Kristin Bartik

Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by two-dimensional 1H NMR.

The pH dependence of the two-dimensional 1H nuclear magnetic resonance spectra of hen and turkey egg-white lysozymes has been recorded over the pH range 1-7. By monitoring the chemical shifts of the resonances of the various protons of ionizable residues, individual pKa values for the acidic residues have been determined for both proteins. The pKa values are displaced, with the exception of those of the residues in the active site cleft, by an average of 1 unit to low pH compared to model compounds.

Polyoxometalates as a Novel Class of Artificial Proteases: Selective Hydrolysis of Lysozyme under Physiological pH and Temperature Promoted by a Cerium(IV) Keggin-Type Polyoxometalate

Hen-egg-white lysozyme (HEWL) is specifically cleaved at the Trp28-Val29 and Asn44-Arg45 peptide bonds in the presence of a Keggin-type [Ce(α-PW(11)O(39))(2)](10-) polyoxometalate (POM; 1) at pH 7.4 and 37 °C. The reactivity of 1 towards a range of dipeptides was also examined and the calculated reaction rates were comparable to those observed for the hydrolysis of HEWL. Experiments with α-lactalbumin (α-LA), a protein that is structurally highly homologous to HEWL but has a different surface potential, showed no evidence of hydrolysis, which indicates the importance of electrostatic interactions between 1 and the protein surface for the hydrolytic reaction to occur. A combination of spectroscopic techniques was used to reveal the molecular interactions between HEWL and 1 that lead to hydrolysis. NMR spectroscopy titration experiments showed that on protein addition the intensity of the (31)P NMR signal of 1 gradually decreased due to the formation of a large protein/polyoxometalate complex and completely disappeared when the HEWL/1 ratio reached 1:2. Circular dichroism (CD) measurements of HEWL indicate that addition of 1 results in a clear decrease in the signal at λ=208 nm, which is attributed to changes in the α-helical content of the protein. (15)N-(1)H heteronuclear single quantum coherence (HSQC) NMR measurements of HEWL in the presence of 1 reveal that the interaction is mainly observed for residues that are located in close proximity to the first site in the α-helical part of the structure (Trp28-Val29). The less pronounced NMR spectroscopic shifts around the second cleavage site (Asn44-Arg45), which is found in the β-strand region of the protein, might be caused by weaker metal-directed binding, compared with strong POM-directed binding at the first site.

Aromatic–Carbohydrate Interactions: An NMR and Computational Study of Model Systems

The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar-aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl beta-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent-sugar and aromatic-sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations.

UV–Vis and NMR study of the formation of gold nanoparticles by citrate reduction: Observation of gold–citrate aggregates

The citrate reduction of gold(III) in water is one of the most commonly used synthetic pathways for the preparation of gold colloids. In order to gain insight into the formation of gold nanoparticles (GNPs) using this method, the synthesis of GNPs was undertaken under different experimental conditions and monitored in operando by UV-Vis spectroscopy. These experiments highlight that citrate should be polydeprotonated and that Au(III) should not be polyhydroxylated in order to obtain GNPs with a narrow size distribution. Samples taken during the reaction were also characterized by Nuclear Magnetic Resonance Spectroscopy (NMR) to monitor the various reaction products as a function of time. Diffusion Ordered SpectroscopY (DOSY) experiments allowed us to identify slow diffusing citrate - Au(I) or Au(0) complexes which could play a role in the formation of GNPs.

Fluoride binding in water: a new environment for a known receptor.

(Figure Presented) Binding in a micelle: In the presence of CTABr micelles (see picture), the salophen-UO2 complex 1 binds fluoride in water with the highest affinity ever recorded for a neutral receptor (K≈ ca. 104M-1). The receptors location and its orientation within the micellar system are determined by PRE and NOE NMR experiments.

Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry

Many scientists, including one of the authors of the present paper, have devoted time to try to find a definition for life (Bersini and Reisse 2007). It is clear that a consensus will never be reached but, more importantly, it seems that the issue itself could be without major interest. It is indeed impossible to define a “natural” frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living). Fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria. It also offers the possibility to avoid losing time with unnecessary controversies such as deciding whether a virus is, or is not, a living system.

Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex.

Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.

Fluorescent Chemosensors for Anions and Contact Ion Pairs with a Cavity-Based Selectivity

The association of a concave macrocyclic compound to one or multiple fluorophores is an appealing strategy for the design of chemosensors. Indeed, as with biological systems, a cavity-based selectivity can be expected with such fluorescent receptors. Examples of calix[6]arene-based systems using this strategy are rare in the literature, and to our knowledge, no examples of fluorescent receptors that can bind organic contact ion pairs have been reported. This report describes the straightforward synthesis of fluorescent calix[6]arene-based receptors 4a and 4b bearing three pyrenyl subunits and the study of their binding properties toward anions and ammonium salts using different spectroscopies. It was found that receptor 4a exhibits a remarkable selectivity for the sulfate anion in DMSO, enabling its selective sensing by fluorescence spectroscopy. In CDCl3, the receptor is able to bind ammonium ions efficiently only in association with the sulfate anion. Interestingly, this cooperative binding of ammonium sulfate salts was also evidenced in a protic environment. Finally, a cavity-based selectivity in terms of size and shape of the guest was observed with both receptors 4a and 4b, opening interesting perspectives on the elaboration of fluorescent cavity-based systems for the selective sensing of biologically relevant ammonium salts such as neurotransmitters.

Comparison of the NMR Enantiodifferentiation of a Chiral Ruthenium(II) Complex of C2 Symmetry Using the TRISPHAT Anion and a Lanthanide Shift Reagent

The tris[tetrachlorobenzenediolato]phosphate(V) anion (TRISPHAT) is known to be an efficient NMR chiral shift agent for various chiral cationic species. Here we compare the efficiency of TRISPHAT and of a chiral lanthanide shift reagent for the determination of the enantiomeric purity of the chiral building block [Ru(phen)2py2]2+ which possesses C2 symmetry. We also discuss our results in terms of the geometry of interaction between the Ru(II) complex and the TRISPHAT anion.

A method for the estimation of χ1 torsion angles in proteins

SummaryA method for estimating αCH-βCH coupling constants from the shape and fine structure of NH-αCH fingerprint-region cross peaks of COSY spectra is presented. Spectral simulations have been used to analyse the effect of variations in 3JNH-αCH, 3JαCH-βCH, linewidths and digital resolution on the appearance of NH-αCH COSY cross peaks. On the basis of these simulations a set of rules for broadly categorising experimental NH-αCH cross peaks according to αCH-βCH coupling constants has been devised. The method has been applied to the analysis of NH-αCH cross peaks of hen lysozyme. The results are compared to previous measurements of αCH-βCH coupling constants using E.COSY techniques.