilic activation of the Asn side chain by removing one of its proton decreases the free energy barrier by approximately 20 kcal/mol. A full pathway of the reaction was also characterized in a larger model, including two imidazole molecules and two water molecules. The proposed reaction mechanism consists of two main steps: Asn side chain activation by a proton transfer to one of the imidazole groups, and cleavage of the peptide bond upon protonation of its nitrogen atom by the other imidazole. The overall free energy barrier in solution was determined to be 29.3 kcal/mol, in reasonable agreement with the apparent experimental barrier in the enzyme. The proposed mechanism suggests that the penultimate histidine stabilizes the tetrahedral intermediate and protonates the nitrogen of the scissile peptide bond, while a second histidine (located 10 amino acids upstream) activates the Asn side chain by deprotonating it.

NMR resonance assignment of DnaE intein from Nostoc punctiforme

DnaE intein from Nostoc punctiforme (Npu) is one of naturally occurring split inteins, which has robust protein splicing activity. Highly efficient trans-splicing activity of NpuDnaE intein could widen various biotechnological applications. However, structural basis of the efficient protein splicing activity is poorly understood. As a first step toward better understanding of protein trans-splicing mechanism, we present the backbone and side-chain resonance assignments of a single chain variant NpuDnaE intein as determined by triple resonance experiments with [(13)C,(15)N]-labeled protein.

Metal ions binding to recA inteins from Mycobacterium tuberculosis

Zinc has been found in the crystal structures of inteins and the zinc ion can inhibit intein splicing both in vitro and in vivo. The interactions between metal ions and three minimized recA inteins have been studied in this work. Isothermal titration calorimetry (ITC) results show that the zinc binding affinity to three inteins is in the order of DeltaI-SM > DeltaDeltaI(hh)-SM approximately DeltaDeltaI(hh)-CM, but is much weaker than to EDTA. These data explain the reversible inhibition and the presence of zinc only in the crystal structure of DeltaI-SM of recA intein. A positive correlation between binding constants and inhibition efficiency was observed upon the titration of different metal ions. Single-site binding modes were detected in all interactions, except DeltaDeltaI(hh)-CM which has two Zn sites. Zinc binding sites on DeltaDeltaI(hh)-CM were analyzed by NMR spectroscopy and ITC titration on inteins with chemical modifications. Results indicate that the Cys1 and His73 are the second zinc binding sites in DeltaDeltaI(hh)-CM. CD studies show the metal coordinations have negligible influence on protein structure. This work suggests that the mobility restriction of key residues from metal coordination is likely the key cause of metal inhibition of intein splicing.

In vivo and in vitro protein ligation by naturally occurring and engineered split DnaE inteins

Background

Protein trans-splicing by naturally occurring split DnaE inteins is used for protein ligation of foreign peptide fragments. In order to widen biotechnological applications of protein trans-splicing, it is highly desirable to have split inteins with shorter C-terminal fragments, which can be chemically synthesized.

Principal Findings

We report the identification of new functional split sites in DnaE inteins from Synechocystis sp. PCC6803 and from Nostoc punctiforme. One of the newly engineered split intein bearing C-terminal 15 residues showed more robust protein trans-splicing activity than naturally occurring split DnaE inteins in a foreign context. During the course of our experiments, we found that protein ligation by protein trans-splicing depended not only on the splicing junction sequences, but also on the foreign extein sequences. Furthermore, we could classify the protein trans-splicing reactions in foreign contexts with a simple kinetic model into three groups according to their kinetic parameters in the presence of various reducing agents.

Conclusion

The shorter C-intein of the newly engineered split intein could be a useful tool for biotechnological applications including protein modification, incorporation of chemical probes, and segmental isotopic labelling. Based on kinetic analysis of the protein splicing reactions, we propose a general strategy to improve ligation yields by protein trans-splicing, which could significantly enhance the applications of protein ligation by protein trans-splicing.