Synthesis and Self-assembly Properties of Acylated Cyclodextrins and Nitrilotriacetic Acid (NTA)-modified Inclusion Ligands for Interfacial Protein Crystallization

Design and Synthesis of Porphyrin-Nitrilotriacetic Acid Dyads with Potential Applications in Peptide Labeling through Metallochelate Coupling

The need to detect and monitor biomolecules, especially within cells, has led to the emerging growth of fluorescent probes. One of the most commonly used labeling techniques for this purpose is reversible metallochelate coupling via a nitrilotriacetic acid (NTA) moiety. In this study, we focus on the synthesis and characterization of three new porphyrin-NTA dyads, TPP-Lys-NTA, TPP-CC-Lys-NTA, and Py ₃ P-Lys-NTA composed of a porphyrin derivative covalently connected with a modified nitrilotriacetic acid chelate ligand (NTA), for possible metallochelate coupling with Ni²⁺ ions and histidine sequences. Emission spectroscopy studies revealed that all of the probes are able to coordinate with Ni²⁺ ions and consequently can be applied as fluorophores in protein/peptide labeling applications. Using two different histidine-containing peptides as His₆-tag mimic, we demonstrated that the porphyrin-NTA hybrids are able to coordinate efficiently with the peptides through the metallochelate coupling process. Moving one step forward, we examined the ability of these porphyrin-peptide complexes to penetrate and accumulate in cancer cells, exploring the potential utilization of our system as anticancer agents.

Active Ester Functionalized Azobenzenes as Versatile Building Blocks

Azobenzenes are important molecular switches that can still be difficult to functionalize selectively. A high yielding Pd-catalyzed cross-coupling method under mild conditions for the introduction of NHS esters to azobenzenes and diazocines has been established. Yields were consistently high with very few exceptions. The NHS functionalized azobenzenes react with primary amines quantitatively. These amines are ubiquitous in biological systems and in material science.

Evidence of sulfur mustard poisoning by detection of the albumin-derived dipeptide biomarker C(-HETE)P after nicotinylation

Sulfur mustard (SM, bis[2-chloroethyl]-sulfide) is a banned chemical warfare agent that was frequently used in recent years and led to numerous poisoned victims who developed painful erythema and blisters. Post-exposure analysis of SM incorporation can be performed by the detection of human serum albumin (HSA)-derived peptides. HSA alkylated by SM contains a hydroxyethylthioethyl (HETE)-moiety bound to the cysteine residue C³⁴ yielding the dipeptide biomarker C(-HETE)P after pronase-catalyzed proteolysis. We herein present a novel procedure for the selective precolumn nicotinylation of its N-terminus using 1-nicotinoyloxy-succinimide. The reaction was carried out for 2 h at ambient temperature with a yield of 81%. The derivative NA-C(-HETE)P was analyzed by micro liquid chromatography-electrospray ionization tandem-mass spectrometry working in the selected reaction monitoring mode (μLC-ESI MS/MS SRM). The derivative was shown to be stable in the autosampler at 15°C for at least 24 h. The single protonated precursor ion (m/z 428.1) was subjected to collision-induced dissociation yielding product ions at m/z 116.1, m/z 137.0, and m/z 105.0 used for selective monitoring without any plasma-derived interferences. NA-C(-HETE)P showed a mass spectrometric response superior to the non-derivatized dipeptide thus yielding larger peak areas (factor 1.3 ± 0.2). The lower limit of identification corresponded to 80 nM SM spiked to plasma in vitro. The presented procedure was applied to real case plasma samples from 2015 collected in the Middle East confirming SM poisoning.

Nonfouling NTA-PEG-Based TEM Grid Coatings for Selective Capture of Histidine-Tagged Protein Targets from Cell Lysates

We report the preparation and performance of TEM grids bearing stabilized nonfouling lipid monolayer coatings. These films contain NTA capture ligands of controllable areal density at the distal end of a flexible poly(ethylene glycol) 2000 (PEG2000) spacer to avoid preferred orientation of surface-bound histidine-tagged (His-tag) protein targets. Langmuir-Schaefer deposition at 30 mN/m of mixed monolayers containing two novel synthetic lipids-1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[(5-amido-1-carboxypentyl)iminodiacetic acid]polyethylene glycolamide 2000) (NTA-PEG2000-DSPE) and 1,2-(tricosa-10',12'-diynoyl)-sn-glycero-3-phosphoethanolamine-N-(methoxypolyethylene glycolamide 350) (mPEG350-DTPE)-in 1:99 and 5:95 molar ratios prior to treatment with a 5 min, 254 nm light exposure was used for grid fabrication. These conditions were designed to limit nonspecific protein adsorption onto the stabilized lipid coating by favoring the formation of a mPEG350 brush layer below a flexible, mushroom conformation of NTA-PEG2000 at low surface density to enable specific immobilization and random orientation of the protein target on the EM grid. These grids were then used to capture His6-T7 bacteriophage and RplL from cell lysates, as well as purified His8-green fluorescent protein (GFP) and nanodisc solubilized maltose transporter, His6-MalFGK2. Our findings indicate that TEM grid supported, polymerized NTA lipid monolayers are capable of capturing His-tag protein targets in a manner that controls their areal densities, while efficiently blocking nonspecific adsorption and limiting film degradation, even upon prolonged detergent exposure.

Challenges and opportunities for new protein crystallization strategies in structure-based drug design

Structure-based drug design (SBDD) has emerged as a valuable pharmaceutical lead discovery tool, showing potential for accelerating the discovery process,while reducing developmental costs and boosting potencies of the drug that is ultimately selected. SBDD is an iterative, rational, lead compound sculpting process that involves both the synthesis of new derivatives and the evaluation of their binding to the target structure either through computational docking or elucidation of the target structure as a complex with the lead compound. This method heavily relies on the production of high resolution(< 2 Å) 3D structures of the drug target, obtained through X-ray crystallographic analysis, in the presence or absence of the drug candidate.The lack of generalized methods for high quality crystal production is still a major bottleneck in the process of macromolecular crystallization. This review provides a brief introduction to SBDD and describes several macromolecular crystallization strategies, with an emphasis on advances and challenges facing researchers in the field today. Recent trends in the development of more universal macromolecular crystallization techniques, particularly nucleation-based techniques that are applicable to both soluble and integral membrane proteins, are also discussed.

Crystallographic characterization of N-oxide tripod amphiphiles

Tripod amphiphiles are designed to promote the solubilization and stabilization of intrinsic membrane proteins in aqueous solution; facilitation of crystallization is a long-range goal. Membrane proteins are subjects of extensive interest because of their critical biological roles, but proteins of this type can be difficult to study because of their low solubility in water. The nonionic detergents that are typically used to achieve solubility can have the unintended effect of causing protein denaturation. Tripod amphiphiles differ from conventional detergents in that the lipophilic segment contains a branchpoint, and previous work has shown that this unusual amphiphilic architecture can be advantageous relative to traditional detergent structures. Here, we report the crystal structures of several tripod amphiphiles that contain an N-oxide hydrophilic group. The data suggest that tripods can adapt themselves to a nonpolar surface by altering the hydrophobic appendage that projects toward that surface and their overall orientation relative to that surface. Although it is not possible to draw firm conclusions regarding amphiphile association in solution from crystallographic data, trends observed among the packing patterns reported here suggest design strategies to be implemented in future studies.

Specific adsorption of histidine-tagged proteins on silica surfaces modified with Ni2+/NTA-derivatized poly(ethylene glycol)

Silica surfaces modified with nitrilotriacetic acid (NTA)-polyethylene glycol (PEG) derivatives were used to immobilize hexahistidine-tagged green fluorescent protein (His6-GFP), biotin/streptavidin-AlexaFluor555 (His6-biotin/SA-AF), and gramicidin A-containing vesicles (His6-gA). Three types of surface-reactive PEG derivatives-NTA-PEG3400-Si(OMe)3, NTA-PEG3400-vinylsulfone, and mPEG5000-Si(OMe)3 (control)-were grafted onto silica and tested for their ability to capture His6-tag species via His6/Ni2+/NTA chelation. The composition and thicknesses of the PEG-modified surfaces were characterized using X-ray photoelectron spectroscopy, contact angle, and ellipsometry. Protein capture efficiencies of the NTA-PEG-grafted surfaces were evaluated by measuring fluorescence intensities of these surfaces after exposure to His6-tag species. XPS and ellipsometry data indicate that surface adsorption occurs via specific interactions between the His6-tag and the Ni2+/NTA-PEG-grafted surface. Protein immobilization was most effective for NTA-PEG3400-Si(OMe)3-modified surfaces, with maximal areal densities achieved at 45 pmol/cm2 for His6-GFP and 95 fmol/cm2 for His6-biotin/SA-AF. Lipid vesicles containing His6-gA in a 1:375 gA/lipid ratio could also be immobilized on Ni2+/NTA-PEG3400-Si(OMe)3-modified surfaces at 0.5 mM total lipid. Our results suggest that NTA-PEG-Si(OMe)3 conjugates may be useful tools for immobilizing His6-tag proteins on solid surfaces to produce protein-functionalized surfaces.