Protein Function In Living Cells Research Articles

Genetically Encoded Lysine Analogues with Differential Light Sensitivity for Activation of Protein Function

AbstractGenetically encoded unnatural amino acids are versatile tools for controlling protein function, but options for regulating multiple proteins in a single experiment are limited. Here, we report the genetic encoding of two new photocaged lysine derivatives, 1‐(2‐nitrophenyl)‐ethyl lysine and nitrodibenzylfuranyl lysine, for sequential light‐activation of protein function in live cells. Nitrodibenzylfuranyl (NDBF) caging groups have a redshifted absorbance maximum and high sensitivity to light compared to the 1‐(2‐nitrophenyl)‐ethyl group (NPE), enabling selective decaging and protein activation. We characterized the responses of these new caged amino acids by optically triggering nuclear localization and firefly luciferase activity. The ability to selectively activate distinct proteins through simple light titration makes this a useful approach with broad applications.

Tethering-based chemogenetic approaches for the modulation of protein function in live cells.

Proteins are the workhorse molecules performing various tasks to sustain life. To investigate the roles of a protein under physiological conditions, the rapid modulation of the protein with high specificity in a living system would be ideal, but achieving this is often challenging. To address this challenge, researchers have developed chemogenetic strategies for the rapid and selective modulation of protein function in live cells. Here, the target protein is modified genetically to become sensitive to a designer molecule that otherwise has no effect on other cellular biomolecules. One powerful chemogenetic strategy is to introduce a tethering point into the target protein, allowing covalent or non-covalent attachment of the designer molecule. In this tutorial review, we focus on tethering-based chemogenetic approaches for modulating protein function in live cells. We first describe genetic, optogenetic and chemical means to study protein function. These means lay the basis for the chemogenetic concept, which is explained in detail. The next section gives an overview, including advantages and limitations, of tethering tactics that have been employed for modulating cellular protein function. The third section provides examples of the modulation of cell-surface proteins using tethering-based chemogenetics through non-covalent tethering and covalent tethering for irreversible modulation or functional switching. The fourth section presents intracellular examples. The last section summarizes key considerations in implementing tethering-based chemogenetics and shows perspectives highlighting future directions and other applications of this burgeoning research field.

Affinity Conjugation for Rapid and Covalent Labeling of Proteins in Live Cells.

Protein labeling is enormously useful for characterization of protein function in live cells and study of the related cellular processes. Covalent labeling of protein using affinity conjugation confers stable and selective labeling of protein in cells. Affinity conjugation combines a specific ligand-protein interaction with a proximity-induced reaction to selectively label the protein of interest (POI) in the cell. Therefore, either a fluorogenic probe is directly introduced to the POI or a bioorthogonal group is incorporated to the POI, which is subsequently labeled with a fluorescent probe. Here, we describe a method for affinity conjugation of protein with a fluorogenic probe and a "tagging-then-labeling" approach by a combination of affinity conjugation with bioorthogonal reactions.

Genetically Encoded Optochemical Probes for Simultaneous Fluorescence Reporting and Light Activation of Protein Function with Two-Photon Excitation

The site-specific incorporation of three new coumarin lysine analogues into proteins was achieved in bacterial and mammalian cells using an engineered pyrrolysyl-tRNA synthetase system. The genetically encoded coumarin lysines were successfully applied as fluorescent cellular probes for protein localization and for the optical activation of protein function. As a proof-of-principle, photoregulation of firefly luciferase was achieved in live cells by caging a key lysine residue, and excellent OFF to ON light-switching ratios were observed. Furthermore, two-photon and single-photon optochemical control of EGFP maturation was demonstrated, enabling the use of different, potentially orthogonal excitation wavelengths (365, 405, and 760 nm) for the sequential activation of protein function in live cells. These results demonstrate that coumarin lysines are a new and valuable class of optical probes that can be used for the investigation and regulation of protein structure, dynamics, function, and localization in live cells. The small size of coumarin, the site-specific incorporation, the application as both a light-activated caging group and as a fluorescent probe, and the broad range of excitation wavelengths are advantageous over other genetically encoded photocontrol systems and provide a precise and multifunctional tool for cellular biology.

A bioorthogonal small-molecule-switch system for controlling protein function in live cells.

Chemically induced dimerization (CID) has proven to be a powerful tool for modulating protein interactions. However, the traditional dimerizer rapamycin has limitations in certain in vivo applications because of its slow reversibility and its affinity for endogenous proteins. Described herein is a bioorthogonal system for rapidly reversible CID. A novel dimerizer with synthetic ligand of FKBP' (SLF') linked to trimethoprim (TMP). The SLF' moiety binds to the F36V mutant of FK506-binding protein (FKBP) and the TMP moiety binds to E. coli dihydrofolate reductase (eDHFR). SLF'-TMP-induced heterodimerization of FKBP(F36V) and eDHFR with a dissociation constant of 0.12 μM. Addition of TMP alone was sufficient to rapidly disrupt this heterodimerization. Two examples are presented to demonstrate that this system is an invaluable tool, which can be widely used to rapidly and reversibly control protein function in vivo.

Effects Of Reactive Oxygen Species On Cyan Fluorescent Protein

Recent advances in microscopy techniques and the development of many different colour variants of the GFP family of proteins allow for a more direct analysis of protein function in live cells. The advantage of genetically coded fluorescent protein probes is often offset by their photophysical properties which usually make them very sensitive to cellular environmental changes.Among these, reactive oxygen species (ROS) are an essential part of key cellular processes (mitochondria respiration, apoptosis) and are also involved in the pathogenesis of various diseases (cancer, atherosclerosis, Alzheimer's disease, etc.). We studied the effects of ROS on the cyan fluorescent protein (CFP) in vitro, as this fluorescent protein is currently one of the most widely used in protein interaction studies. We studied the fluorescence and absorption changes of recombinant CFP protein using γ-radiolysis for ROS production. γ-radiolysis ROS production allowed us to have an exact control over the radical concentrations delivered unto the protein samples. The radicals used in this study were OH°, O2− or a mixture of OH° and O2−. We also determined the chemical modifications that take place upon ROS induced protein oxidation by mass spectrometry. We show that the targets of oxidation are one tyrosine and four methionine residues located on the protein surface and that the chromophore is not likely modified through these oxidation processes.

Labeling of fusion proteins with synthetic fluorophores in live cells.

A general approach for the sequential labeling of fusion proteins of O(6)-alkylguanine-DNA alkyltransferase (AGT) with different fluorophores in mammalian cells is presented. AGT fusion proteins with different localizations in the cell can be labeled specifically with different fluorophores, and the fluorescence labeling can be used for applications such as multicolor analysis of dynamic processes and fluorescence resonance energy transfer measurements. The facile access to a variety of different AGT substrates as well as the specificity of the labeling reaction should make the approach an important tool to study protein function in live cells.