An In-Cell Fluorogenic Tag–Probe System for Protein Dynamics Imaging Enabled by Cell-Penetrating Peptides

Orthogonal Versatile Interacting Peptide Tags for Imaging Cellular Proteins

Genetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a protein's behavior in situ. Some proteins can be analyzed by fusion to a protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here, we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in cells. Labeling is mediated by the formation of a high-affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific for one- or two-color imaging. Last, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin) in fixed cells, highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.

Amine-incorporated quinoxaline based fluorescent sensor for detection of trace water: Solvent influenced self-assembly

Polarity is a complex parameter, with important effect in chemistry and biology. In recent years, polarity exploration attracted more and more attention hence, it's of great importance to exploit new methods for polarity determination. A novel class of long, coplanar, and amine incorporated electron-rich quinoxaline scaffold(L₁) furnished maximum solvatochromic effect and large Stokes shift and was chosen to determine water content in organic solvents e.g. acetonitrile, THF, DMF, and methanol through fluorescence spectroscopy. Moreover, the probe was found to perform as an effective fluorescent sensor for the quantitative detection of low-level moisture content in four commonly-used organic solvents with low detection limits (0.018%, 0.027%, 0.012%, and 0.43% respectively). This study also describes the morphological transformation of L₁ form a fibrous network to spherical aggregates upon increasing water content in several organic solvents. Real-life implementation of the probe was successfully employed for the detection of moisture content in commercial food products and building materials such as cement, sand, limestone, salt, wheat, and detergent powder. Furthermore, probe L₁-immersed easy-to-prepare test strips provide a reliable approach for qualitative monitoring of water content in organic solvents by a simple color-changing method under UV irradiation via smartphone-assisted RGB analysis.

Live-cell imaging of membrane proteins by a coiled-coil labeling method-Principles and applications

In situ investigations in living cell membranes are important to elucidate the dynamic behaviors of membrane proteins in complex biomembrane environments. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence imaging. The use of post-translational labeling methods using a genetically encodable tag and synthetic probes targeting the tag offer a smaller label size, labeling with synthetic fluorophores, and precise control of the labeling ratio in multicolor labeling compared with conventional genetic fusions with fluorescent proteins. This review focuses on tag-probe labeling studies for live-cell analysis of membrane proteins based on heterodimeric peptide pairs that form coiled-coil structures. The robust and simple peptide-peptide interaction enables not only labeling of membrane proteins by noncovalent interactions, but also covalent crosslinking and acyl transfer reactions guided by coiled-coil assembly. A number of studies have demonstrated that membrane protein behaviors in live cells, such as internalization of receptors and the oligomeric states of various membrane proteins (G-protein-coupled receptors, epidermal growth factor receptors, influenza A M2 channel, and glycopholin A), can be precisely analyzed using coiled-coil labeling, indicating the potential of this labeling method in membrane protein research.

Development of Toolboxes for Precision Genome/Epigenome Editing and Imaging of Epigenetics

Zinc finger (ZF) proteins are composed of repeated ββα modules and coordinate a zinc ion. ZF domains recognizing specific DNA target sequences can be substituted for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methyltransferases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the CRISPR-Cas9 system has expanded the range of possibilities for genome-editing technologies. In addition, these DNA binding domains can also be utilized to build a toolbox for epigenetic controls by fusing them with protein- or DNA-modifying enzymes. Here, our research on epigenome editing including the development of artificial zinc finger recombinase (ZFR), split DNA methyltransferase, and fluorescence imaging of histone proteins by ZIP tag-probe system is introduced. Advances in the ZF, TALE, and CRISPR-Cas9 platforms have paved the way for the next generation of genome/epigenome engineering approaches.

Novel polyethyleneimine-R8-heparin nanogel for high-efficiency gene delivery in vitro and in vivo

Gene therapy is an efficient and promising approach to treat malignant tumors. However, protecting the nucleic acid from degradation in vivo and efficient delivering it into tumor cells remain challenges that require to be addressed before gene therapy could be applied in clinic. In this study, we prepared novel polyethyleneimine-RRRRRRRR(R8)-heparin (HPR) nanogel as an efficient gene delivery system, which consists of heparin and cell penetrating peptide R8 grafted low-molecule-weight polyethyleneimine (PEI). Due to the shielding effect of heparin, crosslinking PEI-R8 with heparin was designed to diminish the toxicity of the gene delivery system. Meanwhile, a partial of R8 peptide which located on the surface of HPR nanogel could significantly enhance the cellular uptake. The formed HPR/pDNA complex exhibited effective endolysosomal escape, resulting in a high-efficiency transfection. Furthermore, the HPR could deliver the plasmid which could transcribe human TNF-related apoptosis inducing ligand (phTRAIL), into HCT-116 cells and induce significant cell apoptosis. In addition, HPR/phTRAIL complex showed satisfactory antitumor activity in abdominal metastatic colon carcinoma model. Finally, the antitumor mechanism of HPR/phTRAIL was also explored by western blot and histological analysis. The above results suggested that the HPR nanogel could serve as a promising gene delivery system.

Creation of Functional Molecules Based on Biomolecular Interactions; Development toward Chemical Biology

Interactions between bio-macromolecules such as proteins, DNA, and polysaccharides play pivotal roles in maintaining homeostasis in living systems. For elucidating the function of biomolecules, peptides are powerful tools, compared to native proteins, because of their lower molecular weights, compatibility with chemical modification, and predictability of interaction with the target molecules. These advantages enabled us to develop peptide-based functional molecules. However, for the purposes of controlling or regulating biomolecule functions, designing artificial proteins is also an effective approach. Not only rational protein design, but also directed molecular evolution, are now regarded as powerful methods for optimizing protein function. The interactions of proteins with bio-macromolecules are usually highly specific and show high affinity because of larger interaction surfaces as compared to small molecules or peptides. Thus, the use of proteins for designing biofunctional molecules is also important for wider applications in the biotechnology field. In this review, four topics will be discussed: 1) the development of fluorescently-labeled ligands for G protein-coupled receptors (GPCR), as well as bivalent ligands for GPCR imaging and function analysis, 2) the design and synthesis of gp41 trimer mimics as HIV-1 inhibitors or vaccines, 3) the development of a ZIP tag-probe system and its application to intracellular protein imaging, and 4) the functional analysis of sequence-specific DNA recombinase for expanding the scope of genome editing. The results of these studies indicate the importance of precision in the design of peptides or proteins for regulating bio-macromolecular interactions.

Current Understanding of Direct Translocation of Arginine-Rich Cell-Penetrating Peptides and Its Internalization Mechanisms

Arginine-rich cell-penetrating peptides (CPPs) including Tat, Penetratin and oligoarginine peptides are a series of short peptides that can be efficiently internalized into cells and have been widely used as carriers for intracellular delivery of bioactive molecules. In the early phase of the study, CPPs, as well as their conjugates, were thought to rapidly enter cells by direct penetration through membranes, which was later found to be an experimental artifact that was concluded from observations in fixed cells. Although re-evaluation using living unfixed cells revealed that endocytosis has a major role in internalization of these peptides, there are a number of studies reporting that, even if fixation is avoided, direct translocation across plasma membranes and cytosolic distribution of arginine-rich CPPs are still observed in cells without membrane perturbation. In addition, amphiphilic counteranions such as pyrenebutyrate dramatically accelerate direct translocation of these peptides into cells. These results suggest that there are at least two pathways, i.e., endocytosis and direct translocation, both of which would contribute to cellular internalization of arginine-rich CPPs. In this review, we first introduce the story of fixation artifact, which indeed led to the critical progress in CPP study, and then summarize the current understanding for direct translocation of arginine-rich CPPs. Comprehensive understanding of direct translocation of these peptides and its mechanistic elucidation would provide useful knowledge for developing methodologies that would enable efficient intracellular delivery.

Peptide-tags for site-specific protein labelling in vitro and in vivo

Peptide-tag based labelling can be achieved by (i) enzymes (ii) recognition of metal ions or small molecules and (iii) peptide–peptide interactions and enables site-specific protein visualization to investigate protein localization and trafficking.