Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme

Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were applied to the study of millisecond to microsecond time scale motions in a cavity mutant of T4 lysozyme (L99A) using methyl groups as probes of dynamics. Protein expressed in E. coli cells with (13)CH(3)-pyruvate as the sole carbon source contained high levels of (13)C enrichment at a total of 80 Val gamma, Leu delta, Ile gamma (2), Ala beta, and Met epsilon methyl positions with little extraneous incorporation. Data for 72 methyl groups were available for analysis. Dispersion profiles with large amplitudes were measured for many of these residues and were well fit to a two-state exchange model. The interconversion rates and populations of the states, obtained from fitting relaxation dispersion profiles of each individual probe, were remarkably homogeneous and data for nearly all methyl groups in the protein could be collectively fit to a single cooperative conformational transition. The present study demonstrates the general applicability of methyl relaxation dispersion measurements for the investigation of millisecond time scale protein motions at a large number of side-chain positions. Potential artifacts associated with the experiments are described and methods to minimize their effects presented. These experiments should be particularly well suited for probing dynamics in high molecular weight systems due to the favorable NMR spectroscopic properties of methyl groups.     

Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions

In the previous paper in this issue we have demonstrated that it is possible to measure the five different relaxation rates of a deuteron in (13)CH(2)D methyl groups of (13)C-labeled, fractionally deuterated proteins. The extensive set of data acquired in these experiments provides an opportunity to investigate side-chain dynamics in proteins at a level of detail that heretofore was not possible. The data, acquired on the B1 domain of peptostreptococcal protein L, include 16 (9) relaxation measurements at 4 (2) different magnetic field strengths, 25 degrees C (5 degrees C). These data are shown to be self-consistent and are analyzed using a spectral density mapping procedure which allows extraction of values of the spectral density function at a number of frequencies with no assumptions about the underlying dynamics. Dynamics data from 31 of 35 methyls in the protein for which data could be obtained were well-fitted using the two-parameter Lipari-Szabo model (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546). The data from the remaining 4 methyls can be fitted using a three-parameter version of the Lipari-Szabo model that takes into account, in a simple manner, additional nanosecond time-scale local dynamics. This interpretation is supported by analysis of a molecular dynamics trajectory where spectral density profiles calculated for side-chain methyl sites reflect the influence of slower (nanosecond) time-scale motions involving jumps between rotameric wells. A discussion of the minimum number of relaxation measurements that are necessary to extract the full complement of dynamics information is presented along with an interpretation of the extracted dynamics parameters.     

Accelerated screening of phage-display output with alkaline phosphatase fusions

When using multiple targets and libraries, selection of affinity reagents from phage-displayed libraries is a relatively time-consuming process. Herein, we describe an automation-amenable approach to accelerate the process by using alkaline phosphatase (AP) fusion proteins in place of the phage ELISA screening and subsequent confirmation steps with purified protein. After two or three rounds of affinity selection, the open reading frames that encode the affinity selected molecules (i.e., antibody fragments, engineered scaffold proteins, combinatorial peptides) are amplified from the phage or phagemid DNA molecules by PCR and cloned en masse by a Ligation Independent Cloning (LIC) method into a plasmid encoding a highly active variant of E. coli AP. This time-saving process identifies affinity reagents that work out of context of the phage and that can be used in various downstream enzyme linked binding assays. The utility of this approach was demonstrated by analyzing single-chain antibodies (scFvs), engineered fibronectin type III domains (FN3), and combinatorial peptides that were selected for binding to the Epsin N-terminal Homology (ENTH) domain of epsin 1, the c-Src SH3 domain, and the appendage domain of the gamma subunit of the clathrin adaptor complex, AP-1, respectively.     

Purity assessment for avoparcin

Well-characterized pure-substance reference materials for the use as calibrants are essential to establish the metrological traceability of the results of chemical measurements. Normally, the characterization of this type of reference material is conducted through a thorough purity assessment of the compound concerned. For this reason, studies on purity assessment, especially for neat organic compounds, continues as an important part of work being undertaken by metrological institutions around the world. Among others, the need for certified pure reference standards continues to increase for residues analysis in foods, particularly for those compounds which have been banned for food safety reasons, but their residues in foods are still monitored under food surveillance program in many countries. In this respect, avoparcin serves as a very good example where testing laboratories have difficulties in obtaining traceable and comparable results on determination of avoparcin in food matrix samples due, in part, to the unavailability of certified pure-substance reference material as calibrant. In this study, it was attempted to assess the purity of a commercially available test material of avoparcin using the mass balance approach. The objective of this paper is to share the difficulties encountered during the course of purity assessment and how they were addressed. As expected, the most challenging part of work was to identify and estimate the amount of unknown impurities, both organic and inorganic-related ones, given the chemical structure and properties of avoparcin. For instance, avoparcin exists in two forms in the test material, i.e., α- and β-avoparcin, and they were found to be susceptible to hydrolysis under certain conditions.     

The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

Stabilization of the Charge‐Separated States of Covalently Linked Zinc Porphyrin–Triphenylamine–[60]Fullerene

Spectroscopic, redox, computational, and electron transfer reactions of the covalently linked zinc porphyrin–triphenylamine–fulleropyrrolidine system are investigated in solvents of varying polarity. An appreciable interaction between triphenylamine and the porphyrin π system is revealed by steady‐state absorption and emission, redox, and computational studies. Free‐energy calculations suggest that the light‐induced processes via the singlet‐excited porphyrin are exothermic in benzonitrile, dichlorobenzene, toluene, and benzene. The occurrence of fast and efficient charge‐separation processes (≈10¹² s^?1) via the singlet‐excited porphyrin is confirmed by femtosecond transient absorption measurements in solvents with dielectric constants ranging from 25.2 (benzonitrile) to 2.2 (benzene). The rates of the charge separation processes are much less solvent‐dependent, which suggests that the charge‐separation processes occur at the top region of the Marcus parabola. The lifetimes of the singlet radical‐ion pair (70–3000 ps at room temperature) decrease substantially in more polar solvents, which suggests that the charge‐recombination process is occurring in the Marcus inverted region. Interestingly, by utilizing the nanosecond transient absorption spectral technique we can obtain clear evidence about the existence of triplet radical‐ion pairs with relatively long lifetimes of 0.71 μs (in benzonitrile) and 2.2 μs (in o‐dichlorobenzene), but not in toluene and benzene due to energetic considerations. From the point of view of mechanistic information, the synthesized zinc porphyrin–triphenylamine–fulleropyrrolidine system has the advantage that both the lifetimes of the singlet and triplet radical‐ion pair can be determined.     

Cross‐Reactive Sensor Arrays for the Detection of Peptides in Aqueous Solution by Fluorescence Spectroscopy

A simple but powerful method for the sensing of peptides in aqueous solution has been developed. The transition‐metal complexes [PdCl₂(en)], [{RhCl₂Cp*}₂], and [{RuCl₂(p‐cymene)}₂] were combined with six different fluorescent dyes to build a cross‐reactive sensor array. The fluorescence response of the individual sensor units was based on competitive complexation reactions between the peptide analytes and the fluorescent dyes. The collective response of the sensor array in a time‐resolved fashion was used as an input for multivariate analyses. A sensor array comprised of only six metal–dye combinations was able to differentiate ten different dipeptides in buffered aqueous solution at a concentration of 50 μM . Furthermore, the cross‐reactive sensor could be used to obtain information about the identity and the quantity of the pharmacologically interesting dipeptides carnosine and homocarnosine in a complex biological matrix, such as deproteinized human blood serum. The sensor array was also able to sense longer peptides, which was demonstrated by differentiating mixtures of the nonapeptide bradykinin and the decapeptide kallidin.     

Detecting the "afterglow" of 13C NMR in proteins using multiple receivers

We show that the weak signal that remains after (13)C-detected experiments (the (13)C "afterglow") can still be measured with high sensitivity by proton detection. This is illustrated by the incorporation of two experiments, 2D (HA)CACO and 3D (HA)CA(CO)NNH, into a single pulse sequence that makes use of two receivers in parallel. In cases where the sensitivity is not limiting, such as applications to small proteins, the inclusion of the projection-reconstruction method permits the recording of both spectra in only 15 min. High-quality data sets for the 143 residue nuclease A inhibitor (2 °C, correlation time 17.5 ns) were obtained in 3 h, illustrating the utility of the method even in studies of moderately sized proteins.     

Uranium speciation in biofilms studied by laser fluorescence techniques

Biofilms may immobilize toxic heavy metals in the environment and thereby influence their migration behaviour. The mechanisms of these processes are currently not understood, because the complexity of such biofilms creates many discrete geochemical microenvironments which may differ from the surrounding bulk solution in their bacterial diversity, their prevailing geochemical properties, e.g. pH and dissolved oxygen concentration, the presence of organic molecules, e.g. metabolites, and many more, all of which may affect metal speciation. To obtain such information, which is necessary for performance assessment studies or the development of new cost-effective strategies for cleaning waste waters, it is very important to develop new non-invasive methods applicable to study the interactions of metals within biofilm systems. Laser fluorescence techniques have some superior features, above all very high sensitivity for fluorescent heavy metals. An approach combining confocal laser scanning microscopy and laser-induced fluorescence spectroscopy for study of the interactions of biofilms with uranium is presented. It was found that coupling these techniques furnishes a promising tool for in-situ non-invasive study of fluorescent heavy metals within biofilm systems. Information on uranium speciation and uranium redox states can be obtained.