Peptide and protein carboxyl-terminal labeling through carboxypeptidase Y-catalyzed transpeptidation

Engineered peptide ligases for cell signaling and bioconjugation

Enzymes that catalyze peptide ligation are powerful tools for site-specific protein bioconjugation and the study of cellular signaling. Peptide ligases can be divided into two classes: proteases that have been engineered to favor peptide ligation, and protease-related enzymes with naturally evolved peptide ligation activity. Here, we provide a review of key natural peptide ligases and proteases engineered to favor peptide ligation activity. We cover the protein engineering approaches used to generate and improve these tools, along with recent biological applications, advantages, and limitations associated with each enzyme. Finally, we address future challenges and opportunities for further development of peptide ligases as tools for biological research.

ProC-TEL: Profiling of Protein C-Termini by Enzymatic Labeling

Proteins are frequently processed by proteases in cell signaling pathways to perform their biological functions in response to environmental stimuli. Identification of the exact cleavage sites provides necessary information for the study of their biological functions. Although proteomic approaches for profiling of protein N-termini have been developed extensively in the past few years, the N-terminal profiling strategy has its inherent disadvantages. Therefore, C-terminal profiling approaches might be a complementary approach for the identification of protein cleavages although it has similar shortcomings as N-terminal profiling methods. In this protocol, we describe an approach, termed ProC-TEL: Profiling of Protein C-Termini by Enzymatic Labeling, for affinity labeling of protein C-termini for a protein or proteome. This method uses the transpeptidase activity of carboxypeptidase Y to label protein C-termini with an affinity biotin tag for subsequent isolation with avidin beads and identification by mass spectrometer. It is complementary to the N-terminal profiling approaches and can be used to identify proteolytic cleavages for a specific protease or in cell signaling events, such as apoptosis.

C-terminomics: Targeted analysis of natural and posttranslationally modified protein and peptide C-termini

The C-terminus (where C is carboxyl) of a protein can serve as a recognition signature for a variety of biological processes, including protein trafficking and protein complex formation. Hence, the identity of the in vivo protein C-termini provides valuable information about biological processes. Analysis of protein C-termini is also crucial for the study of C-terminal PTMs, particularly for monitoring proteolytic processing by endopeptidases and carboxypeptidases. Although technical difficulties have limited the study of C-termini, a range of technologies have been proposed in the last couple of years. Here, we review the current proteomics technologies for C-terminal analysis, with a focus on the biological information that can be derived from C-terminomics studies.

Chemoenzymatic labeling of protein C-termini for positive selection of C-terminal peptides

Many proteomic experiments require selective labeling of either N- or C-termini of proteins and recovery of terminal peptides. Although N-termini can be selectively labeled, selective labeling of protein C-termini has not been possible due to the difficulty in discriminating between the carboxyl group on the C-terminus versus that on aspartate and glutamate residues. Here we describe the first simple proteomic approach for positive selection of protein C-termini, Profiling Protein C-Termini by Enzymatic Labeling (ProC-TEL). ProC-TEL uses carboxypeptidase Y and other readily available reagents to selectively add an affinity tag to protein C-termini and to capture C-terminal peptides from complex cell lysates for mass spectrometry (MS) identification. Using ProC-TEL, we identify novel C-terminal processing and internal proteolytic cleavage events. These results indicate that ProC-TEL provides a straightforward approach for profiling C-terminal peptides and identifying protein processing in complex biological samples.

Controlled coupling of peptides at their C-termini

Fusion of two proteins has become an important tool in biotechnology. Whereas biotechnological methods easily can produce C-terminal to N-terminal fused compounds, methods to couple two proteins to each of their C-termini are not easily accessible. Herein, peptides are used as models for larger proteins. A method is described exploiting the possibility to attach different reactive handles to their C-termini using a reaction catalyzed by the enzyme carboxypeptidase Y (CPY). It is possible to attach pairs of reaction handles which can react with each other to each of the peptides to be coupled. In a second step, the two modified peptides can be linked together by a chemical reaction, such as an oxime-forming reaction or a copper(I) catalyzed [2+3]-cycloaddition reaction of an azide with an alkyne.

Enzymatic degradation of endomorphins

Centrally acting plant opiates, such as morphine, are the most frequently used analgesics for the relief of severe pain, even though their undesired side effects are serious limitation to their usefulness. The search for new therapeutics that could replace morphine has been mainly focused on the development of peptide analogs or peptidomimetics with high selectivity for one receptor type and high bioavailability, that is good blood-brain barrier permeability and enzymatic stability. Drugs, in order to be effective, must be able to reach the target tissue and to remain metabolically stable to produce the desired effects. The study of naturally occurring peptides provides a rational and powerful approach in the design of peptide therapeutics. Endogenous opioid peptides, endomorphin-1 and endomorphin-2, are two potent and highly selective mu-opioid receptor agonists, discovered only a decade ago, which display potent analgesic activity. However, extensive studies on the possible use of endomorphins as analgesics instead of morphine met with failure due to their instability. This review deals with the recent investigations that allowed determine degradation pathways of endomorphins in vitro and in vivo and propose modifications that will lead to more stable analogs.

The endomorphin system and its evolving neurophysiological role

Endomorphin-1 (Tyr-Pro-Trp-Phe-NH2) and endomorphin-2 (Tyr-Pro-Phe-Phe-NH2) are two endogenous opioid peptides with high affinity and remarkable selectivity for the mu-opioid receptor. The neuroanatomical distribution of endomorphins reflects their potential endogenous role in many major physiological processes, which include perception of pain, responses related to stress, and complex functions such as reward, arousal, and vigilance, as well as autonomic, cognitive, neuroendocrine, and limbic homeostasis. In this review we discuss the biological effects of endomorphin-1 and endomorphin-2 in relation to their distribution in the central and peripheral nervous systems. We describe the relationship between these two mu-opioid receptor-selective peptides and endogenous neurohormones and neurotransmitters. We also evaluate the role of endomorphins from the physiological point of view and report selectively on the most important findings in their pharmacology.

C-Terminally PEGylated hGH-derivatives

A two-step strategy was used for the preparation of C-terminally PEGylated hGH-derivatives. In a first step a CPY-catalyzed transpeptidation was performed on hGH-Leu-Ala, introducing reaction handles, which were used in the second step for the ligation of PEG-moieties. Both oxime-ligation and copper(I) catalyzed [2+3]-cycloaddition reactions were used for the attachment of PEG-moieties. The biological data show a dependency of the potency of the hGH-derivatives on both size as well as shape of the PEG-group.

Influence of degradation on binding properties and biological activity of endomorphin 1

The recently-isolated endogenous peptide endomorphin 1 has high affinity for the mu opioid receptor and plays an important role in analgesia. Several of its degradation products have been isolated from the central nervous system. Degradation products present structural similarities and may influence the receptor binding properties and biological activity of the parent compound. Therefore, we investigated how degradation of endomorphin 1 might influence ligand binding to the mu opioid receptor, the consequent activation of G proteins and its antinociceptive effect. Both N- and C-terminal truncation of endomorphin 1 resulted in peptides presenting considerably lower opioid receptor binding potency. None of these peptides had an effect on GTP binding, nor was able to produce analgesia, suggesting that degradation destroys the biological activity of endomorphin 1.

C-Terminal labeling of immunoglobulin G with a cysteine derivative by carboxypeptidase Y catalyzed transpeptidation

We describe a new method for the site-specific incorporation of an extrinsic cysteine to the C-termini of immunoglobulin G (IgG) using carboxypeptidase Y (CPase Y) catalyzed transpeptidation. The transpeptidase activity of CPase Y was employed to attach cysteine esters to the C-termini of the IgG molecule (cysteinylation) at alkaline pH. No CPase Y catalyzed transpeptidation products were found when native IgG was used as the substrate or when cysteine was used as the nucleophile. However, C-terminal labeling occurred when cysteine ethyl ester (CysOEt) or cysteine isobutyl ester (CysOiBu) was used as the nucleophile and IgG methyl ester as the substrate. When CysOiBu was used as the nucleophile, the maximal labeling yield obtained with IgG methyl ester as substrate was 25%, assuming all four C-termini in the IgG molecule were labeled equally. The C-terminal labeling pattern of cysteinylated IgG was determined by autoradiography followed by the integration of radiodensity. It revealed that both the C-termini of the heavy and light chains of IgG methyl ester were labeled with CysOiBu.

The absolute configuration of belactin A, a beta-lactone-containing serine carboxypeptidase inhibitor: importance of the beta-lactone structure for serine carboxypeptidase inhibition

The absolute configuration of belactin A, a beta-lactone-containing serine carboxypeptidase inhibitor was studied by a crystal X-ray diffraction analysis and its absolute structure was determined to be (2R,3S)-2-¿(3S)-3-[(2-amino-5-chlorophenyl)carboxamido]-1,1-dimethyl-2-o xobutyl¿-3-methyl-4-oxooxetane. The importance of the beta-lactone structure for inhibitory activity was found by preparing several derivatives of belactin A.

Covalent glycoinositolphospholipid binding to hemoglobin: a new post-translational modification of Hb occurring in hyperinsulinism with concomitant hypoglycemia

In this work a novel hitherto unrecognised minor hemoglobin (Hb) fraction, which we detected previously in hemolysates of erythrocytes exposed to a high concentration of insulin under hypoglycemic conditions, both in vivo and in vitro, is analysed. The modification of Hb in HbA1x was shown to be due the addition of glycoinositolphospholipid (GPI) to the C termini of both beta polypeptide chains. A structurally related minor Hb fraction was identified in erythrocytes exposed in vitro to insulin-mimetic agent, trypsin. To our knowledge this is the first demonstration of such a modification of Hb, as well as the first demonstration of post-translational GPI binding to proteins in response to insulin. The mechanism proposed for GPI-Hb formation is briefly described.

Belactins A and B, new serine carboxypeptidase inhibitors produced by Actinomycete. I. Taxonomy, production, isolation and biological activities

Belactins A and B, new inhibitors of serine carboxypeptidase were discovered in the fermentation broth of Saccharopolyspora sp. MK19-42F6. They were purified by ethyl acetate extraction, silica gel chromatography, Sephadex LH20 chromatography, Capcellpak C18 SG120 reversed phase HPLC and centrifugal partition chromatography (CPC) following their inhibitory activity against carboxypeptidase Y (CP-Y). The inhibition constants (Ki) of belactins A and B against CP-Y are 0.14 and 0.27 microM respectively. Belactins A and B have highly specific inhibitory activities for CP-Y among various peptidases, have no antimicrobial activities at 100 micrograms/ml and have low toxicities.

Performances and limits of plasma desorption mass spectrometry in the primary structure determination of proteins

The resolution, sensitivity, matrix effect, cationization and spectral suppression in plasma desorption mass spectrometry (PD-MS) were investigated in the context of peptide analysis. Excessive cationization may be avoided by the addition of citric acid on the target. The importance of the relative net charge of peptides in PD-MS spectra suppression was confirmed. Esterification of peptides is shown to be an easy way to overcome spectral suppression. Provided that cationization and spectral suppression of peptides are under control, PD-MS is an excellent tool for protein sequence analysis, affording the necessary complement to automated Edman degradation.