The complex of apomyoglobin with the fluorescent dye coumarin 153

Solvation dynamics in protein environments: Comparison of fluorescence upconversion measurements of coumarin 153 in monomeric hemeproteins with molecular dynamics simulations

The complexes of the fluorescence probe coumarin 153 with apomyoglobin and apoleghemoglobin are used as model systems to study solvation dynamics in proteins. Time-resolved Stokes shift experiments are compared with molecular dynamics simulations, and very good agreement is obtained. The solvation of the coumarin probe is very rapid with approximately 60% occurring within 300 fs and is attributed to interactions with water (or possibly to the protein itself). Differences in the solvation relaxation (or correlation) function C(t) for the two proteins are attributed to differences in their hemepockets.

Bioanalytical interaction studies executed by preincubation affinity capillary electrophoresis

The versatility of CE is beneficial for the study of many types of molecular interactions, because different experimental designs can be made to suit the characteristics of a particular interaction. A very versatile starting point is the preequilibration type of affinity CE that has been used extensively for characterizing biomolecular interactions in the last 15 years. We review this field here and include a comprehensive overview of the existing preincubation ACE modes including their advantages and limitations as well as the methodological developments and applications within the bioanalytical field.

A femtosecond study of excitation wavelength dependence of solvation dynamics in a PEO-PPO-PEO triblock copolymer micelle

Excitation wavelength (lambdaex) dependence of solvation dynamics of coumarin 480 (C480) in the micellar core of a water soluble triblock copolymer, PEO20-PPO70-PEO20 (Pluronic P123), is studied by femtosecond and picosecond time resolved emission spectroscopies. In the P123 micelle, the width of the emission spectrum of C480 is found to be much larger than that in bulk water. This suggests that the P123 micelle is more heterogeneous than bulk water. The steady state emission maximum of C480 in P123 micelle shows a significant red edge excitation shift by 25 nm from 453 nm at lambdaex=345 nm to 478 nm at lambdaex=435 nm. The solvation dynamics in the interior of the triblock copolymer micelle is found to depend strongly on the excitation wavelength. The excitation wavelength dependence is ascribed to a wide distribution of locations of C480 molecules in the P123 micelle with two extreme environments-a bulklike peripheral region with very fast solvent response and a very slow core region. With increase in lambdaex, contribution of the bulklike region having an ultrafast component (< or =2 ps) increases from 7% at lambdaex=375 nm to 78% at lambda(ex)=425 nm while the contribution of the ultraslow component (4500 ps) decreases from 79% to 17%.

Temperature dependence of solvation dynamics and anisotropy decay in a protein: ANS in bovine serum albumin

Temperature dependence of solvation dynamics and fluorescence anisotropy decay of 8-anilino-1-naphthalenesulfonate (ANS) bound to a protein, bovine serum albumin (BSA), are studied. Solvation dynamics of ANS bound to BSA displays a component (300 ps) which is independent of temperature in the range of 278-318 K and a long component which decreases from 5800 ps at 278 K to 3600 ps at 318 K. The temperature independent part is ascribed to a dynamic exchange of bound to free water with a low barrier. The temperature variation of the long component of solvation dynamics corresponds to an activation energy of 2.1 kcal mol(-1). The activation energy is ascribed to local segmental motion of the protein along with the associated water molecules and polar residues. The time scale of solvation dynamics is found to be very different from the time scale of anisotropy decay. The anisotropy decays are analyzed in terms of the wobbling motion of the probe (ANS) and the overall tumbling of the protein.

Recent applications of affinity interactions in capillary electrophoresis

Systems biology depends on a comprehensive assignment and characterization of the interactions of proteins and polypeptides (functional proteomics) and of other classes of biomolecules in a given organism. High‐capacity screening methods are in place for ligand capture and interaction screening, but a detailed dynamic characterization of molecular interactions under physiological conditions in efficiently separated mixtures with minimal sample consumption is presently provided only by electrophoretic interaction analysis in capillaries, affinity CE (ACE). This has been realized in different fields of biology and analytical chemistry, and the resulting advances and uses of ACE during the last 2.5 years are covered in this review. Dealing with anything from small divalent metal ions to large supramolecular assemblies, the applications of ACE span from low‐affinity binding of broad specificity being exploited in optimizing selectivity, e.g., in enantiomer analysis to miniaturized affinity technologies, e.g., for fast processing immunoassay. Also, approaches that provide detailed quantitative characterization of analyte–ligand interaction for drug, immunoassay, and aptamer development are increasingly important, but various approaches to ACE are more and more generally applied in biological research. In addition, the present overview emphasizes that distinct challenges regarding sensitivity, parallel processing, information‐rich detection, interfacing with MS, analyte recovery, and preparative capabilities remain. This will be addressed by future technological improvements that will ensure continuing new applications of ACE in the years to come.

Capillary electrophoresis of proteins 2003-2005

This review article with 304 references describes recent developments in CE of proteins, and covers the two years since the previous review (Hutterer, K., Dolník, V., Electrophoresis 2003, 24, 3998-4012) through Spring 2005. It covers topics related to CE of proteins, including modeling of the electrophoretic migration of proteins, sample pretreatment, wall coatings, improving separation, various forms of detection, special electrophoretic techniques such as affinity CE, CIEF, and applications of CE to the analysis of proteins in real-world samples including human body fluids, food and agricultural samples, protein pharmaceuticals, and recombinant protein preparations.

Characterization of the Interactions of Fluorescent Probes with Proteins: Coumarin 153 and 1,8-ANS in Complex with Holo- and Apomyoglobin

In order to provide a thorough characterization of a system with which to study the dielectric response of a protein, a well-defined system complex of a fluorescent probe and protein is required. We have argued that such a system is provided by coumarin 153 and apomyoglobin (Photochem. Photobiol. 79, 440-446 [2004]). In order to demonstrate further that coumarin 153 exhibits negligible nonspecific binding to the surface of apomyoglobin, we study its interactions with both the apo and holo proteins. We further make a similar comparison with 8-anilino-l-naphthalenesulfonic acid, for which an NMR structure with apomyoglobin has been obtained. Our results confirm the appropriateness of the system of coumarin 153 and apomyoglobin for the investigation of solvation by the protein matrix.

Femtosecond Study of Partially Folded States of Cytochrome C by Solvation Dynamics

Using femtosecond time-resolved fluorescence spectroscopy, it is shown that the solvation dynamics in the two partially folded states (IS' and IS' ') of a protein, cytochrome C, are very different. In the case of IS' (formed by the addition of 2 mM sodium dodecyl sulfate, SDS) almost the entire dynamic solvent shift of coumarin 153 (C153) is captured in a picosecond setup and the contribution of the ultrafast component (0.5 ps) is very small (5%). Solvation dynamics of IS' ' (formed by 2 mM SDS and 5 M urea) displays a major component (47%) of 1.3 ps. This indicates that the structure of IS' ' is much more open and exposed compared to that of IS'. The difference in the dynamics of IS' and IS' ' is attributed to differences in their structure, particularly near the heme region, and the presence of urea in IS' '.