Use of intein-mediated protein ligation strategies for the fabrication of functional protein arrays

Chemical synthesis of proteins using N-sulfanylethylanilide peptides, based on N-S acyl transfer chemistry

Native chemical ligation (NCL), which features the use of peptide thioesters, is among the most reliable ligation protocols in chemical protein synthesis. Thioesters have conventionally been synthesized using tert-butyloxycarbonyl (Boc)-based solid-phase peptide synthesis (SPPS); however, the increasing use of 9-fluorenylmethyloxycarbonyl (Fmoc) SPPS requires an efficient preparative protocol for thioesters which is fully compatible with Fmoc chemistry. We have addressed this issue by mimicking the naturally occurring thioester-forming step seen in intein-mediated protein splicing of the intein-extein system, using an appropriate chemical device to induce N-S acyl transfer reaction, avoiding the problems associated with Fmoc strategies. We have developed N-sulfanylethylanilide (SEAlide) peptides, which can be synthesized by standard Fmoc SPPS and converted to the corresponding thioesters through treatment under acidic conditions. Extensive examination of SEAlide peptides showed that the amide-type SEAlide peptides can be directly and efficiently involved in NCL via thioester species in the presence of phosphate salts, even under neutral conditions. The presence or absence of phosphate salts provided kinetically controllable chemoselectivity in NCL for SEAlide peptides. This allowed SEAlide peptides to be used in both one-pot/N-to-C-directed sequential NCL under kinetically controlled conditions, and the convergent coupling of large peptide fragments, which facilitated the chemical synthesis of proteins over about 100 residues. The use of SEAlide peptides, enabling sequential NCL operated under kinetically controlled conditions, and the convergent coupling, were used for the total chemical synthesis of a 162-residue monoglycosylated GM2-activator protein (GM2AP) analog.

Semi-synthesis of labeled proteins for spectroscopic applications

Since the introduction of SPPS by Merrifield in the 60s, peptide chemists have considered the possibility of preparing large proteins. The introduction of native chemical ligation in the 90s and then of expressed protein ligation have opened the way to the preparation of synthetic proteins without size limitations. This review focuses on semi-synthetic strategies useful to prepare proteins decorated with spectroscopic probes, like fluorescent labels and stable isotopes, and their biophysical applications. We show that expressed protein ligation, combining the advantages of organic chemistry with the easy and size limitless recombinant protein expression, is an excellent strategy for the chemical synthesis of labeled proteins, enabling a single protein to be functionalized at one or even more distinct positions with different probes.

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR.

Diverse organo-peptide macrocycles via a fast and catalyst-free oxime/intein-mediated dual ligation

Macrocyclic Organo-Peptide Hybrids (MOrPHs) can be prepared from genetically encoded polypeptides via a chemoselective and catalyst-free reaction between a trifunctional oxyamino/amino-thiol synthetic precursor and an intein-fusion protein incorporating a bioorthogonal keto group.

Selective and direct immobilization of cysteinyl biomolecules by electrochemical cleavage of azo linkage

Controlled orientation and reserved activity of biomolecules, when site-selectively immobilized in a highly integrated manner on a minimal time scale, are crucial in designing biosensors for the multiplex detection. Here, we describe a novel method for the orientation-controlled immobilization of biomolecules based on site-selective electrochemical activation of p-hydroxyazobenzene self-assembled monolayer (SAM) followed by one-step coupling of cysteinyl biomolecules. The p-aminophenol, a product of reductive cleavage of p-hydroxyazobenzene, was subsequently oxidized to yield p-quinoneimine which then conjugated with cysteinyl biomolecules through 1,4-Michael addition, thus obviating additional linker agents and the related time consumption. Using this method, we selectively activated the electrode surface and immobilized laminin peptide IKVAV, a neurite promoting motif. When we cultured hippocampal neurons on the electrode, the extended neurites were found only within the electrochemically activated area. Hence, the proposed method represents a new promising platform for the patterning of functional peptides, active proteins, and live cells.