Biotinylated fluorescent peptide substrates for the sensitive and specific determination of cathepsin D activity

Genome-wide investigation of maize RAD51 binding affinity through phage display

BACKGROUND

RAD51 proteins, which are conserved in all eukaryotes, repair DNA double-strand breaks. This is critical to homologous chromosome pairing and recombination enabling successful reproduction. Work in Arabidopsis suggests that RAD51 also plays a role in plant defense; the Arabidopsis rad51 mutant is more susceptible to Pseudomonas syringae. However, the defense functions of RAD51 and the proteins interacting with RAD51 have not been thoroughly investigated in maize. Uncovering ligands of RAD51 would help to understand meiotic recombination and possibly the role of RAD51 in defense. This study used phage display, a tool for discovery of protein-protein interactions, to search for proteins interacting with maize RAD51A1.

RESULTS

Maize RAD51A1 was screened against a random phage library. Eleven short peptide sequences were recovered from 15 phages which bound ZmRAD51A1 in vitro; three sequences were found in multiple successfully binding phages. Nine of these phage interactions were verified in vitro through ELISA and/or dot blotting. BLAST searches did not reveal any maize proteins which contained the exact sequence of any of the selected phage peptides, although one of the selected phages had a strong alignment (E-value = 0.079) to a binding domain of maize BRCA2. Therefore, we designed 32 additional short peptides using amino acid sequences found in the predicted maize proteome. These peptides were not contained within phages. Of these synthesized peptides, 14 bound to ZmRAD51A1 in a dot blot experiment. These 14 sequences are found in known maize proteins including transcription factors putatively involved in defense.

CONCLUSIONS

These results reveal several peptides which bind ZmRAD51A1 and support a potential role for ZmRAD51A1 in transcriptional regulation and plant defense. This study also demonstrates the applicability of phage display to basic science questions, such as the search for binding partners of a known protein, and raises the possibility of an iterated approach to test peptide sequences that closely but imperfectly align with the selected phages.

Solid-phase fluorescent BODIPY-peptide synthesis via in situ dipyrrin construction

Traditional fluorescent peptide chemical syntheses hinge on the use of limited fluorescent/dye-taggable unnatural amino acids and entail multiple costly purifications. Here we describe a facile and efficient protocol for in situ construction of dipyrrins on the N-terminus with 20 natural and five unnatural amino acids and the lysine's side chain of selected peptides/peptide drugs through Fmoc-based solid-phase peptide synthesis. The new strategy enables the direct formation of boron-dipyrromethene (BODIPY)-peptide conjugates from simple aldehyde and pyrrole derivatives without pre-functionalization, and only requires a single-time chromatographic purification at the final stage. As a model study, synthesized EBNA1-targeting BODIPY1-Pep4 demonstrates intact selectivity in vitro, responsive fluorescence enhancement, and higher light cytotoxicity due to the photo-generation of cytotoxic singlet oxygen. This work offers a novel practical synthetic platform for fluorescent peptides for multifaceted biomedical applications.

Enzyme-responsive multifunctional surfaces for controlled uptake/release of (bio)molecules

The current trend in the development of biomaterials is towards bioactive and biodegradable systems. In particular, enzyme-responsive structures are useful tools to realize biodegradable surfaces for the controlled delivery of biomolecules/drugs through a triggered surface erosion process. Up to now, enzyme-responsive structures have been designed by covalent linkage between synthetic polymers and biodegradable functionalities that are responsive to chemical and biological cues (i.e. proteases or pH) [1-4]. Here, we present a novel approach to achieve enzyme-responsive surface-attached networks by exploiting the non-covalent interaction between streptavidin and biotin. The functional component of this three-dimensional (3D) structure is a layer of biotinylated peptides that are degraded by the action of specific proteases. The system was stable under typical physiological conditions; however, it was efficiently degraded upon enzyme exposure. Further, the controlled release of biomolecules and drugs--previously entrapped into the surface-attached network--was demonstrated to occur as a consequence of the enzymatic cleavage. This versatile approach does not require complex chemical procedures. Interestingly, it can be easily adapted to different enzyme-peptide partners and therefore is very attractive for tissue replacement, drug delivery and biosensing.

A dual magnetic resonance imaging/fluorescent contrast agent for Cathepsin-D detection

Currently there are no approved biomarkers for the pre-symptomatic diagnosis of Alzheimer's disease (AD). Cathepsin-D (Cat-D) is a lysosomal protease that is present at elevated levels in amyloid plaques and neurons in patients with AD and is also elevated in some cancers. We have developed a magnetic resonance imaging (MRI)/fluorescent contrast agent to detect Cat-D enzymatic activity. The purpose of this study was to investigate the cellular and tissue uptake of this MRI/fluorescent contrast agent. The agent consists of an MRI probe [DOTA-caged metal ion (Gd³⁺ or Tm³⁺)] and a fluorescent probe coupled to a cell-penetrating-peptide sequence by a Cat-D recognition site. The relaxivity of Gd³⁺-DOTA-CAT(cleaved) was measured in 10% heat-treated bovine serum albumin (BSA) phantoms to assess contrast efficacy at magnetic fields ranging from 0.24 mT to 9.4 T. In vitro, Tm³⁺-DOTA-CAT was added to neuronal SN56 cells over-expressing Cat-D and live-cell confocal microscropy was performed at 30 min. Tm³⁺-DOTA-CAT was also intravenously injected into APP/PS1-dE9 Alzheimer's disease mice (n = 9) and controls (n = 8). Cortical and hippocampal uptake was quantified at 30, 60 and 120 min post-injection using confocal microscopy. The liver and kidneys were also evaluated for contrast agent uptake. The relaxivity of Gd³⁺-DOTA-CAT(cleaved) was 3.3 (mM s)⁻¹ in 10% BSA at 9.4 T. In vitro, cells over-expressing Cat-D preferentially took up the contrast agent in a concentration-dependent manner. In vivo, the contrast agent effectively crossed the blood-brain barrier and exhibited a distinct time course of uptake and retention in APP/PS1-dE9 transgenic mice compared with age-matched controls. At clinical and high magnetic field strengths, Gd³⁺-DOTA-CAT produced greater T₁ relaxivity than Gd³⁺-DTPA. Tm³⁺-DOTA-CAT was taken up in a dose-dependent manner in cells over-expressing Cathepsin-D and was shown to transit the blood-brain barrier in vivo. This strategy may be useful for the in vivo detection of enzyme activity and for the diagnosis of Alzheimer's disease.

Molecular imaging of Cathepsin E-positive tumors in mice using a novel protease-activatable fluorescent probe

The purpose of this study is to demonstrate the ability of imaging Cathepsin E (Cath E) positive tumors in living animals through selective targeting of Cath E proteolytic activity using a sensitive molecular imaging agent.

METHODS

A peptide-based Cath E imaging probe and a control probe were synthesized for this study. Human Cath E-positive cancer cells (MPanc96-E) were implanted subcutaneously in nude mice. Tumor-bearing mice were examined in vivo with near-infrared fluorescence (NIRF) imaging at various time points after intravenous injection of the Cath E sensing imaging probe. Excised organs and tissues of interest were further imaged ex vivo.

RESULTS

Upon specific Cath E proteolytic activation, the NIRF signal of the imaging probe a was converted from an optically quenched initial state to a highly fluorescent active state. Imaging probe a was able to highlight the Cath E-positive tumors as early as 24 h post injection. Fluorescent signal in tumor was 3-fold higher than background. The confined specificity of imaging probe a to tumor associated Cath E was verified by using control imaging probe b. Both in vivo and ex vivo imaging results confirmed the superior selectivity and sensitivity of imaging probe a in Cath E imaging.

CONCLUSIONS

The small animal studies demonstrated the capability of probe a for imaging Cath E-positive tumors. The developed optical probe could be applied in early diagnostic imaging and guiding subsequent surgical procedure.

Selective detection of Cathepsin E proteolytic activity

BACKGROUND

Aspartic proteases Cathepsin (Cath) E and D are two different proteases, but they share many common characteristics, including molecular weight, catalytic mechanism, substrate preferences, proteolytic conditions and inhibition susceptibility. To define the biological roles of these proteases, it is necessary to elucidate their substrate specificity. In the present study, we report a new peptide-substrate that is only sensitive to Cath E but not Cath D.

METHODS

Substrate e, Mca-Ala-Gly-Phe-Ser-Leu-Pro-Ala-Lys(Dnp)-DArg-CONH₂, designed in such a way that due to the close proximity of a Mca-donor and a Dnp-acceptor, near complete intramolecular quenching effect was achieved in its intact state. After the proteolytic cleavage of the hydrophobic motif of peptide substrate, both Mca and Dnp would be further apart, resulting in bright fluorescence.

RESULTS

Substrate e showed a 265 fold difference in the net fluorescence signals between Cath E and D. This Cath E selectivity was established by having -Leu**Pro- residues at the scissile peptide bond. The confined cleavage site of substrate e was confirmed by LC-MS. The catalytic efficiency (K(cat)/K(M)) of Cath E for substrate e was 16.7 μM⁻¹S⁻¹. No measurable catalytic efficiency was observed using Cath D and no detectable fluorescent changes when incubated with Cath S and Cath B.

CONCLUSIONS

This study demonstrated the promise of using the developed fluorogenic substrate e as a selective probe for Cath E proteolytic activity measurement.

GENERAL SIGNIFICANCE

This study forms the foundation of Cath E specific inhibitor development in further studies.

Quantitative determination and localization of cathepsin D and its inhibitors

A literature survey was performed of the methods of quantitative assessment of the activity and concentration of cathepsin D and its inhibitors. Usefulness of non-modified and modified proteins and synthetic peptides as measurement substrates was evaluated. The survey includes also chemical and immunochemical methods used to determine the distribution of cathepsin D and its inhibitors in cells and tissues.

A new approach for distinguishing cathepsin E and D activity in antigen-processing organelles

Cathepsin E (CatE) and D (CatD) are the major aspartic proteinases in the endolysosomal pathway. They have similar specificity and therefore it is difficult to distinguish between them, as known substrates are not exclusively specific for one or the other. In this paper we present a substrate-based assay, which is highly relevant for immunological investigations because it detects both CatE and CatD in antigen-processing organelles. Therefore it could be used to study the involvement of these proteinases in protein degradation and the processing of invariant chain. An assay combining a new monospecific CatE antibody and the substrate, MOCAc-Gly-Lys-Pro-Ile-Leu-Phe-Phe-Arg-Leu-Lys(Dnp)-D-Arg-NH2[where MOCAc is (7-methoxycoumarin-4-yl)acetyl and Dnp is dinitrophenyl], is presented. This substrate is digested by both proteinases and therefore can be used to detect total aspartic proteinase activity in biological samples. After depletion of CatE by immunoprecipitation, the remaining activity is due to CatD, and the decrease in activity can be assigned to CatE. The activity of CatE and CatD in cytosolic, endosomal and lysosomal fractions of B cells, dendritic cells and human keratinocytes was determined. The data clearly indicate that CatE activity is mainly located in endosomal compartments, and that of CatD in lysosomal compartments. Hence this assay can also be used to characterize subcellular fractions using CatE as an endosomal marker, whereas CatD is a well-known lysosomal marker. The highest total aspartic proteinase activity was detected in dendritic cells, and the lowest in B cells. The assay presented exhibits a lower detection limit than common antibody-based methods without lacking the specificity.

Muropeptide modification-amidation of peptidoglycan D-glutamate does not affect the proinflammatory activity of Staphylococcus aureus

Peptidoglycan muropeptides, potent proinflammatory components, are amidated in Staphylococcus aureus for unknown reasons. To study whether this modification may modulate proinflammatory capacity, cytokine induction by isogenic S. aureus strains with different amidation levels and by synthetic amidated/nonamidated muramyldipeptides was evaluated. However, amidation did not significantly affect cytokine induction. This finding contributes to defining peptidoglycan receptor specificities and indicates that further rationales for muropeptide amidation have to be considered.

A Targeted Protease Substrate for a Quantitative Determination of Protease Activities in the Endolysosomal Pathway

Inside the cell, proteases act in concert in the degradation of proteins and peptides. In order to understand the significance of an individual proteolytic activity within an ensemble of proteases, protocols and probes are required that enable a quantitative determination of the contribution of a protease to the break-down of a given substrate. Here we present a fluorescence resonance energy transfer-based probe and protocols for a quantitative determination of proteolytic activities inside the endolysosomal compartment. A peptide substrate that is readily cleaved by different cathepsins is flanked by fluorescein and tetramethylrhodamine-labeled lysine residues. Efficient endolysosomal targeting of the substrate is achieved by N-terminal elongation with the cell-penetrating peptide nona-arginine. The proteasome inhibitor lactacystin has a small, but significant effect on the break-down of the substrate, thus demonstrating that only a minor fraction of the peptide reaches the cytoplasm in its intact form. Nona-arginine therefore constitutes a highly efficient low-molecular-weight moiety for targeting the endolysosomal compartment.

Cathepsin D is present in human eccrine sweat and involved in the postsecretory processing of the antimicrobial peptide DCD-1L

The protein pattern of healthy human eccrine sweat was investigated and 10 major proteins were detected from which apolipoprotein D, lipophilin B, and cathepsin D (CatD) were identified for the first time in human eccrine sweat. We focused our studies on the function of the aspartate protease CatD in sweat. In vitro digestion experiments using a specific fluorescent CatD substrate showed that CatD is enzymatically active in human sweat. To identify potential substrates of CatD in human eccrine sweat LL-37 and DCD-1L, two antimicrobial peptides present in sweat, were digested in vitro with purified CatD. LL-37 was not significantly digested by CatD, whereas DCD-1L was cleaved between Leu(44) and Asp(45) and between Leu(29) and Glu(30) almost completely. The DCD-1L-derived peptides generated in vitro by CatD were also found in vivo in human sweat as determined by surface-enhanced laser desorption/ionization (SELDI) mass spectrometry. Furthermore, besides the CatD-processed peptides we identified additionally DCD-1L-derived peptides that are generated upon cleavage with a 1,10-phenanthroline-sensitive carboxypeptidase and an endoprotease. Taken together, proteolytic processing generates 12 DCD-1L-derived peptides. To elucidate the functional significance of postsecretory processing the antimicrobial activity of three CatD-processed DCD-1L peptides was tested. Whereas two of these peptides showed no activity against Gram-positive and Gram-negative bacteria, one DCD-1L-derived peptide showed an even higher activity against Escherichia coli than DCD-1L. Functional analysis indicated that proteolytic processing of DCD-1L by CatD in human sweat modulates the innate immune defense of human skin.