Ultrafast and selective labeling of endogenous proteins using affinity-based benzotriazole chemistry

Chemical modification of proteins is enormously useful for characterizing protein function in complex biological systems and for drug development. Selective labeling of native or endogenous proteins is challenging owing to the existence of distinct functional groups in proteins and in living systems. Chemistry for rapid and selective labeling of proteins remains in high demand. Here we have developed novel affinity labeling probes using benzotriazole (BTA) chemistry. We showed that affinity-based BTA probes selectively and covalently label a lysine residue in the vicinity of the ligand binding site of a target protein with a reaction half-time of 28 s. The reaction rate constant is comparable to the fastest biorthogonal chemistry. This approach was used to selectively label different cytosolic and membrane proteins in vitro and in live cells. BTA chemistry could be widely useful for labeling of native/endogenous proteins, target identification and development of covalent inhibitors.

Affinity-based benzotriazole (BTA) probes selectively and covalently label native proteins or endogenous proteins in cells with a fast reaction rate. It is enormously useful for characterizing protein function in biological systems and for drug development.     

Salting-out gradients in centrifugal partition chromatography for the isolation of chlorogenic acids from green coffee beans

In addition to sample solubility constraints, the use of polarity gradients in normal-phase centrifugal partition chromatography (CPC) for the purification of complex mixtures is also limited by the instability of biphasic systems as a consequence of dramatic changes in the settling times along the gradient, leading in many cases to column bleeding when working under maximum efficiency conditions. In this paper an electrostriction approach is proposed as a strategy in reversed-phase CPC to fractionate intermediate polarity extracts in a single run by bringing its components into the “sweet spot” in a controlled fashion through a stepwise reduction of salt concentration in the aqueous mobile phase. The salting-out gradient method was successfully tested with the separation of the major chlorogenic acids (CGAs, hydroxycinnamoylquinic acids) present in green coffee beans (5-caffeoylquinic acid (5-CQA), 5-feruloylquinic acid (5-FQA) and 3,5-dicaffeoylquinic acid (3,5-diCQA)) using ethyl acetate-hexane as the stationary phase and an ionic gradient of LiCl (5.0, 2.5 and 0.1 M) as the mobile phase in one case and (NH₄)₂SO₄/KNO₃ (3.0 and 1.5 M/1.5 M) in another. Regioisomers of each chlorogenic acid obtained by base-catalyzed isomerisation were also separated by CPC using isocratic elution. The best resolution for both FQAs and diCQAs was achieved with a chloroform–n-butanol–0.01 M pH 2.5 phosphate buffer (84:16:100; v/v) system, while CQAs were best isolated using chloroform–n-butanol–0.01 M pH 2.5 phosphate buffer/5.0 M LiCl (82:18:100; v/v).     

Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure

First results are reported on the application of ECD in analysis of 2+ and 3+ ions of stereoisomers of Trp-cage (NLYIQWLKDGGPSSGRPPPS), the smallest and fastest-folding protein, which exhibits a tightly folded tertiary structure in solution. The chiral recognition based on the ratios of the abundances of z(18) and z(19) fragments in ECD of 2+ ions was excellent even for a single amino acid (Tyr) D-substitution (R(chiral) = 8.6). The chiral effect decreased with an increase of temperature at the electrospray ion source, as well as at a higher degree of ionization, 3+ ions (R(chiral) = 1.5). A general approach is suggested for charge localization in n+ ions by analysis of ECD mass spectra of (n + 1)+ ions. Application of this approach to 3+ Trp-cage ions revealed the protonation probability order in 2+ ions: Arg(16) > Gln(5) > approximately N-terminus. The ECD results for native form of the 2+ ions favor the preservation of the solution-phase tertiary structure, and chiral recognition through the interaction between the charges and the neutral bond network. Conversely, ECD of 3+ ions supports the dominance of ionic hydrogen bonding which determines a different gas-phase structure than found in solution. Vibrational activation of 2+ ions indicated greater stability of the native form, but the fragmentation patterns did not provide stereoisomer differentiation, thus underlying the special position of ECD among other MS/MS fragmentation techniques. Further ECD studies should yield more structural information as well as quantitative single-amino acid D/L content measurements in proteins.     

Phase behavior and mesophase structures of 1,3,5-benzene- and 1,3,5-cyclohexanetricarboxamides: towards an understanding of the losing order at the transition into the isotropic phase

One of the simplest and most-versatile motifs in supramolecular chemistry is based on 1,3,5-benzenetricarboxamides. Variation of the core structure and subtle changes in the structures of the lateral substituents govern the self-assembly and determine the phase behavior. Herein, we provide a comprehensive comparison between the phase behavior and mesophase structure of a series of 1,3,5-benzene- and 1,3,5-cyclohexanetricarboxamides that contain linear and branched alkyl substituents. Depending on the substituent, different crystalline, plastic crystalline, and liquid crystalline phases were formed. The relatively rare columnar nematic (N(C)) phase was only observed in cyclohexane-based trisamides that contained linear alkyl substituents. Of fundamental interest in liquid crystalline supramolecular systems is the transition from the mesomorphic state into the isotropic state and, in particular, the question of how the order decreases. Temperature-dependent IR spectroscopy and XRD measurements revealed that columnar H-bonded aggregates were still present in the isotropic phase. At the clearing transition, mainly the lateral order was lost, whilst shorter columnar aggregates still remained. A thorough understanding of the phase behavior and the mesophase structure is relevant for selecting processing conditions that use supramolecular structures in devices or as fibrillar nanomaterials.     

C?X⋅⋅⋅O Halogen Bonding: Interactions of Trifluoromethyl Halides with Dimethyl Ether

The formation of weakly bound molecular complexes between dimethyl ether (DME) and the trifluoromethyl halides CF₃Cl, CF₃Br and CF₃I dissolved in liquid argon and in liquid krypton is investigated, using Raman and FTIR spectroscopy. For all halides evidence is found for the formation of C? X???O halogen‐bonded 1:1 complexes. At higher concentrations of CF₃Br, a weak absorption due to a 1:2 complex is also observed. Using spectra recorded at temperatures between 87 and 125 K, the complexation enthalpies for the complexes are determined to be ?6.8(3) kJ mol^?1 (DME?CF₃Cl), ?10.2(1) kJ mol^?1 (DME?CF₃Br), ?15.5(1) kJ mol^?1 (DME?CF₃I), and ?17.8(5) kJ mol^?1 [DME(?CF₃Br)₂]. Structural and spectral information on the complexes is obtained from ab initio calculations at the MP2/ 6‐311++G(d,p) and MP2/6‐311++G(d,p)+LanL2DZ* levels. By applying Monte Carlo free energy perturbation calculations to account for the solvent influences, and statistical thermodynamics to estimate the zero‐point vibrational and thermal influences, the ab initio complexation energies are converted into complexation enthalpies for the solutions in liquid argon. The resulting values are compared with the experimental data deduced from the cryosolutions.     

Palladium‐Mediated Cleavage of Proteins with Thiazolidine‐Modified Backbone in Live Cells

Chemical protein synthesis and biorthogonal modification chemistries allow production of unique proteins for a range of biological studies. Bond‐forming reactions for site‐selective protein labeling are commonly used in these endeavors. Selective bond‐cleavage reactions, however, are much less explored and still pose a great challenge. In addition, most of studies with modified proteins prepared by either total synthesis or semisynthesis have been applied mainly for in vitro experiments with very limited extension to live cells. Reported here is an approach for studying uniquely modified proteins containing a traceless cell delivery unit and palladium‐based cleavable element for chemical activation, and monitoring the effect of these proteins in live cells. This approach is demonstrated for the synthesis of a caged ubiquitin‐aldehyde, which was decaged for the inhibition of deubiquitinases in live cells.     

Dielectric studies of two liquid crystalline benzoates with coupled and decoupled CN groups

The results of dielectric studies performed in a broad frequency range for two compounds, 4-cyanophenyl 4-n-heptylbenzoate (7BBCN) and 4-(4-cyanobutyloxy)phenyl 4- n-heptylbenzoate (7BB4CN), are compared. They have the same molecular core whereas the strongly polar CN group is attached to the benzene ring in 7BBCN or is separated from it by the butyloxy chain in 7BB4CN. 7BBCN has a nematic phase, whereas 7BB4CN exhibits a monotropic nematic and smectic A₂ polymorphism. Large differences in the dielectric properties of the two substances were found. The analysis of the results led to the conclusion that the antiparallel dipole-dipole associations are considerably stronger in the substance with a decoupled CN group.