Biomedical subjects

Cees Gooijer

Publications and source records attributed to Cees Gooijer.

At least 19 recordsLinked to original sources

PubMed2006

Hexamerization of the bacteriophage T4 capsid protein gp23 and its W13V mutant studied by time-resolved tryptophan fluorescence.

The bacteriophage T4 capsid protein gp23 was studied using time-resolved and steady-state fluorescence of the intrinsic protein fluorophore tryptophan. In-vitro gp23 consists mostly of monomers at low temperature but forms hexamers at room temperature. To extend our knowledge of the structure and hexamerization characteristics of gp23, the temperature-dependent fluorescence properties of a tryptophan mutant (W13V) were compared to those of wild-type gp23. The W13V mutation is located in the N-terminal part of the protein, which is cleaved off after prohead formation in the live bacteriophage. Results show that W13 plays a role in the hexamerization process but is not needed to stabilize the hexamer once it is formed. Furthermore, besides the monomer-to-hexamer temperature transition (15-23 degrees C and 12-43 degrees C for wild-type and W13V gp23, respectively), we were able to observe denaturation of the N-terminus in hexameric wild-type gp23 around 40 degrees C. In addition, with the aid of a recently published homology model of gp23, the lifetimes obtained from time-resolved fluorescence measurements could tentatively be assigned to specific tryptophan residues.

Capsid Proteins↗

PubMed2006

Towards combined electrochemistry and surface-enhanced resonance Raman of heme proteins: Improvement of diffusion electrochemistry of cytochrome c at silver electrodes chemically modified with 4-mercaptopyridine.

To date, a successful combination of surface-enhanced resonance Raman spectroscopy (SERRS) and electrochemistry to study heme proteins is inhibited by the problems raised by the prerequisite to use silver as electrode metal. This paper indicates an approach to overcome these problems. It describes a quick and reproducible procedure to prepare silver electrodes chemically modified with 4-mercaptopyridine suitable to perform diffusion electrochemistry of cytochrome c (cyt c). The method involves the employment of a mechanical and a chemical treatment and avoids the use of alumina slurries and any electrochemical pretreatment. Cyclic voltammetry (CV) was used to test the electrochemical response of cyt c, and the CV signals were found identical with those obtained on gold electrodes under the same experimental conditions. Compared to previous literature, a significant improvement of the CV signal of cyt c at silver electrodes was achieved. Preliminary results show that this treatment can be also successfully employed for the preparation of SERRS-active electrodes.

Animals↗

PubMed2006

Strong overtones and combination bands in ultraviolet resonance Raman spectroscopy.

Ultraviolet resonance Raman spectroscopy is carried out using a continuous wave frequency-doubled argon ion laser operated at 229, 244, and 257 nm in order to characterize the overtones and combination bands for several classes of organic compounds in liquid solutions. Contrary to what is generally anticipated, for molecules such as pyrene and anthracene, strong overtones and combination bands can show up; it is demonstrated that their intensity depends critically on the applied laser wavelength. If the excitation wavelength corresponds with a purely electronic transition--this applies to a good approximation for 244-nm excitation in the case of pyrene and for 257-nm excitation in the case of anthracene--mostly fundamental vibrations (up to 1700 cm(-1)) are observed. Overtones and combination bands are detected but are rather weak. However, if the laser overlaps with the vibronic region--as holds for 229- and 257-nm excitation for pyrene and 244-nm excitation for anthracene--very strong bands are found in the region 1700-3400 cm(-1). As illustrated for pyrene at 257 nm, all these bands can be assigned to first overtones or binary combinations of fundamental vibrations. Their intensity distribution can roughly be simulated by multiplying the relative intensities of the fundamental bands. Significant bands can also be found in the region 3400-5000 cm(-1), corresponding with second overtones and ternary combinations. It is shown that these findings are not restricted to planar and rigid molecules with high symmetry. Substituted pyrenes exhibit similar effects, and relatively strong overtones are also observed for adenosine monophosphate and for abietic acid. The reasons for these observations are discussed, as well as the potential applicability for analytical purposes.

Journal Article↗

PubMed2006

Binding of bufuralol, dextromethorphan, and 3,4-methylenedioxymethylamphetamine to wild-type and F120A mutant cytochrome P450 2D6 studied by resonance Raman spectroscopy.

Cytochrome P450 2D6 (CYP2D6) is one of the most important drug-metabolizing enzymes in humans. Resonance Raman data, reported for the first time for CYP2D6, show that the CYP2D6 heme is found to be in a six-coordinated low-spin state in the absence of substrates, and it is perturbed to different extents by bufuralol, dextromethorphan, and 3,4-methylenedioxymethylamphetamine (MDMA). Dextromethorphan and MDMA induce in CYP2D6 a significant amount of five-coordinated high-spin heme species and reduce the polarity of its heme-pocket, whereas bufuralol does not. Spectra of the F120A mutant CYP2D6 suggest that Phe120 is involved in substrate-binding of dextromethorphan and MDMA, being responsible for the spectral differences observed between these two compounds and bufuralol. These differences could be explained postulating a different substrate mobility for each compound in the CYP2D6 active site, consistently with the role previously suggested for Phe120 in binding dextromethorphan and MDMA.

Amino Acid Substitution↗

PubMed2006

Analytical separation and detection methods for flavonoids.

Flavonoids receive considerable attention in the literature, specifically because of their biological and physiological importance. This review focuses on separation and detection methods for flavonoids and their application to plants, food, drinks and biological fluids. The topics that will be discussed are sample treatment, column liquid chromatography (LC), but also methods such as gas chromatography (GC), capillary electrophoresis (CE) and thin-layer chromatography (TLC), various detection methods and structural characterization. Because of the increasing interest in structure elucidation of flavonoids, special attention will be devoted to the use of tandem-mass spectrometric (MS/MS) techniques for the characterization of several important sub-classes, and to the potential of combined diode-array UV (DAD UV), tandem-MS and nuclear magnetic resonance (NMR) detection for unambiguous identification. Emphasis will be on recent developments and trends.

Beverages↗

PubMed2006

Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy.

Enzyme structure and dynamics may play a main role in substrate binding and the subsequent steps in the CYP (cytochrome P450) catalytic cycle. In the present study, changes in the structure of human CYP2D6 upon binding of the substrate are studied using steady-state and time-resolved fluorescence methods, focusing not only on the emission of the tryptophan residues, but also on emission of the substrate. As a substrate, MAMC [7-methoxy-4-(aminomethyl)-coumarin] was selected, a compound exhibiting native fluorescence. As well as the wild-type, the W128F (Trp128-->Phe) mutant of CYP2D6 was studied. After binding, a variety of energy transfer possibilities exist, and molecular dynamics simulations were performed to calculate distances and relative orientations of donors and acceptors. Energy transfer from Trp128 to haem appeared to be important; its emission was related to the shortest of the three average tryptophan fluorescence lifetimes observed for CYP2D6. MAMC to haem energy transfer was very efficient as well: when bound in the active site, the emission of MAMC was fully quenched. Steady-state anisotropy revealed that besides the MAMC in the active site, another 2.4% of MAMC was bound outside of the active site to wild-type CYP2D6. The tryptophan residues in CYP2D6 appeared to be less accessible for the external quenchers iodide and acrylamide in presence of MAMC, indicating a tightening of the enzyme structure upon substrate binding. However, the changes in the overall enzyme structure were not very large, since the emission characteristics of the enzyme were not very different in the presence of MAMC.

Amino Acid Substitution↗

PubMed2005

Coupling of size-exclusion chromatography to a continuous assay for subtilisin using a fluorescence resonance energy transfer peptide substrate: testing of two standard inhibitors.

Liquid chromatography (LC) was coupled on-line to a homogeneous continuous-flow protease assay using fluorescence resonance energy transfer (FRET) as a readout for the screening of inhibitors of an enzyme (e.g., Subtilisin Carlsberg). The inhibitors aprotinin (a protein of approximately 6500 g/mol) and 4-(2-aminoethyl)benzenesulfonyl fluoride hydrochloride (AEBSF, 240 g/mol) were mixed with other, non-active compounds and separated on a size-exclusion chromatography column. After the separation, the analytes were eluted to the postcolumn reactor unit where the enzyme solution and subsequently the FRET peptide substrate were added; by measuring the fluorescence intensity the degree of inhibition was monitored on-line. As expected, only the two inhibitors caused a change in the FRET response. Detection limits for aprotinin were 5.8 microM in the flow injection analysis (FIA) mode and 12 microM in the on-line LC mode. System validation was performed by determining IC50 values for aprotinin for the FIA mode (19 microM) and the on-line mode (22 microM). These IC50 values were in line with the value determined in batch experiments (25 microM). With this system, chemical information (i.e., chromatographic retention time) and biological information (i.e., enzyme inhibition) can be combined to characterize mixtures.

Aprotinin↗

PubMed2005

Combined theoretical and experimental deep-UV resonance raman studies of substituted pyrenes.

The results of time-dependent density functional theory (TDDFT) calculations of resonance Raman intensities are combined with experimental deep-ultraviolet resonance Raman measurements at a single wavelength, i.e., 244 nm, in order to test the possibility to distinguish several very similar compounds. Pyrene and three of its substituted derivatives, in which a single hydrogen atom has been replaced by a halogen atom, are compared. The fixed 244 nm excitation wavelength overlapped with the same electronic transition of the four pyrenes. Ground-state calculations using the BP86 exchange-correlation functional were used to predict the Raman frequencies, whereas excited-state calculations have been carried out employing the "statistical averaging of (model) orbital potentials" (SAOP) potential within a linear-response TDDFT framework in combination with the short-time approximation of resonance Raman intensities. In view of the simplistic theoretical approach, we find a surprisingly good agreement between the simulated and measured resonance Raman spectra of pyrene and its substituted analogues in terms of frequencies and intensities, which shows that the calculations can be used reliably to interpret the experimental spectra. With this combined information, it is possible to find criteria to distinguish the compounds under investigation, although many features of their vibrational spectra are similar.

Journal Article↗

PubMed2005

Fast excited-state intramolecular proton transfer and subnanosecond dynamic stokes shift of time-resolved fluorescence spectra of the 5-methoxysalicylic acid/diethyl ether complex.

Excited-state intramolecular proton transfer (ESIPT) occurring in the salicylic acid (SA) derivative 5-methoxysalicylic acid (5-MeOSA) in an apolar solvent (cyclohexane) and in the presence of the hydrogen bond accepting agent diethyl ether (DEE) is investigated. Analysis of the directly measured subnanosecond time-resolved emission spectra (TRES) together with conventional steady-state fluorescence and time-correlated single-photon-counting (TCSPC) decays indicates that ESIPT in this system occurs much faster than fluorescence, and that the equilibrium between normal and tautomeric excited states is established before the emission from both states takes place. However, changes in time- and frequency-resolved fluorescence of the 5-MeOSA/DEE complex are observed due to structural relaxation within the complex, which is reflected in the dynamic Stokes shift of the tautomeric fluorescence band. The normal fluorescence band of 5-MeOSA/DEE does not exhibit marked changes within the investigated time range. A single-exponential relaxation time of 460 ps was determined for the dynamic Stokes shift of the tautomeric band, and it is attributed to a geometric change within the 5-MeOSA/DEE complex upon excitation. Since both tautomeric and normal emission bands are well resolved and exhibit different time-dependent behaviors, a double-well potential appears to be adequate to describe the excited state of the system studied.

Journal Article↗

PubMed2005

Time-resolved fluorescence of the bacteriophage T4 capsid protein gp23.

The time-resolved fluorescence properties of the bacteriophage T4 capsid protein gp23 are investigated. The structural characteristics of this protein are largely unknown and can be probed by recording time-resolved and decay-associated fluorescence spectra and intensity decay curves using a 200 ps-gated intensified CCD-camera. Spectral and decay data are recorded simultaneously, which makes data acquisition fast compared to time-correlated single-photon counting. A red-shift of the emission maximum within the first nanosecond of decay is observed, which can be explained by the different decay-associated spectra of fluorescence lifetimes of the protein in combination with dipolar relaxation. In addition, iodide quenching experiments are performed, to study the degree of exposure of the various tryptophan residues. A model for the origin of the observed lifetimes of 0.032 +/- 0.003, 0.39 +/- 0.06, 2.1 +/- 0.1 and 6.8 +/- 0.8 ns is presented: the 32 ps lifetime can be assigned to the emission of a buried tryptophan residue, the 0.4 and 2.1 ns lifetimes to two partly buried residues, and the 6.8 ns lifetime to a single tryptophan outside the bulk of the folded gp23.

Capsid Proteins↗

PubMed2005

Changed isoflavone levels in red clover (Trifolium pratense L.) leaves with disturbed root nodulation in response to waterlogging.

The effect of disturbed root nodulation on the quantitative and qualitative composition of the main isoflavonoid glucoside malonates, glucosides, and aglycones in the leaves of Trifolium pratense L. grown under waterlogging conditions was investigated. Isoflavonoids are involved in the regulation of root nodule activity and the establishment of the mycorrhizal association. Isoflavonoid determination was performed using reversed-phase liquid chromatography coupled to mass spectrometric and UV absorbance detection. In response to waterlogging, the concentrations of biochanin A and biochanin A-7-O-glucoside malonate, biochanin A-7-O-glucoside, and genistein-7-O-glucoside in the leaves increased two- to threefold after a lag period of 3 wk because of disturbed root nodulation. The other isoflavones detected formononetin, formononetin-7-O-glucoside malonate, and formononetin-7-O-glucoside-did not show any significant changes related to waterlogging. After restoring normal soil water conditions, the concentrations of biochanin A and its glucoside and glucoside-malonate rapidly returned to the initial values, whereas the concentration of genistein-7-O-glucoside remained high.

Adaptation, Physiological↗

PubMed2005

The chemical interaction between the estrogen receptor and monohydroxybenzo[a]pyrene derivatives studied by fluorescence line-narrowing spectroscopy.

A novel approach is presented for studying the chemical interaction between receptor binding sites and ligands. Monohydroxylated polyaromatic compounds were found to be environmentally sensitive ligands when applying a special mode of fluorescence: fluorescence line-narrowing spectroscopy (FLNS). With this technique, solvent dependencies and ligand-receptor interactions can be studied in great detail, due to the high spectral resolution and the fact that at cryogenic temperatures (4 K), no solvent reorientation effects complicate the interpretation. The FLN spectrum of a ligand bound to the receptor is compared to the spectra of the free ligand in solvent mixtures that mimic the functionalities present within the receptor's binding site. It is shown that for the well-known estrogen receptor (ER), the orientations of two xenoestrogenic ligands 3- and 9-hydroxybenzo[a]pyrene (3- and 9-OH-BaP) can be determined. The FLN results clearly indicate that an H-bond accepted by HIS524 plays a major role in the binding of these ligands to the ER. Furthermore, the spectra indicated a pi-pi stacking aromatic interaction for 9-OH-BaP with PHE404. These results are in line with molecular modeling studies published earlier.

Benzo(a)pyrene↗

PubMed2004

A flow injection kinase assay system based on time-resolved fluorescence resonance energy-transfer detection in the millisecond range.

A flow injection analysis (FIA) system for biochemical assays using time-resolved fluorescence resonance energy transfer (TR-FRET) in the millisecond time scale was developed. As a model system, we studied a kinase assay, measuring the phosphorylation of poly(GT)-biotin (substrate) by a receptor tyrosine kinase (epidermal growth factor receptor). A streptavidin labeled with XL665 (SA-XL665)-the acceptor-was coupled to the biotin moiety, and an antiphosphotyrosine antibody labeled with europium cryptate (Ab-EuK)-the donor-was coupled to the phosphorylated tyrosine group(s). Long-lived FRET can only occur if the substrate is successfully phosphorylated. For the time-resolved detection of such long-lived luminescence phenomena in a flow system, the repetition rate of the excitation source plays a crucial role. Good results were obtained for a small-sized commercially available quadrupled Nd:YAG laser emitting at 266 nm with a repetition rate of 7.8 kHz and a pulse width of 0.3 ns. The long-lived emissions of the donor at 625 nm and that of the acceptor at 665 nm were monitored simultaneously with two photomultipliers, using a delay time of 50 micros and a gate time of 75 micros to exclude background fluorescence interferences. In the FIA experiments, the Ab-EuK concentration was 6 nM and the substrate concentration and SA-XL665 concentrations were 7 nM. By monitoring the intensity changes at 625 and 665 nm, the inhibition of tyrosine kinase by tyrphostin AG1478 was studied and an IC(50) value of 5.1 +/- 0.4 nM obtained.

Binding Sites↗

PubMed2004

Citrate-reduced silver hydrosol modified with omega-mercaptoalkanoic acids self-assembled monolayers as a substrate for surface-enhanced resonance Raman scattering. A study with cytochrome c.

A new citrate-reduced silver hydrosol coated with omega-mercaptoalkanoic acids (mercaptopropionic and mercaptoundecanoic acids) self-assembled monolayers was prepared and characterized with surface-enhanced Raman spectroscopy. The structure and the quality of the coating monolayers are discussed and compared to similar coated and uncoated silver hydrosols previously developed. As an application, the new hydrosol was used as a biocompatible and efficient metal substrate for a surface-enhanced resonance Raman scattering (SERRS) study of cytochrome c. The high-quality SERRS spectra reported of cytochrome c (obtained using only 1 microL of a micromolar cytochrome solution) are discussed and compared with data available from literature studies.

Journal Article↗

PubMed2004

Linearly moving low-volume spectroelectrochemical cell for microliter-scale surface-enhanced resonance Raman spectroscopy of heme proteins.

Surface-enhanced resonance Raman spectra of cytochrome c on silver electrodes coated with self-assembled monolayers of mercaptopropionic acid were recorded at different potentials using 50 microL of a micromolar solution. For this purpose, a linearly moving, low-volume, small spectroelectrochemical cell was designed and used together with a Raman microprobe. The quality of the spectra obtained is good, and the spectra show essentially the same features reported by other authors using much larger volumes. The cell described in this paper is shown to be useful for studying the spectroelectrochemistry of photosensitive compounds such as heme proteins, which are available only in very small amounts (nanomoles to picomoles).

Animals↗

PubMed2004

Probing the interaction of benzo[a]pyrene adducts and metabolites with monoclonal antibodies using fluorescence line-narrowing spectroscopy.

A new approach for studying antibody-antigen interactions of DNA adducts and metabolites of polycyclic aromatic hydrocarbons (PAHs) is demonstrated in which fluorescence line-narrowing spectroscopy (FLNS) is used. It is based on the fact that in an FLN spectrum the relative intensities of the line-narrowed bands (that correspond to the excited-state vibrations) are, in general, strongly dependent on the local environment of the fluorophore. Information on the nature of the interactions can be obtained by comparing the FLN spectra of the antigen-antibody complexes to the spectra of the antigen in different types of solvents (H-bonding, aprotic, and pi-electron-containing solvent molecules) recorded under the same conditions. The antigens used were the DNA adduct 7-(benzo[a]pyren-6-yl)guanine (BP-6-N7Gua) and the metabolite (+)-trans-anti-7,8,9,10-benzo[a]pyrenetetrol (BP-tetrol) of benzo[a]pyrene; two monoclonal antibodies (MAbs) have been developed to selectively bind these compounds. It is shown that, for BP-tetrol, H-bonding solvents have a pronounced effect on the FLN spectra. The presence of pi electrons in the solvent molecules results in relatively small but still significant changes in the spectra. When BP-tetrol is bound to its MAb, however, neither of these effects is observed; its spectrum is very similar to the one obtained with an aprotic solvent, methylcyclohexane. Therefore, we can conclude that this MAb has an internal binding site in which the interaction with BP-tetrol is of a hydrophobic character. For BP-6-N7Gua, however, there is a strong effect of the presence of pi electrons in the solvent molecules. The FLN spectrum of this antigen bound to its MAb is very similar to its spectrum in acetone, indicating that pi-pi interactions play an important role in the binding.

Antibodies, Monoclonal↗

PubMed2004

Quenched phosphorescence as a detection method in capillary electrophoretic chiral separations. Monitoring the stereoselective biodegradation of camphorquinone by yeast.

Quenched phosphorescence detection of camphorquinone in cyclodextrin-based electrokinetic chromatography provides very favorable detection limits, i.e., 7 x 10(-)(7) M, 3 orders of magnitude lower than conventional UV absorption detection at 200 nm. The detection is based on the dynamic quenching by the analyte of the strong phosphorescence emission of brominated naphthalenesulfonate, under deoxygenated buffer solution conditions. This approach has been used to detect (1S)-(+)- and (1R)-(-)-camphorquinone after enantiomeric separation by CE. Although the use of the negatively charged carboxymethyl beta-cyclodextrin (CM-beta-CD) alone was not successful, the addition of a second, neutral cyclodextrin, alpha-CD, provided an adequate enantiomeric separation of camphorquinone. Using 25 mM borate buffer (pH 8.5) with 10 mM CM-beta-CD and 20 mM alpha-CD (applied voltage 20 kV, ambient temperature), the enantiomeric separation was performed in approximately 14 min. The chiral method was applied to monitor the stereoselectivity of the biotransformation of a racemic mixture of camphorquinone by yeast. It was found that the enantiomeric ratio calculated from the peak areas in the electropherogram (RSD = 5%) after 24 h of incubation decreased from 0.92 for the control solution (culture medium without yeast) to 0.24 for the culture medium; a similar ratio of 0.25 was observed for cell extract solutions. Therefore, racemic camphorquinone is enantioselectively degraded by yeast, the biodegradation of (1S)-(+)-camphorquinone being faster than that of the (1R)-(-)-enantiomer.

Bromine↗

PubMed2004

Liquid chromatography coupled to nuclear magnetic resonance spectroscopy for the identification of isoflavone glucoside malonates in T. pratense L. leaves.

Previous studies revealed that the main isoflavones in extracts of leaves of T. pratense L. are biochanin A and formononetin, their 7-O-glucosides, and two glucoside malonate isomers of each of them. Since LC-MS(/MS) did not provide sufficient information to distinguish the glucoside malonate isomers, in the present paper LC-NMR as well as off-line two-dimensional NMR were used to obtain further structural information. Matrix solid-phase dispersion (MSPD) was applied to obtain sufficiently high analyte concentrations to perform LC-NMR. Stop-flow reversed-phase LC-NMR was performed using a gradient of deuterated water and deuterated acetonitrile. Offline COSY and NOESY experiments were carried out to determine the positions of the glucose moiety on the flavonoid aglycone, and of the malonate moiety on the glucose. Based on the fragmentation patterns in MS/MS and the NMR spectra, the two formononetin glucoside malonate isomers were identified as 7-O-beta-D-glucoside 6"-O-malonate and 7-O-beta-D-glucoside 4"-O-malonate; i.e. they only differ in the substitution position of the malonate group on the glucoside ring. The biochanin A glucoside malonate isomers, however, have quite different structures. The main and later eluting isomer is biochanin A 7-O-beta-D-glucoside 6"-O-malonate, and the minor and earlier eluting isomer is 5-hydroxy-7-methoxyisoflavone 4'-O-beta-D-glucoside 4"-O-malonate: the positions of the methoxy group and the glucoside 6"-O-malonate group on the flavonoid skeleton are interchanged.

Chromatography, Liquid↗