Engineering A Uranyl‐Specific Binding Protein from NikR

A new pick‐up line : The first uranyl‐selective DNA‐binding protein is designed using the E. coli nickel(II)‐responsive protein NikR as the template. The resulting NikR′ protein binds uranyl (see picture) with a dissociation constant K_d=53 nM and selectively binds to DNA in the presence of uranyl.

     

New Insight into the Water‐Soluble Chlorophyll‐Binding Protein from Lepidium virginicum

This study describes new recombinant water‐soluble chlorophyll (Chl)‐binding proteins (WSCP) from Lepidium virginicum (LvWSCP). This complex binds four Chls (i.e. two dimers of Chls) per protein tetramer. We show that absorption, emission, hole‐burned (HB) spectra and the shape of the zero‐phonon hole (ZPH) action spectrum are consistent with the presence of uncorrelated excitation energy transfer between two Chl dimers. Thus, there is no need to include slow protein relaxation within the lowest excited state (as suggested in a previous analysis of cauliflower WSCP [Schmitt, F.‐J. et al. (2008) J. Phys. Chem. B, 112, 13951; Pieper, J. et al. (2011) J. Phys. Chem. B, 115, 4053]) in order to explain the large shift observed between the maxima of the ZPH action and emission spectra. Experimental evidence is provided which shows that electron exchange between lowest energy Chls and the protein may occur, i.e. electrons can be trapped at low temperature by nearby aromatic amino acids. The latter explains the shape of nonresonant HB spectra (i.e. the absence of antihole), demonstrating that the hole‐burning process in LvWSCP is largely photochemical in nature, though a small contribution from nonphotochemical hole burning (in resonant holes) is also observed.     

On Penicillin‐Binding Protein 1b Affinity‐Labeling Reagents

The synthesis of some 3‐aryl‐3‐(trifluoromethyl)3H‐diazirine and benzophenone‐based photoaffinity labels is reported. The photolabile group is bound to a scaffold that also accommodates functional groups to which an indicator unit (biotin) and the bioactive ligand can be attached orthogonally. To three of the labels, moenomycin was conjugated with the aim to provide tools for the identification of the moenomycin binding site within the transglycosylase domain of the enzyme PBP 1b. Some preliminary photoaffinity‐labeling experiments were carried out.     

Investigation of Protein Binding With All Solid‐State Ion‐Selective Electrodes

A potentiometric sensor for studying charge based adsorption of proteins was created using a single‐piece polyaniline‐PVC ion‐selective electrode (ISE). Three different ISEs, two for Na⁺ and one for Cl^? ion determination, were studied. The Na⁺‐ISEs consisted of a neutral calixarene‐based ionophore and one with a charged carrier dinonylnapthalenesulfonic acid (DNNSA) whereas for the Cl^? ISE, an anion exchanger tridodecylmethylammonium chloride (TDDMA⁺Cl^?), was used. The Na⁺ ISE with DNNSA as the charged carrier was successfully able to discriminate the binding of two different proteins (bovine serum albumin and lysozyme) based on their intrinsic charge.     

Enzyme‐Mediated,Site‐Specific Protein Coupling Strategies for Surface‐Based Binding Assays

Covalent surface immobilization of proteins for binding assays is typically performed non‐specifically via lysine residues. However, receptors that either have lysines near their binding pockets, or whose presence at the sensor surface is electrostatically disfavoured, can be hard to probe. To overcome these limitations and to improve the homogeneity of surface functionalization, we adapted and optimized three different enzymatic coupling strategies (4′‐phosphopantetheinyl transferase, sortase A, and asparaginyl endopeptidase) for biolayer interferometry surface modification. All of these enzymes can be used to site‐specifically and covalently ligate proteins of interest via short recognition sequences. The enzymes function under mild conditions and thus immobilization does not affect the receptors’ functionality. We successfully employed this enzymatic surface functionalization approach to study the binding kinetics of two different receptor–ligand pairs.     

Enzyme‐Mediated,Site‐Specific Protein Coupling Strategies for Surface‐Based Binding Assays

Covalent surface immobilization of proteins for binding assays is typically performed non‐specifically via lysine residues. However, receptors that either have lysines near their binding pockets, or whose presence at the sensor surface is electrostatically disfavoured, can be hard to probe. To overcome these limitations and to improve the homogeneity of surface functionalization, we adapted and optimized three different enzymatic coupling strategies (4′‐phosphopantetheinyl transferase, sortase A, and asparaginyl endopeptidase) for biolayer interferometry surface modification. All of these enzymes can be used to site‐specifically and covalently ligate proteins of interest via short recognition sequences. The enzymes function under mild conditions and thus immobilization does not affect the receptors’ functionality. We successfully employed this enzymatic surface functionalization approach to study the binding kinetics of two different receptor–ligand pairs.     

Water‐Mediated Recognition of Simple Alkyl Chains by Heart‐Type Fatty‐Acid‐Binding Protein

Long‐chain fatty acids (FAs) with low water solubility require fatty‐acid‐binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown. To address this question, we employed a newly developed calorimetric method for comprehensively evaluating the affinity of FAs, sub‐Angstrom X‐ray crystallography to accurately determine their 3D structure, and energy calculations of the coexisting water molecules using the computer program WaterMap. Our results clearly showed that the heart‐type FABP (FABP3) preferentially incorporates a U‐shaped FA of C10–C18 using a lipid‐compatible water cluster, and excludes longer FAs using a chain‐length‐limiting water cluster. These mechanisms could help us gain a general understanding of how proteins recognize diverse lipids with different chain lengths.     

Synthesis and Protein Binding of (4‐Carboxybutyl)carbamoyl‐ Substituted Taxoids

(4‐Carboxybutyl)carbamates 5 and 6 , as well as 10 , derived from 10‐O‐deacetylbaccatin III ( 1 ) and paclitaxel ( 2 ), respectively, were synthesized by reaction of unprotected 1 and 2′‐O‐(methoxyacetyl)paclitaxel ( 8 ), respectively, with trimethylsilyl 5‐isocyanatopentanoate in good yields. The carbamoyl‐taxoids were conjugated to bovine‐serum albumin and analyzed by MALDI‐TOF mass spectrometry.     

Size‐Controlled Construction of Magnetic Nanoparticle Clusters Using DNA‐Binding Zinc Finger Protein

Nanoparticle clusters (NPCs) have attracted significant interest owing to their unique characteristics arising from their collective individual properties. Nonetheless, the construction of NPCs in a structurally well‐defined and size‐controllable manner remains a challenge. Here we demonstrate a strategy to construct size‐controlled NPCs using the DNA‐binding zinc finger (ZnF) protein. Biotinylated ZnF was conjugated to DNA templates with different lengths, followed by incubation with neutravidin‐conjugated nanoparticles. The sequence specificity of ZnF and programmable DNA templates enabled a size‐controlled construction of NPCs, resulting in a homogeneous size distribution. We demonstrated the utility of magnetic NPCs by showing a three‐fold increase in the spin–spin relaxivity in MRI compared with Feridex. Furthermore, folate‐conjugated magnetic NPCs exhibited a specific targeting ability for HeLa cells. The present approach can be applicable to other nanoparticles, finding wide applications in many areas such as disease diagnosis, imaging, and delivery of drugs and genes.     

Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane‐Spanning Protein

Mapping the interaction sites between membrane‐spanning proteins is a key challenge in structural biology. In this study a carbene‐footprinting approach was developed and applied to identify the interfacial sites of a trimeric, integral membrane protein, OmpF, solubilised in micelles. The diazirine‐based footprinting probe is effectively sequestered by, and incorporated into, the micelles, thus leading to efficient labelling of the membrane‐spanning regions of the protein upon irradiation at 349 nm. Areas associated with protein–protein interactions between the trimer subunits remained unlabelled, thus revealing their location.     

12‐ to 22‐Membered Bridged β‐Lactams as Potential Penicillin‐Binding Protein Inhibitors

As potential inhibitors of penicillin‐binding proteins (PBPs), we focused our research on the synthesis of non‐traditional 1,3‐bridged β‐lactams embedded into macrocycles. We synthesized 12‐ to 22‐membered bicyclic β‐lactams by the ring‐closing metathesis (RCM) of bis‐ω‐alkenyl‐3(S)‐aminoazetidinone precursors. The reactivity of 1,3‐bridged β‐lactams was estimated by the determination of the energy barrier of a concerted nucleophilic attack and lactam ring‐opening process by using ab initio calculations. The results predicted that 16‐membered cycles should be more reactive. Biochemical evaluations against R39 DD‐peptidase and two resistant PBPs, namely, PBP2a and PBP5, revealed the inhibition effect of compound 4d , which featured a 16‐membered bridge and the N‐tert‐butyloxycarbonyl chain at the C3 position of the β‐lactam ring. Surprisingly, the corresponding bicycle, 12d , with the PhOCH₂CO side chain at C3 was inactive. Reaction models of the R39 active site gave a new insight into the geometric requirements of the conformation of potential ligands and their steric hindrance; this could help in the design of new compounds.     

3‐Mercapto‐2,6‐Pyridinedicarboxylic Acid: A Small Lanthanide‐Binding Tag for Protein Studies by NMR Spectroscopy

Paramagnetic effects from lanthanide ions present powerful tools for protein studies by nuclear magnetic resonance (NMR) spectroscopy provided that the lanthanide can be site‐specifically and rigidly attached to the protein. A new, particularly small and rigid lanthanide‐binding tag, 3‐mercapto‐2,6‐pyridinedicarboxylic acid (3MDPA), was synthesized and attached to two different proteins via a disulfide bond. The complexes of the N‐terminal domain of the E. coli arginine repressor (ArgN) with seven different paramagnetic lanthanide ions and Co²⁺ were analyzed in detail by NMR spectroscopy. The magnetic susceptibility anisotropy (Δχ) tensors and metal position were determined from pseudocontact shifts. The 3MDPA tag generated very different Δχ tensor orientations compared to the previously studied 4‐mercaptomethyl‐DPA tag, making it a highly complementary and useful tool for protein NMR studies.     

Protein p53 Binding to Cisplatin‐modified DNA Targets Evaluated by Modification‐specific Electrochemical Immunoprecipitation Assay

Studies of protein interactions with chemically modified nucleic acids are of importance in various areas of biomolecular and biomedical research, including investigations of the binding of proteins important in medicine with DNA modified with drugs and diagnostic applications of modified DNAs in biosensing and bioanalysis. Chemical modification of DNA substrates with various species inside or outside specific protein binding sites can affect the protein‐DNA recognition. In this paper we present a simple electrochemical immunoprecipitation technique designed for evaluation of the effects of antitumor drug cisplatin on the p53‐DNA binding. The cisplatin‐DNA adducts are utilized as electroactive labels allowing a facile determination of the p53‐bound modified DNA. Effects observed using this technique accord with results of previous biochemical assays. This approach is potentially applicable in studies that deal with the influence of any electroactive DNA modifications on the protein‐DNA binding.