SLAP: Small Labeling Pair for Single‐Molecule Super‐Resolution Imaging

Protein labeling with synthetic fluorescent probes is a key technology in chemical biology and biomedical research. A sensitive and efficient modular labeling approach (SLAP) was developed on the basis of a synthetic small‐molecule recognition unit (Ni‐trisNTA) and the genetically encoded minimal protein His_6‐10‐tag. High‐density protein tracing by SLAP was demonstrated. This technique allows super‐resolution fluorescence imaging and fulfills the necessary sampling criteria for single‐molecule localization‐based imaging techniques. It avoids masking by large probes, for example, antibodies, and supplies sensitive, precise, and robust size analysis of protein clusters (nanodomains).     

The Scaffold Design of Trivalent Chelator Heads Dictates Affinity and Stability for Labeling His‐tagged Proteins in vitro and in Cells

Small chemical/biological interaction pairs are at the forefront in tracing protein function and interaction at high signal‐to‐background ratios in cellular pathways. However, the optimal design of scaffold, linker, and chelator head still deserve systematic investigation to achieve the highest affinity and kinetic stability for in vitro and especially cellular applications. We report on a library of N‐nitrilotriacetic acid (NTA)‐based multivalent chelator heads (MCHs) built on linear, cyclic, and dendritic scaffolds and compare these with regard to their binding affinity and stability for the labeling of cellular His‐tagged proteins. Furthermore, we describe a new approach for tracing cellular target proteins at picomolar probe concentrations in cells. Finally, we outline fundamental differences between the MCH scaffolds and define a cyclic trisNTA chelator that displays the highest affinity and kinetic stability of all reported reversible, low‐molecular‐weight interaction pairs.     

Make them Blink: Probes for Super‐Resolution Microscopy

In recent years, a number of approaches have emerged that enable far‐field fluorescence imaging beyond the diffraction limit of light, namely super‐resolution microscopy. These techniques are beginning to profoundly alter our abilities to look at biological structures and dynamics and are bound to spread into conventional biological laboratories. Nowadays these approaches can be divided into two categories, one based on targeted switching and readout, and the other based on stochastic switching and readout of the fluorescence information. The main prerequisite for a successful implementation of both categories is the ability to prepare the fluorescent emitters in two distinct states, a bright and a dark state. Herein, we provide an overview of recent developments in super‐resolution microscopy techniques and outline the special requirements for the fluorescent probes used. In combination with the advances in understanding the photophysics and photochemistry of single fluorophores, we demonstrate how essentially any single‐molecule compatible fluorophore can be used for super‐resolution microscopy. We present examples for super‐resolution microscopy with standard organic fluorophores, discuss factors that influence resolution and present approaches for calibration samples for super‐resolution microscopes including AFM‐based single‐molecule assembly and DNA origami.     

Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria

Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.     

High‐Fidelity Protein Targeting into Membrane Lipid Microdomains in Living Cells

Lipid analogues carrying three nitrilotriacetic acid (tris‐NTA) head groups were developed for the selective targeting of His‐tagged proteins into liquid ordered (l_o) or liquid disordered (l_d) lipid phases. Strong partitioning into the l_o phase of His‐tagged proteins bound to tris‐NTA conjugated to saturated alkyl chains (tris‐NTA DODA) was achieved, while tris‐NTA conjugated to an unsaturated alkyl chain (tris‐NTA SOA) predominantly resided in the l_d phase. Interestingly, His‐tag‐mediated lipid crosslinking turned out to be required for efficient targeting into the l_o phase by tris‐NTA DODA. Robust partitioning into l_o phases was confirmed by using viral lipid mixtures and giant plasma membrane vesicles. Moreover, efficient protein targeting into l_o and l_d domains within the plasma membrane of living cells was demonstrated by single‐molecule tracking, thus establishing a highly generic approach for exploring lipid microdomains in situ.     

New Tris(hydroxypyridinones) as Iron and Aluminium Sequestering Agents: Synthesis,Complexation and In Vivo Studies

Two new tripodal tris(3‐hydroxy‐4‐pyridinone) hexadentate chelators—NTA(BuHP)₃ and NTP(PrHP)₃ (NTA=nitrilotriacetic acid, NTP=nitrilotripropionic acid, HP=hydroxypyridone)—have been developed and studied in solution for their iron and aluminium binding affinity, and also assayed in vivo for their capacity to remove metal from an animal model that is overloaded. These chelators are positional isomers, possessing identical general structures based on aminotricarboxylic acid skeletons attached to three bidentate 3‐hydroxy‐4‐pyridinones (3,4‐HPs), but differing in the position of the amide linkage along the chelating “arm”. In spite of expected differences in the tripodal ligands, such as acidity and hydrogen‐bonding networks, they share important properties, namely, a mild hydrophilic character (log P ca. ?1.2 to ?1.4) and a strong chelating affinity for Fe and Al (pFe=27.9 and pAl=22.0 for NTA(BuHP)₃; pFe=29.4 and pAl=22.4 for NTP(PrHP)₃). They also evidenced identical effects on the biodistribution and on the excretion of a radiotracer (⁶⁷Ga) previously administered to mice, as models of iron overload animals. Comparison of the new compounds with reported analogues shows good improvement in terms of solution and in vivo sequestering properties, thus giving support to expectations about their potential clinical application as metal removal agents.     

Single‐Molecule Localization Microscopy using mCherry

We demonstrate the potential of the commonly used red fluorescent protein mCherry for single‐molecule super‐resolution imaging. mCherry can be driven into a light‐induced dark state in the presence of a thiol from which it can recover spontaneously or by irradiation with near UV light. We show imaging of subcellular protein structures such as microtubules and the nuclear pore complex with a resolution below 40 nm. We were able to image the C‐terminus of the nuclear pore protein POM121, which is on the inside of the pore and not readily accessible for external labeling. The photon yield for mCherry is comparable to that of the latest optical highlighter fluorescent proteins. Our findings show that the widely used mCherry red fluorescent protein and the vast number of existing mCherry fusion proteins are readily amenable to super‐resolution imaging. This obviates the need for generating novel protein fusions that may compromise function or the need for external fluorescent labeling.     

A De Novo Designed Metalloenzyme for the Hydration of CO2

Protein design will ultimately allow for the creation of artificial enzymes with novel functions and unprecedented stability. To test our current mastery of nature’s approach to catalysis, a Zn^II metalloenzyme was prepared using de novo design. α₃DH₃ folds into a stable single‐stranded three‐helix bundle and binds Zn^II with high affinity using His₃O coordination. The resulting metalloenzyme catalyzes the hydration of CO₂ better than any small molecule model of carbonic anhydrase and with an efficiency within 1400‐fold of the fastest carbonic anhydrase isoform, CAII, and 11‐fold of CAIII.     

In‐Situ Spin Labeling of His‐Tagged Proteins: Distance Measurements under In‐Cell Conditions

New spin labeling strategies have immense potential in studying protein structure and dynamics under physiological conditions with electron paramagnetic resonance (EPR) spectroscopy. Here, a new spin‐labeled chemical recognition unit for switchable and concomitantly high affinity binding to His‐tagged proteins was synthesized. In combination with an orthogonal site‐directed spin label, this novel spin probe, Proxyl‐trisNTA (P‐trisNTA) allows the extraction of structural constraints within proteins and macromolecular complexes by EPR. By using the multisubunit maltose import system of E. coli: 1) the topology of the substrate‐binding protein, 2) its substrate‐dependent conformational change, and 3) the formation of the membrane multiprotein complex can be extracted. Notably, the same distance information was retrieved both in vitro and in situ allowing for site‐specific spin labeling in cell lysates under in‐cell conditions. This approach will open new avenues towards in‐cell EPR.     

Reversibly Triggered Protein–Ligand Assemblies in Giant Vesicles

External small‐molecule triggers were used to reversibly control dynamic protein–ligand interactions in giant vesicles. An alcohol dehydrogenase was employed to increase or decrease the interior pH upon conversion of two different small‐molecule substrates, thereby modulating the pH‐sensitive interaction between a Ni‐NTA ligand on the vesicle membrane and an oligohistidine‐tagged protein in the lumen. By alternating the small‐molecule substrates the interaction could be reversed.     

Visible‐light‐driven self‐cleaning SERS substrate of silver nanoparticles and graphene oxide decorated nitrogen‐doped titania nanotube array

Graphene oxide (GO) and silver nanoparticles (Ag NPs) sequentially decorated nitrogen‐doped titania nanotube array (N‐TiO₂ NTA) had been designed as visible‐light‐driven self‐cleaning surface‐enhanced Raman scattering (SERS) substrate for a recyclable SERS detection application. N‐TiO₂ NTA was fabricated by anodic oxidation and then doping nitrogen treatment in ammonia atmosphere, acting as a visible‐light‐driven photocatalyst and supporting substrate. Ag/GO/N‐TiO₂ NTA was prepared by decorating GO monolayer through an impregnation process and then depositing Ag NPs through a polyol process on the surface of N‐TiO₂ NTA, acting as the collection of organic molecule and Raman enhancement. The SERS activity of Ag/GO/N‐TiO₂ NTA was evaluated using methyl blue as an organic probe molecule, revealing the analytical enhancement factor of 4.54 × 10⁴. Ag/GO/N‐TiO₂ NTA was applied as active SERS substrate to determine a low‐affinity organic pollutant of bisphenol A, revealing the detection limit of as low as 5 × 10^?7 m . Ag/GO/N‐TiO₂ NTA could also achieve self‐cleaning function for a recycling utilization through visible‐light‐driven photocatalytic degradation of the adsorbed organic molecules. Ag/GO/N‐TiO₂ NTA has been successfully reused for five times without an obvious decay in accuracy and sensitivity for organic molecule detection. The unique properties of this SERS substrate enable it to have a promising application for the sensitive and recyclable SERS detection of low‐affinity organic molecules. Copyright © 2016 John Wiley & Sons, Ltd.     

Active site labeling with dansyl-glutamyl-glycyl-arginyl chloromethyl ketone demonstrates the full activity of the refolded and purified tissue-type plasminogen activator variant BM 06.022

BM 06.022 is a tissue-type plasminogen activator deletion variant that is comprised of the kringle 2 and the protease domain of the native molecule. BM 06.022 is expressed as inactive inclusion bodies inE. coli and transferred into the active enzyme by an in vitro folding process. Active site labeling with dansyl-glutamyl-glycyl-arginyl chloromethyl ketone provides evidence that the purified BM 06.022 is fully active and that misfolded species are completely removed by affinity chromatography on ETI-Sepharose. The comparison of the kinetics of the inhibition of BM 06.022 with that of CHO-t-PA indicates that the active centers of both enzymes are rather similar. The further evaluation of the site of interaction of BM 06.022 and DnsEGRck by mass spectroscopy and amino acid sequence analysis revealed that the inhibitor is bound selectively to His₃₂₂, which is part of the catalytic triad of this serine protease.     

Hydrogen‐bonding patterns in two aroylthiocarbamates and two aroylimidothiocarbonates

In O‐ethyl N‐benzoylthiocarbamate, C₁₀H₁₁NO₂S, the molecules are linked into sheets by a combination of two‐centre N—H...O and C—H...S hydrogen bonds and a three‐centre C—H...(O,S) hydrogen bond. A combination of two‐centre N—H...O and C—H...O hydrogen bonds links the molecules of O‐ethyl N‐(4‐methylbenzoyl)thiocarbamate, C₁₁H₁₃NO₂S, into chains of rings, which are linked into sheets by an aromatic π–π stacking interaction. In O,S‐diethyl N‐(4‐methylbenzoyl)imidothiocarbonate, C₁₃H₁₇NO₂S, pairs of molecules are linked into centrosymmetric dimers by pairs of symmetry‐related C—H...π(arene) hydrogen bonds, while the molecules of O,S‐diethyl N‐(4‐chlorobenzoyl)imidothiocarbonate, C₁₂H₁₄ClNO₂S, are linked by a single C—H...O hydrogen bond into simple chains, pairs of which are linked by an aromatic π–π stacking interaction to form a ladder‐type structure.     

Capillary electrophoretic studies on quantum dots and histidine appended peptides self‐assembly

Herein, we designed four peptides appended with different numbers of histidine (His_n‐peptide). We launched a systematic investigation on quantum dots (QDs) and His_n‐peptide self‐assembly in solution using fluorescence coupled CE (CE‐FL). The results indicated that CE‐FL was a powerful method to probe how ligands interaction on the surface of nanoparticles. The self‐assembly of QDs and peptide was determined by the numbers of histidine. We also observed that longer polyhistidine tags (n ≤ 6) could improve the self‐assembly efficiency. Furthermore, the formation and separation of QD‐peptide assembly were also studied by CE‐FL inside a capillary. The total time for the mixing, self‐assembly, separation, and detection was less than 10 min. Our method greatly expands the application of CE‐FL in QDs‐based biolabeling and bioanalysis.     

A Triazacyclononane‐Based Bifunctional Phosphinate Ligand for the Preparation of Multimeric 68Ga Tracers for Positron Emission Tomography

For application in positron emission tomography (PET), PrP9 , a N,N′,N′′‐trisubstituted triazacyclononane with methyl(2‐carboxyethyl)phosphinic acid pendant arms, was developed as ⁶⁸Ga³⁺ complexing agent. The synthesis is short and inexpensive. Ga^III and Fe^III complexes of PrP9 were characterized by single‐crystal X‐ray diffraction. Stepwise protonation constants and thermodynamic stabilities of metal complexes were determined by potentiometry. The Ga^III complex possesses a high thermodynamic stability (log K_[GaL]=26.24) and a high degree of kinetic inertness. ⁶⁸Ga labeling of PrP9 is possible at ambient temperature and in a wide pH range, also at pH values as low as 1. This means that for the first time, the neat eluate of a TiO₂‐based ⁶⁸Ge/⁶⁸Ga generator (typically consisting of 0.1 M HCl) can be directly used for labeling purposes. The rate of ⁶⁸Ga activity incorporation at pH 3.3 and 20 °C is higher than for the established chelators DOTA and NOTA. Tris‐amides of PrP9 with amino acid esters were synthesized to act as models for multimeric peptide conjugates. These conjugates exhibit radiolabeling properties similar to those of unsubstituted PrP9 .     

Novel Lanthanide(III) Ternary Complexes with Naphthoyltrifluoroacetone: A Synthetic and Spectroscopic Study

A series of lanthanide complexes with general formula [Ln(NTA)₃X] were prapared [Ln = Y ( a ), Er ( b ), Eu ( c ), NTA = naphthoyltrifluoroacetone, X = H₂O ( 1 ), phen = phenanthroline ( 2 ), bpyO1 = 2, 2′‐bipyridine N‐oxide ( 3 ), and bpyO2 = 2, 2′‐bipyridine‐N,N′‐dioxide ( 4 )]. The crystal structures of [Eu(NTA)₃bpyO2] ( 4b ), [Er(NTA)₃bpyO1] ( 3c ), and [Er(NTA)₃phen] ( 2c ) were determined. X‐ray crystallographic analysis reveals that the complexes are of mononuclear structure with three NTA and one ancillary ligand. The photoluminescence spectra of 3c and 4b exhibit strong characteristic emissions arising from Eu³⁺ central ion due to the efficient sensitization of bpyO1 and bpyO2, respectively.     

5，10，15，20-四 [4-(4''-乙基哌嗪基)苯基]卟啉的合成及其与DNA的相互作用

基于卟啉对癌细胞的特殊亲和作用和哌嗪化合物的抗肿瘤、抗病毒作用，设计并合成了具有哌嗪结构的新型卟啉化合物5，10，15，20-四[4-(4'-乙基哌嗪基)苯基]卟啉（TEPPPH₂），其结构经UV-Vis, 元素分析，¹H NMR等手段证明。采用UV-Vis光谱和荧光光谱研究了TEPPPH₂和小牛胸腺DNA 的相互作用模式和结合机理。实验发现，TEPPPH₂能嵌入到DNA的碱基对中，1个小牛胸腺DNA分子对TEPPPH₂分子的最大结合数n约为88，结合常数为8.4×10⁶mol•L^-1 。TEPPPH₂与DNA的结合数和结合常数大于已知的四（4-N-甲基吡啶基）卟啉和Ca/sal-his、Ni/sal–aln型席夫碱抗癌药物。     

Tag‐Convertible Photocrosslinker with Click‐On/Off N‐Acylsulfonamide Linkage for Protein Identification

The N‐acylsulfonamide group, known as a safety‐catch linker, has been applied to photoaffinity labeling (PAL) using a cinnamate‐type photocrosslinker to improve the efficiency of PAL‐based target identification. A bioorthogonal sulfo‐click reaction was used to stably link a photocrosslinker unit with N‐acylsulfonamide linkage to produce a photoactivatable probe without any protection. In addition, the crosslinked protein was selectively isolated with a small cinnamate tag via linkage disruption upon N‐alkylation. Furthermore, the tag moiety was photochemically converted to a stable coumarin derivative by losing a water molecule, which is a useful property in MS‐based identification.     

Transient Incomplete Separation Facilitates Finding Accurate Equilibrium Dissociation Constant of Protein–Small Molecule Complex

Current practical methods for finding the equilibrium dissociation constant, K_d, of protein–small molecule complexes have inherent sources of inaccuracy. Introduced here is “accurate constant via transient incomplete separation” (ACTIS), which appears to be free of inherent sources of inaccuracy. Conceptually, a short plug of the pre‐equilibrated protein–small molecule mixture is pressure‐propagated in a capillary, causing fast transient incomplete separation of the complex from the unbound small molecule. A superposition of signals from these two components is measured near the capillary exit and used to calculate a fraction of unbound small molecule, which, in turn, is used to calculate K_d. Herein the validity of ACTIS is proven theoretically, its accuracy is verified by computer simulation, and its practical use is demonstrated. ACTIS has the potential to become a reference‐standard method for determining K_d values of protein–small molecule complexes.