1.5 Proteinanalytik
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Erscheinungsjahr
- 2019 (4) (entfernen)
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- Englisch (4)
Schlagworte
- Mass spectrometry (2)
- Peptide library (2)
- Array (1)
- Binder (1)
- Biochip (1)
- Collision induced dissociation (CID) (1)
- Combinatorial chemistry (1)
- Combinatorial polymer libraries (1)
- Combinatorial screening (1)
- Conjugates (1)
Organisationseinheit der BAM
Screening of one-bead-one-compound (OBOC) libraries is a proven procedure for the identification of protein-binding ligands. The demand for binders with high affinity and specificity towards various targets has surged in the biomedical and pharmaceutical field in recent years. The traditional peptide screening involves tedious steps such as affinity selection, bead picking, sequencing, and characterization. Herein, we present a high-throughput “all-on-one chip” system to avoid slow and technically complex bead picking steps. On a traditional glass slide provided with an electrically conductive tape, beads of a combinatorial peptide library are aligned and immobilized by application of a precision sieve. Subsequently, the chip is incubated with a fluorophore-labeled target protein. In a fluorescence scan followed by matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry, high-affinity binders are directly and unambiguously sequenced with high accuracy without picking of the positive beads. The use of an optimized ladder sequencing approach improved the accuracy of the de-novo sequencing step to nearly 100%. The new technique was validated by employing a FLAG-based model system, identifying new peptide binders for the monoclonal M2 anti-FLAG antibody, and was finally utilized to search for IgG-binding peptides. In the present format, more than 30,000 beads can be screened on one slide.
Screening of one-bead-one-peptide libraries is a powerful analytical tool for the identification of protein ligands. However, the traditional peptide screening procedure involves tedious steps such as manual selection, sequencing, and characterization. We present a high-throughput “all in one chip” system, allowing the screening of a high number of resin beads in short time. Here, beads of a combinatorial one-bead one compound peptide library are immobilized on an in-house produced chip, on which every bead has a well-defined position. The chip is then incubated with a fluorophore-labeled protein, identifying suitable peptides by a high-resolution fluorescence scan. The screening is followed by MALDI-MS experiments directly on the respective glass chip. To circumvent the need for peptide fragmentation normally used for peptide de novo sequencing, which can result in incomplete sequence information, an approach based on ladder sequencing has been used. This allows the peptide sequence identification by fragmentation-free MS with almost 100 % accuracy. For this purpose, a software tool was developed automatically translating MALDI-MS spectra into the corresponding peptide sequences.
DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences – bearing mismatch positions and abasic sites of complementary DNA 15-mers – were investigated to unravel general trends in their stability in the gas phase. Single stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.
Functional sequences of precision polymers based on thiolactone/Michael chemistry are identified from a large one-bead one-compound library. Single-bead readout by MALDI-TOF MS/MS identifies sequences that host m-THPC that is a second Generation photo-sensitizer drug. The corresponding Tla/Michael-PEG conjugates make m-THPC available in solution and drug payload as well as drug release kinetics can be fine-tuned by the precision segment.