Biomedical subjects

F van Mourik

Publications and source records attributed to F van Mourik.

18 recordsLinked to original sources

PubMed2006

The ultrafast structural response of solid parahydrogen: a complementary experimental/simulation investigation.

We present a complete characterization, based on femtosecond pump-probe spectroscopy and molecular dynamics simulations, of the ultrafast dynamics of electronic bubble formation in solid parahydrogen upon impulsive excitation of impurity-doped sites, which correlate with the lowest Rydberg state of the NO impurity. The high temporal resolution of the experiment allows us to identify three time scales in the structural dynamics. A first ultrafast expansion (<150 fs), associated with the release of approximately 80% of the excess energy available to the system after excitation, is accompanied by a transient narrowing of the spatial distribution of the first shell of H2 molecules around the impurity. In a subsequent stage (up to approximately 800 fs), the cavity expansion slows down, and energy starts to flow irreversibly into the crystal. Finally, the lattice undergoes a slow structural reorganization at the impurity site (5-10 ps). A weak low-frequency recurrence, probably associated with an elastic response of the crystal, is observed at approximately 10 ps. The absence of polarization dependence indicates that the dynamics is largely dominated by translational (radial) motions of the molecules surrounding NO and not by the rotational motion of the impurity. Molecular dynamics simulations with temperature corrections, to mimic zero-point fluctuations, fully support the experimental results and show that the bubble model is suited to describe the dynamics of the system. It appears that the response of the medium around the impurity at short times is typical of a liquid solvent rather than that of a solid.

Journal Article↗

PubMed2006

Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption.

A visible-pump/UV-probe transient absorption is used to characterize the ultrafast dynamics of bacteriorhodopsin with 80-fs time resolution. We identify three spectral components in the 265- to 310-nm region, related to the all-trans retinal, tryptophan (Trp)-86 and the isomerized photoproduct, allowing us to map the dynamics from reactants to products, along with the response of Trp amino acids. The signal of the photoproduct appears with a time delay of approximately 250 fs and is characterized by a steep rise ( approximately 150 fs), followed by additional rise and decay components, with time scales characteristic of the J intermediate. The delayed onset and the steep rise point to an impulsive formation of a transition state on the way to isomerization. We argue that this impulsive formation results from a splitting of a wave packet of torsional modes on the potential surface at the branching between the all-trans and the cis forms. Parallel to these dynamics, the signal caused by Trp response rises in approximately 200 fs, because of the translocation of charge along the conjugate chain, and possible mechanisms are presented, which trigger isomerization.

Bacteriorhodopsins↗

PubMed2005

Probing the ultrafast charge translocation of photoexcited retinal in bacteriorhodopsin.

The ultrafast evolution of the electric field within bacteriorhodopsin was measured by monitoring the absorption changes of a tryptophan residue after excitation of retinal. The Trp absorption decreases within the first 200 femtoseconds and then recovers on time scales typical for retinal isomerization and vibrational relaxation. A model of excitonic coupling between retinal and tryptophans shows that the signal reflects a gradual rise of the retinal difference dipole moment, which precedes and probably drives isomerization. The results suggest an intimate connection between the progressive dipole moment change and the retinal skeletal changes reported over the same time scale.

Bacteriorhodopsins↗

PubMed2005

Lattice response of quantum solids to an impulsive local perturbation.

The lattice response of solid para-H2 to an impulsive electronic excitation was studied using femtosecond pump-probe spectroscopy. The evolution of an electronic bubble in the crystal, created upon excitation of the A(3ssigma) Rydberg state of an NO impurity, was followed in real time, with a resolution of 100 fs. The experimental results, interpreted in connection with molecular dynamics simulations with quantum corrections, indicate the presence of three stages in the dynamics: a sub-100 fs "adiabatic" phase, a 0.5-1 ps phase, corresponding to the interaction of the first with the next shells driven by the bubble expansion, and a 5 ps phase, corresponding to a slow rearrangement of the environment surrounding the impurity. These findings indicate that the lattice response in solid para-H2 resembles that of a liquid.

Journal Article↗

PubMed2001

Long-lived charge-separated states in bacterial reaction centers isolated from Rhodobacter sphaeroides.

We studied the accumulation of long-lived charge-separated states in reaction centers isolated from Rhodobacter sphaeroides, using continuous illumination, or trains of single-turnover flashes. We found that under both conditions a long-lived state was produced with a quantum yield of about 1%. This long-lived species resembles the normal P(+)Q(-) state in all respects, but has a lifetime of several minutes. Under continuous illumination the long-lived state can be accumulated, leading to close to full conversion of the reaction centers into this state. The lifetime of this accumulated state varies from a few minutes up to more than 20 min, and depends on the illumination history. Surprisingly, the lifetime and quantum yield do not depend on the presence of the secondary quinone, Q(B). Under oxygen-free conditions the accumulation was reversible, no changes in the normal recombination times were observed due to the intense illumination. The long-lived state is responsible for most of the dark adaptation and hysteresis effects observed in room temperature experiments. A simple method for quinone extraction and reconstitution was developed.

Electromagnetic Fields↗

PubMed1999

Primary charge separation routes in the BChl:BPhe heterodimer reaction centers of Rhodobacter sphaeroides.

Energy transfer and the primary charge separation process are studied as a function of excitation wavelength in membrane-bound reaction centers of Rhodobacter sphaeroides in which the excitonically coupled bacteriochlorophyll homodimer is converted to a bacteriochlorophyll-bacteriopheophytin heterodimer, denoted D [Bylina, E. J., and Youvan, D. C. (1988) Proc. Natl. Acad. Sci. U.S. A. 85, 7226]. In the HM202L heterodimer reaction center, excitation of D using 880 nm excitation light results in a 43 ps decay of the excited heterodimer, D. The decay of D results for about 30% in the formation of the charge separated state D+QA- and for about 70% in a decay directly to the ground state. Upon excitation of the monomeric bacteriochlorophylls using 798 nm excitation light, approximately 60% of the excitation energy is transferred downhill to D, forming D. Clear evidence is obtained that the other 40% of the excitations results in the formation of D+QA- via the pathway BA --> BA+HA- --> D+HA- --> D+QA-. In the membrane-bound "reversed" heterodimer reaction center HL173L, the simplest interpretation of the transient absorption spectra following B excitation is that charge separation occurs solely via the slow D-driven route. However, since a bleach at 812 nm is associated with the spectrum of D in the HL173L reaction center, it cannot be excluded that a state including BB is involved in the charge separation process in this complex.

Bacteriochlorophylls↗

PubMed1999

Multiple pathways for ultrafast transduction of light energy in the photosynthetic reaction center of Rhodobacter sphaeroides.

A pathway of electron transfer is described that operates in the wild-type reaction center (RC) of the photosynthetic bacterium Rhodobacter sphaeroides. The pathway does not involve the excited state of the special pair dimer of bacteriochlorophylls (P*), but instead is driven by the excited state of the monomeric bacteriochlorophyll (BA*) present in the active branch of pigments along which electron transfer occurs. Pump-probe experiments were performed at 77 K on membrane-bound RCs by using different excitation wavelengths, to investigate the formation of the charge separated state P+HA-. In experiments in which P or BA was selectively excited at 880 nm or 796 nm, respectively, the formation of P+HA- was associated with similar time constants of 1.5 ps and 1. 7 ps. However, the spectral changes associated with the two time constants are very different. Global analysis of the transient spectra shows that a mixture of P+BA- and P* is formed in parallel from BA* on a subpicosecond time scale. In contrast, excitation of the inactive branch monomeric bacteriochlorophyll (BB) and the high exciton component of P (P+) resulted in electron transfer only after relaxation to P*. The multiple pathways for primary electron transfer in the bacterial RC are discussed with regard to the mechanism of charge separation in the RC of photosystem II from higher plants.

Bacteriochlorophylls↗

PubMed1998

Ultrafast evolution of the excited states in the chlorophyll a/b complex CP29 from green plants studied by energy-selective pump-probe spectroscopy.

The energy transfer process in the minor light-harvesting antenna complex CP29 of green plants was probed in multicolor transient absorption experiments at 77 K using selective subpicosecond excitation pulses at 640 and 650 nm. Energy flow from each of the chlorophyll (Chl) b molecules of the complex could thus be studied separately. The analysis of our data showed that the "blue" Chl b (absorption around 640 nm) transfers excitation to a "red" Chl a with a time constant of 350 +/- 100 fs, while the 'red' Chl b (absorption at 650 nm) transfers on a picosecond time scale (2.2 +/- 0.5 ps) toward a "blue" Chl a. Furthermore, both fast (280 +/- 50 fs) and slow (10-13 ps) equilibration processes among the Chl a molecules were observed, with rates and associated spectra very similar to those of the major antenna complex, LHC-II. Based on the protein sequence homology between CP29 and LHC-II, a basic modelling of the observed kinetics was performed using the LHC-II structure and the Förster theory of energy transfer. Thus, an assignment for the spectral properties and orientation of the two Chl's b, as well as for their closest Chl a neighbors, is put forward, and a comparison is made with the previous assignments and models for LHC-II and CP29.

Chlorophyll↗

PubMed1997

Spectroscopy and structure of bacteriochlorophyll dimers. I. Structural consequences of nonconservative circular dichroism spectra.

The origin of the nonconservative nature of the circular dichroism (CD) spectrum of bacteriochlorophyll dimers is investigated. It is shown that coupling between the Qy and Qx transitions can, under rather restricting circumstances, lead to an asymmetrical CD spectrum: only for a limited set of relative orientations of the monomers within the dimer is the spectrum found to be asymmetrical. The relation between intensity and asymmetry of the CD spectrum is elucidated. The results are applied to the B820 subunit of the LH1 antenna system and subsequently to the antenna system LH1 itself. Differences in the geometry of the BChls in LH1 versus the LH2 structure are discussed.

Bacterial Proteins↗

PubMed1995

Direct observation of sub-picosecond equilibration of excitation energy in the light-harvesting antenna of Rhodospirillum rubrum.

Excitation energy transfer in the light-harvesting antenna of Rhodospirillum rubrum was studied at room temperature using sub-picosecond transient absorption measurements. Upon excitation of Rs. rubrum membranes with a 200 fs, 600 nm laser flash in the Qx transition of the bacteriochlorophyll-a (BChl-a) absorption, the induced transient absorption changes in the Qy region were monitored. In Rs. rubrum membranes the observed delta OD spectrum exhibits ground state bleaching, excited state absorption and stimulated emission. Fast Qx --> Qy relaxation occurs in approximately 100-200 fs as reflected by the building up of stimulated emission. An important observation is that the zero-crossing of the transient difference absorption (delta OD) spectrum exhibits a dynamic redshift from 863 to 875 nm that can be described with by a single exponential with 325 fs time constant. The shape of the transient difference spectrum observed in a purified subunit of the core light-harvesting antenna, B820, consisting of only a single interacting pair of BChl-as, is similar to the spectrum observed in Rs. rubrum membranes and clearly different from the spectrum of BChl-a in a protein/detergent mixture. In the B820 and monomeric BChl-a preparations the 100-200 fs Qx --> Qy relaxation is still observed, but the dynamic redshift of the delta OD spectrum is absent. The spectral kinetics observed in the Rs. rubrum membranes are interpreted in terms of the dynamics of excitation equilibration among the antenna subunits that constitute the inhomogeneously broadened antenna. A simulation of this process using a set of reasonable physical parameters is consistent with an average hopping time in the core light harvesting of 220-270 fs, resulting in an average single-site excitation lifetime of 50-70 fs. The observed rate of this equilibration process is in reasonable agreement with earlier estimations for the hopping time from more indirect measurements. The implications of the findings for the process of excitation trapping by reaction centers will be discussed.

Artifacts↗

PubMed1994

Trapping kinetics in mutants of the photosynthetic purple bacterium Rhodobacter sphaeroides: influence of the charge separation rate and consequences for the rate-limiting step in the light-harvesting process.

The primary light-harvesting processes, energy transfer in the light-harvesting antenna, and trapping of the excited states by reaction centers were studied in several mutant strains of the photosynthetic purple bacterium Rhodobacter sphaeroides. The mutants had reaction centers in which the rates of electron transfer were modified by site-directed mutations at the M210 position. Low-intensity pump-probe laser spectroscopy was used to monitor the absorbance transients in the Qy region of the antenna pigments, and it was found that despite a wide variation in charge separation rates within the RC, produced by the alterations at Tyr M210, there was relatively little corresponding variation in the overall trapping rate. These effects of the mutations on the trapping kinetics demonstrate that the rate-limiting step of the overall light-harvesting process is the transfer of the excitations from the antenna to the reaction center.

Electrochemistry↗

PubMed1994

Energy migration and trapping in a spectrally and spatially inhomogeneous light-harvesting antenna.

In this paper, we analyze the process of excitation energy migration and trapping by reaction centres in photosynthesis and discuss the mechanisms that may provide an overall description of this process in the photosynthetic bacterium Rhodospirillum (Rs.) rubrum and related organisms. A wide range of values have been published for the pigment to pigment transfer rate varying from less than 1 ps up to 10 ps. These differences occur because the interpretation of trapping measurements depend on the assumptions made regarding the organization of the photosynthetic system. As we show, they can be reconciled by assuming a spatially inhomogeneous model where the distance of the reaction center to its surrounding pigments is larger than the pigment-pigment distances within the antenna. We estimate their ratio to be 1.7-1.8. The observed spectral inhomogeneity (at low temperature) of the photosynthetic antenna has resulted in various models. We demonstrate that the excitation kinetics can be modelled at all temperatures by assuming an inhomogeneous distribution of spectral shifts for each pigment. A transition temperature can be distinguished where the effects of spectral inhomogeneity become apparent and we discuss the ranges above (e.g., room temperature), around (e.g., 77K) and below (e.g., 4K) this temperature. Although the basic model is the same in all cases, the dominant mechanism differs in each range. We present explicit expressions for the exciton lifetime in the first two cases and demonstrate that at both temperatures the transfer rate from the light-harvesting antenna to the special pair of the reaction center is the rate-limiting step. Furthermore we demonstrate that at all temperatures a finite number of functional "levels" can be distinguished in the spectral distribution. At high temperature all pigments can be considered spectrally identical and only one level is needed. In the intermediate range a blue-shifted fraction is necessary. At low temperature a third redshifted fraction must be introduced.

Biophysical Phenomena↗

PubMed1992

Spectral identification of the electrochromically active carotenoids of Rhodobacter sphaeroides in chromatophores and reconstituted liposomes.

Reaction centers with both light harvesting complexes I and II (B875 and B800/850; i.e., RCLHILHII complexes) have been isolated from Rhodobacter sphaeroides. These complexes have been incorporated into liposomes made from lipids purified from Escherichia coli. The electrochromic bandshift of carotenoids, present in these reconstituted complexes, shows shifted minima and maxima with respect to a similar spectrum in chromatophores of Rb. sphaeroides in a potassium diffusion potential induced difference spectrum (see also Crielaard, W., Hellingwerf, K.J. and Konings, W.N. (1989) Biochim. Biophys. Acta 973, 205-211). The absorbance spectrum, at room temperature or at 77 K, of both membrane preparations did not, however, reveal differences in the carotenoid region. The long-wavelength carotenoid peak in both preparations is located at 513 nm (77 K). A small difference could be observed between the 77 K excitation spectra of the B850 fluorescence. Reconstituted complexes show a carotenoid peak at 513 nm, whereas in chromatophores this peak is located at 514.5 nm. When fluorescence was recorded at 805 nm, to detect B800 excitation, there was a marked difference between both preparations. In liposomes the long wavelength B800-associated carotenoid peak is located at 512.5 nm, whereas in chromatophores this peak is located at 516 nm. These results explain the shifted minima and maxima in a potassium diffusion induced difference spectrum in proteoliposomes. The prediction of two carotenoid pools in chromatophores (De Grooth, B.G. and Amesz, J. (1977) Biochim. Biophys. Acta 462, 247-258) is confirmed, and the field sensitive carotenoids are identified as the pool that is associated with the B800 band (Kramer, H.J.M., Van Grondelle, R., Hunter, C.N., Westerhuis, W.H.J. and Amesz, J. (1984) Biochim. Biophys. Acta 765, 156-165).

Bacterial Chromatophores↗

PubMed1991

Cellular daunomycin fluorescence in multidrug resistant 2780AD cells and its relation to cellular drug localisation.

Multidrug resistant (MDR) 2780AD human ovarian carcinoma cells were loaded with the fluorescent anticancer agent daunomycin (DN). Fluorescence anisotropy was lower than for corresponding A2780 wild-type cells, indicating that DN was less rigidly bound than in the wild-type cells. Average fluorescence quenching of DN was lower for 2780AD cells. Data were fitted into a model with a highly quenched fraction (fraction A), corresponding to DN intercalated in DNA, and an unquenched fraction (fraction B). The ratio A/B was one order of magnitude lower for the MDR cells than for the wild-type cells. Two other MDR cell lines were investigated and low A/B ratios were found in both cases. Thus, evidence has been provided that in MDR cells the DNA-bound fraction is relatively low and that more free DN is present, for example in acidic vesicles.

DNA, Neoplasm↗

PubMed1991

Fluorescence polarization and low-temperature absorption spectroscopy of a subunit form of light-harvesting complex I from purple photosynthetic bacteria.

Measurements of polarized fluorescence and CD were made on light-harvesting complex 1 and a subunit form of this complex from Rhodospirillum rubrum, Rhodobacter sphaeroides, and Rhodobacter capsulatus. The subunit form of LH1, characterized by a near-infrared absorbance band at approximately 820 nm, was obtained by titration of carotenoid-depleted LH1 complexes with the detergent n-octyl beta-D-glucopyranoside as reported by Miller et al. (1987) [Miller J. F., Hinchigeri, S. B., Parkes-Loach, P. S., Callahan, P. M., Sprinkle, J. R., & Loach, P. A. (1987) Biochemistry 26, 5055-5062]. Fluorescence polarization and CD measurements at 77 K suggest that this subunit form must consist of an interacting bacteriochlorophyll a dimer in all three bacterial species. A small, local decrease in the polarization of the fluorescence is observed upon excitation at the blue side of the absorption band of the B820 subunit. This decrease is ascribed to the presence of a high-energy exciton component, perpendicular to the main low-energy exciton component. From the extent of the depolarization, we estimate the oscillator strength of the high-energy component to be at most 3% of the main absorption band. The optical properties of B820 are best explained by a Bchl a dimer that has a parallel or antiparallel configuration with an angle between the Qy transition dipoles not larger than 33 degrees. The importance of this structure is emphasized by the results showing that core antennas from three different purple bacteria have a similar structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriochlorophylls↗

PubMed1988

Linear dichroism of the complex between the gene 32 protein of bacteriophage T4 and poly(1,N6-ethenoadenylic acid).

We performed linear dichroism measurements in compressed polyacrylamide gels on the complex between the helix-destabilizing protein of bacteriophage T4, GP32 and poly(1,N6-ethenoadenylic acid), which is used as a model system for single-stranded DNA. A strong hyperchromism for poly(1,N6-ethenoadenylic acid) in the complex indicates a strongly altered conformation. The positive linear dichroism in the wavelength region where the bases absorb must be explained by a strong tilting of the bases in the complex. This finding is in accordance with results from earlier studies, using electric birefringence and circular dichroism measurements. Our measurements show that the angle between the bases and the local helix axis is 42(+/- 6)degrees. In addition, a pronounced contribution from the tryptophan residues of GP32 can be recognized, indicating that several of these residues have a specific orientation in the complex. The sign of the dichroism due to the tryptophan residues is the same as that due to the DNA bases. However, it is not sufficient to assume that all the observed dichroism is due to one or more intercalated tryptophan residues and there must be one or more additional tryptophan residues that make an angle of less than 40 degrees with the local helix axis. Some possible structures of the DNA-protein complex are discussed.

DNA-Binding Proteins↗

PubMed1988

The internal dynamics of gene 32 protein-DNA complexes studied by quasi-elastic light scattering.

The hydrodynamic properties of large homodisperse single stranded DNAs complexed with the helix destabilizing protein of phage T4, the product of gene 32 (GP32), have been measured. The results suggest a size of the binding site between 8 and 10 nucleotides/GP32 molecule, in reasonable agreement with earlier work on a complex between GP32 and single stranded 145 base DNA. From static light scattering experiments it is concluded that the persistence length of these complexes is about 30 nm, distinctly smaller than the generally accepted value for double stranded DNA. The quasi-elastic light scattering properties of the DNA-GP32 complexes were determined. The variation of the apparent translation diffusion coefficient Dapp with the scattering vector q was analyzed using the discrete ISMF and Rouse-Zimm models [S.C. Lin et al., Biopolymers 17 (1978) 425]. The model parameters that followed from the fit of Dapp versus q2 and from an extensive global analysis of the actually measured autocorrelation functions agreed with the notion that these DNA-protein complexes are indeed rather flexible. The continuous Soda model [K. Soda, Macromolecules 17 (1984) 2365] could successfully explain the variation of Dapp versus q2, assuming a persistence length of 30 nm and a base-base distance in the complex of 0.44 nm.

Bacteriophage lambda↗

PubMedDate not supplied

(Sub)-picosecond spectral evolution of fluorescence in photoactive proteins studied with a synchroscan streak camera system.

The spectral evolution of three photoactive proteins has been investigated by measuring the fluorescence with good temporal and wavelength resolution and a high signal-to-noise ratio. Upon excitation at 400 nm wild-type (wt) PYP both at neutral pH and in the low-pH blueshifted pBdark state exhibited a strong quenching of the fluorescence, the major part of which could be described by lifetimes of about 1.7 and 7.7 ps. The remaining fluorescence decay occurred multiexponentially with lifetimes between 30 and 125 ps. Additionally, in wtPYP at neutral pH, a dynamic Stokes shift was found to occur with a time constant of about 0.25 ps. In a PYP preparation that was reconstituted with the chromophore 7-hydroxy-coumarin-3- carboxylic acid rather than the native coumaric acid, and which is therefore not capable of performing the cis-trans-isomerization that initiates the photocycle in wtPYP, the fluorescence was found to decay multiexponentially with lifetimes of 51 ps, 0.33 and 3.77 ns. Additionally, dynamic Stokes shifts were observed with time constants of about 0.1 and 3.5 ps. Upon comparison of the dynamics of this preparation with that of wtPYP the multiexponential decay with lifetimes of 1.7 and 7.7 ps found in wtPYP was attributed to photochemistry of the p-coumaric-acid chromophore. The emission from bacteriorhodopsin mutant D85S upon excitation at 635 nm decays biexponentially with estimated lifetimes of 5.2 and 19.1 ps. No dynamic Stokes shift was observed here. Four lifetimes were needed to describe the decay of the emission from the A* state in the green fluorescent protein. From a target analysis it was concluded that the longer lifetimes are accompanied by a decreasing probability of forming I*, which approaches zero with the longest A* lifetime of 1.5 ns. These observations may be explained by heterogeneity of A and by relaxation of A*. In all three systems studied, multiexponential decay of emission was present, suggesting that heterogeneity is a common feature of these chromophore protein complexes.

Coumaric Acids↗