Search PubMed⌕ Search

Biomedical subjects

M H Vos

Publications and source records attributed to M H Vos.

At least 19 recordsLinked to original sources
PubMed2006

Functional implications of the propionate 7-arginine 220 interaction in the FixLH oxygen sensor from Bradyrhizobium japonicum.

BjFixL from Bradyrhizobium japonicum is a heme-based oxygen sensor implicated in the signaling cascade that enables the bacterium to adapt to fluctuating oxygen levels. Signal transduction is initiated by the binding of O(2) to the heme domain of BjFixL, resulting in protein conformational changes that are transmitted to a histidine kinase domain. We report structural changes of the heme and its binding pocket in the Fe(II) deoxy and Fe(III) met states of the wild-type BjFixLH oxygen sensor domain and four mutants of the highly conserved residue arginine 220. UV-visible, electron paramagnetic resonance, and resonance Raman spectroscopies all showed that the heme iron of the R220H mutant is unexpectedly six-coordinated at physiological pH in the Fe(III) state but undergoes pH- and redox-dependent coordination changes. This behavior is unprecedented for FixL proteins, but is reminiscent of another oxygen sensor from E. coli, EcDos. All mutants in their deoxy states are five-coordinated Fe(II), although we report rupture of the residue 220-propionate 7 interaction and structural modifications of the heme conformation as well as propionate geometry and flexibility. In this work, we conclude that part of the structural reorganization usually attributed to O(2) binding in the wild-type protein is in fact due to rupture of the Arg220-P7 interaction. Moreover, we correlate the structural modifications of the deoxy Fe(II) states with k(on) values and conclude that the Arg220-P7 interaction is responsible for the lower O(2) and CO k(on) values reported for the wild-type protein.

Arginine↗
PubMed2005

Geminate carbon monoxide rebinding to a c-type haem.

A chemically modified form of cytochrome c(cyt. c), termed carboxymethyl cytochrome c(cm cyt. c), possesses a vacant sixth coordination site to the haem iron that is available to bind external ligands. We present data on the rapid flash photolysis of CO from the ferrous haem iron of cm cyt. c and describe the kinetics and spectral transitions that accompany the recombination. This was achieved using 30-femtosecond laser pulses and a white light continuum to monitor spectral transitions. Whereas the photo-dissociation quantum yield is close to 1, the yield of CO escape from the protein (the apparent quantum yield, varphi) relative to myoglobin (varphi=1) is small due to rapid geminate recombination of CO. On ligand photo-dissociation the haem undergoes a spin-state transition from low-spin ferrous CO bound to penta-coordinate high-spin. Subsequently the system reverts to the CO bound form. The data were fitted with a minimum number of exponentials using global analysis. Recombination of CO with the haem iron of cm cyt. c is multiphasic (tau=16 ps, 120 ps and 1 ns), involving three spectrally distinct components. The fraction of haem (0.11) not recombining with CO within 4 ns is similar to the value of varphi(0.12) measured on the same preparation by the "pulse method" (M. Brunori, G. Giacometti, E. Antonini and J. Wyman, Proc. Natl. Acad. Sci. USA, 1973, 70, 3141-3144, ). This implies that no further geminate recombination occurs at t>4 ns. This unusually efficient CO-haem geminate recombination indicates the sterically hindered ("caged") nature of the distal haem pocket in cm cyt. c from which it is difficult for CO to escape. The large geminate phase may be contrasted with the behaviour of myoglobin in which geminate recombination is small. This is in general agreement with the well-documented extensive structural dynamics in myoglobin that allow ligand passage, and a higher structural rigidity in cyt. c imposed by the restraints of minimising reorganisation energy for electron transfer (M. Brunori, D. Bourgeois and D. Vallone, J. Struct. Biol., 2004, 147, 223-234, ). The high pH ferrous form of cm cyt. c is a low-spin species having a lysine bound to the central iron atom of the haem (M. Brunori, M. Wilson and E. Antonini, J. Biol. Chem., 1972, 247, 6076-6081; G. Silkstone, G. Stanway, P. Brzezinski and M. Wilson, Biophys. Chem., 2002, 98, 65-77, ). This high pH (pH approximately 8) form of deoxy cm cyt. c undergoes photo-dissociation of lysine (although the proximal histidine is possible) after photo-excitation. Recombination occurs with a time constant (tau) of approximately 7 ps. This is similar to that observed for the geminate rebinding of the Met80 residue in native ferrous cyt. c(tau approximately 6 ps) following its photo-dissociation (S. Cianetti, M. Negrerie, M. Vos, J.-L. Martin and S. Kruglik, J. Am. Chem. Soc., 2004, 126, 13 932-13 933; W. Wang, X. Ye, A. Demidov, F. Rosca, T. Sjodin, W. Cao, M. Sheeran and P. Champion, J. Phys. Chem., 2000, 104, 10 789-10 801, ).

Carbon Monoxide↗
PubMed2004

CO vibration as a probe of ligand dissociation and transfer in myoglobin.

We report femtosecond visible pump, midinfrared probe, spectrally integrated experiments resolving the dynamics of CO in myoglobin upon photodissociation. Our results show a progressive change in absorption strength of the CO vibrational transition during its transfer from the heme to the docking site, whereas the vibrational frequency change is faster than our time resolution. A phenomenological model gives good qualitative agreement with our data for a time constant of 400 fs for the change in oscillator strength. Density-functional calculations demonstrate that indeed vibrational frequency and absorption strength are not linearly coupled and that the absorption strength varies in a slower manner due to charge transfer from the heme iron to CO.

Biophysical Phenomena↗
PubMed2001

Dynamics of nitric oxide in the active site of reduced cytochrome c oxidase aa3.

Nitric oxide (NO) is involved in the regulation of respiration by acting as a competitive ligand for molecular oxygen at the binuclear active site of cytochrome c oxidase. The dynamics of NO in and near this site are not well understood. We performed flash photolysis studies of NO from heme a3 in cytochrome c oxidase from Paracoccus denitrificans, using femtosecond transient absorption spectroscopy. The formation of the product state--the unliganded heme a3 ground state--occurs in a similar stepwise manner (period approximately 700 fs) as previously observed for carbon monoxide photolysis from this enzyme and interpreted in terms of ballistic ligand motions in the active site on the subpicosecond time scale [Liebl, U., Lipowski, G., Négrerie, M., Lambry, J.-C., Martin, J.-L., and Vos, M. H. (1999) Nature 401, 181-184]. A fraction (approximately 35% at very low NO concentrations) of the dissociated NO recombines with heme a3 in 200-300 ps. The presence of this recombination phase indicates that a transient bond to the second ligand-binding site, a copper atom (CuB), has a short lifetime or may not be formed. Increasing the NO concentration increases the recombination yield on the hundreds of picoseconds time scale. This effect, unprecedented for heme proteins, implies that, apart from the one NO molecule bound to heme a3, a second NO molecule can be accommodated in the active site, even at relatively low (submicromolar) concentrations. Models for NO accommodation in the active site, based on molecular dynamics energy minimizations are presented. Pathways for NO motion and their relevance for the regulation of respiration are discussed.

Binding Sites↗
PubMed2000

Electrochromic detection of a coherent component in the formation of the charge pair P(+)H(L)(-) in bacterial reaction centers.

We demonstrate coupling of an intraprotein electron transfer reaction to coherent vibrational motions. The kinetics of charge separation toward the radical pair state P(+)H(L)(-) were studied in reaction centers of Rhodobacter sphaeroides at 15 K. The electrochromic shift of the bacteriochlorophyll monomers is the most prominent spectral feature associated with this charge displacement. The newly reported absolute absorption spectrum of the P(+)H(L)(-) state is discussed in terms of this shift. In wild-type reaction centers, the rise kinetics of the electrochromic shift display a small but significant 30 cm(-)(1) periodic modulation (period of approximately 1 ps). This modulation is also present in FL181Y mutant reaction centers, where overall charge separation is somewhat more rapid than in the wild-type reaction center. In contrast, in YM210L mutant reaction centers, where the charge separation is much slower, the modulation is absent. The conclusion that the motion along the reaction coordinate has a 30 cm(-)(1) coherent component is discussed in light of possible mechanisms of electron transfer.

Electrochemistry↗
PubMed2000

Intraprotein radical transfer during photoactivation of DNA photolyase.

Amino-acid radicals play key roles in many enzymatic reactions. Catalysis often involves transfer of a radical character within the protein, as in class I ribonucleotide reductase where radical transfer occurs over 35 A, from a tyrosyl radical to a cysteine. It is currently debated whether this kind of long-range transfer occurs by electron transfer, followed by proton release to create a neutral radical, or by H-atom transfer, that is, simultaneous transfer of electrons and protons. The latter mechanism avoids the energetic cost of charge formation in the low dielectric protein, but it is less robust to structural changes than is electron transfer. Available experimental data do not clearly discriminate between these proposals. We have studied the mechanism of photoactivation (light-induced reduction of the flavin adenine dinucleotide cofactor) of Escherichia coli DNA photolyase using time-resolved absorption spectroscopy. Here we show that the excited flavin adenine dinucleotide radical abstracts an electron from a nearby tryptophan in 30 ps. After subsequent electron transfer along a chain of three tryptophans, the most remote tryptophan (as a cation radical) releases a proton to the solvent in about 300 ns, showing that electron transfer occurs before proton dissociation. A similar process may take place in photolyase-like blue-light receptors.

DNA Repair↗
PubMed2000

Femtosecond resolution of ligand-heme interactions in the high-affinity quinol oxidase bd: A di-heme active site?

Interaction of the two high-spin hemes in the oxygen reduction site of the bd-type quinol oxidase from Escherichia coli has been studied by femtosecond multicolor transient absorption spectroscopy. The previously unidentified Soret band of ferrous heme b(595) was determined to be centered around 440 nm by selective excitation of the fully reduced unliganded or CO-bound cytochrome bd in the alpha-band of heme b(595). The redox state of the b-type hemes strongly affects both the line shape and the kinetics of the absorption changes induced by photodissociation of CO from heme d. In the reduced enzyme, CO photodissociation from heme d perturbs the spectrum of ferrous cytochrome b(595) within a few ps, pointing to a direct interaction between hemes b(595) and d. Whereas in the reduced enzyme no heme d-CO geminate recombination is observed, in the mixed-valence CO-liganded complex with heme b(595) initially oxidized, a significant part of photodissociated CO does not leave the protein and recombines with heme d within a few hundred ps. This caging effect may indicate that ferrous heme b(595) provides a transient binding site for carbon monoxide within one of the routes by which the dissociated ligand leaves the protein. Taken together, the data indicate physical proximity of the hemes d and b(595) and corroborate the possibility of a functional cooperation between the two hemes in the dioxygen-reducing center of cytochrome bd.

Binding Sites↗
PubMed1999

Coherent reaction dynamics in a bacterial cytochrome c oxidase.

Biological reactions in protein complexes involve structural dynamics spanning many orders of magnitude in time. In standard descriptions of catalysis by enzymes, the transition state between reactant and product is reached by thermal, stochastic motion. In the ultrashort time domain, however, the protein moiety and cofactor motions leading to altered conformations can be coherent rather than stochastic in nature. Such coherent motions may play a key role in controlling the accessibility of the transition state and explain the high efficiency of the reaction. Here we present evidence for coherent population transfer to the product state during an ultrafast reaction catalysed by a key enzyme in aerobic organisms. Using the enzyme cytochrome c oxidase aa3 from the bacterium Paracoccus denitrificans, we have studied haem dynamics during the photo-initiated ultrafast transfer of carbon monoxide from haem a3 to CuB by femtosecond spectroscopy. The ground state of the unliganded a3 species is populated in a stepwise manner in time, indicating that the reaction is mainly governed by coherent vibrations (47cm(-1)). The reaction coordinate involves conformational relaxation of the haem group and we suggest that ligand transfer also contributes.

Carbon Monoxide↗
PubMed1999

Geminate recombination of nitric oxide to endothelial nitric-oxide synthase and mechanistic implications.

The nitric-oxide synthase (NOS) catalyzes the oxidation of L-arginine to L-citrulline and NO through consumption of oxygen bound to the heme. Because NO is produced close to the heme and may bind to it, its subsequent role in a regulatory mechanism should be scrutinized. We therefore examined the kinetics of NO rebinding after photodissociation in the heme pocket of human endothelial NOS by means of time-resolved absorption spectroscopy. We show that geminate recombination of NO indeed occurs and that this process is strongly modulated by L-Arg. This NO rebinding occurs in a multiphasic fashion and spans over 3 orders of magnitude. In both ferric and ferrous states of the heme, a fast nonexponential picosecond geminate rebinding first takes place followed by a slower nanosecond phase. The rates of both phases decreased, whereas their relative amplitudes are changed by the presence of L-Arg; the overall effect is a slow down of NO rebinding. For the isolated oxygenase domain, the picosecond rate is unchanged, but the relative amplitude of the nanosecond binding decreased. We assigned the nanosecond kinetic component to the rebinding of NO that is still located in the protein core but not in the heme pocket. The implications for a mechanism of regulation involving NO binding are discussed.

Arginine↗
PubMed1999

Spectroscopic resolution of the picosecond reduction kinetics of the secondary electron acceptor A1 in photosystem I.

Forward electron transfer in photosystem I from Synechocystis sp. PCC 6803 has been studied in the picosecond time range with transient absorption spectroscopy in the blue and near-UV spectral regions. From the direct measurement, at 380-390 nm, of the reduction kinetics of the phylloquinone secondary acceptor A1 and from the absence of spectral evolution between 100 ps and 2 ns, we conclude that electron transfer, from the chlorophyll a primary acceptor A0, to A1 occurs directly and completely with a time constant of about 30 ps.

Cyanobacteria↗
PubMed1999

Identification of SSF1, CNS1, and HCH1 as multicopy suppressors of a Saccharomyces cerevisiae Hsp90 loss-of-function mutation.

Hsp90 functions in a multicomponent chaperone system to promote the maturation and maintenance of a diverse, but specific, set of target proteins that play key roles in the regulation of cell growth and development. To identify additional components of the Hsp90 chaperone system and its targets, we searched for multicopy suppressors of various temperature-sensitive mutations in the yeast Hsp90 gene, HSP82. Three suppressors were isolated for one Hsp90 mutant (glutamate --> lysine at amino acid 381). Each exhibited a unique, allele-specific pattern of suppression with other Hsp90 mutants and had unique structural and biological properties. SSF1 is a member of an essential gene family and functions in the response to mating pheromones. CNS1 is an essential gene that encodes a component of the Hsp90 chaperone machinery. The role of HCH1 is unknown; its sequence has no strong homology to any protein of known function. SSF1 and CNS1 were weak suppressors, whereas HCH1 restored wild-type growth rates at all temperatures tested to cells expressing the E381K mutant. Overexpression of CNS1 or HCH1, but not SSF1, enhanced the maturation of a heterologous Hsp90 target protein, p60(v-src). These results suggest that like Cns1p, Hch1p is a general modulator of Hsp90 chaperone functions, whereas Ssf1p likely is either an Hsp90 target protein or functions in the same pathway as an Hsp90 target protein.

Amino Acid Substitution↗
PubMed1998

Low frequency vibrational modes in proteins: changes induced by point-mutations in the protein-cofactor matrix of bacterial reaction centers.

As a step toward understanding their functional role, the low frequency vibrational motions (<300 cm-1) that are coupled to optical excitation of the primary donor bacteriochlorophyll cofactors in the reaction center from Rhodobacter sphaeroides were investigated. The pattern of hydrogen-bonding interaction between these bacteriochlorophylls and the surrounding protein was altered in several ways by mutation of single amino acids. The spectrum of low frequency vibrational modes identified by femtosecond coherence spectroscopy varied strongly between the different reaction center complexes, including between different mutants where the pattern of hydrogen bonds was the same. It is argued that these variations are primarily due to changes in the nature of the individual modes, rather than to changes in the charge distribution in the electronic states involved in the optical excitation. Pronounced effects of point mutations on the low frequency vibrational modes active in a protein-cofactor system have not been reported previously. The changes in frequency observed indicate a strong involvement of the protein in these nuclear motions and demonstrate that the protein matrix can increase or decrease the fluctuations of the cofactor along specific directions.

Bacterial Proteins↗
PubMed1997

In vivo functions of the Saccharomyces cerevisiae Hsp90 chaperone.

In the highly concentrated environment of the cell, polypeptide chains are prone to aggregation during synthesis (as nascent chains await the emergence of the remainder of their folding domain), translocation, assembly, and exposure to stresses that cause previously folded proteins to unfold. A large and diverse group of proteins, known as chaperones, transiently associate with such folding intermediates to prevent aggregation, but in many cases the specific functions of individual chaperones are still not clear. In vivo, Hsp90 (heat shock protein 90) plays a role in the maturation of components of signal transduction pathways but also exhibits chaperone activity with diverse proteins in vitro, suggesting a more general function. We used a unique temperature-sensitive mutant of Hsp90 in Saccharomyces cerevisiae, which rapidly and completely loses activity on shift to high temperatures, to examine the breadth of Hsp90 functions in vivo. The data suggest that Hsp90 is not required for the de novo folding of most proteins, but it is required for a specific subset of proteins that have greater difficulty reaching their native conformations. Under conditions of stress, Hsp90 does not generally protect proteins from thermal inactivation but does enhance the rate at which a heat-damaged protein is reactivated. Thus, although Hsp90 is one of the most abundant chaperones in the cell, its in vivo functions are highly restricted.

HSP90 Heat-Shock Proteins↗
PubMed1997

Spectral equilibration and primary photochemistry in Heliobacillus mobilis at cryogenic temperature.

We performed multicolor femtosecond transient absorption measurements on membranes of the photosynthetic bacterium Heliobacillus mobilis at 20 K, by selective excitation at either the red or the blue extreme of the bacteriochlorophyll g Q(Y) band, which is split in three spectral forms (Bchl g 778, 793, and 808) at low temperature. In contrast to room temperature, there is no observable uphill energy transfer upon excitation at the red extreme. This provides a direct experimental confirmation of the expected strong temperature dependence of uphill energy transfer in multichromophore systems. Upon excitation at the blue edge, downhill energy transfer is observed on time ranges varying over 2 orders of magnitude and is discussed in terms of four distinct energy transfer processes: Bchl g 778* --> Bchl g 793* (approximately 50 fs); Bchl g 778* --> Bchl g 808* (approximately 400 fs); Bchl g 793* --> Bchl g 808* (approximately 1.4 ps); and within Bchl g 808* (approximately 7 ps). Surprisingly, the amount of oxidized primary donor P798+ formed on the time scale of picoseconds and tens of picoseconds was found to depend on the excitation conditions: trapping occurs mainly in approximately 80 ps and slower from directly excited Bchl g 808* and can additionally occur in a few picoseconds from Bchl g 778* and Bchl g 793* upon blue excitation. This finding implies that spectral equilibration is not complete prior to charge separation and furthermore is inconsistent with a funnel model, in which P798 is surrounded by long-wavelength pigments. More generally, we discuss to what extent our data bring constraints on the spatial distribution of the different spectral forms of the pigments.

Bacteria↗
PubMed1996

Energy and electron transfer upon selective femtosecond excitation of pigments in membranes of Heliobacillus mobilis.

Excitation energy transfer steps in membranes of Heliobacillus mobilis were directly monitored by transient absorption spectroscopy with a time resolution of 30 fs under selective excitation within the inhomogeneously broadened bacteriochlorophyll g QY band. The initial anisotropy was found to be > 0.4, indicating that the pigments are excitonically coupled. After initial decay of this anisotropy in < 50 fs, major sub-picosecond components associated with spectral equilibration were identified, corresponding to uphill energy transfer with a 300 fs time constant (812 nm excitation) and downhill energy transfer with 100 and 500 fs components (770 nm excitation). These equilibrations are ascribed predominantly to single excitation transfer steps, as anisotropy measurements showed that equilibration within spectrally similar pigments occurs on the same time scale as spectral equilibration, a situation which contrasts with that in photosystem I. Downhill energy transfer occurs to a significant extent directly to an energetically heterogeneous population of excited states as well as in a sequential way via gradually lower-lying pools of bacteriochlorophyll g. This finding supports a description in which all pigments, including the bluemost absorbing, are spatially organized in a random way rather than in clusters of spectrally similar species. Spectral equilibration is not entirely completed prior to formation of the primary radical pair P798 + A0-, which was found to proceed in a multiexponential way (time constants of 5 and 30 ps). No indication for the formation of radical species other than P798 + A0- on the time scale up to 100 ps was found.

Bacteria↗
PubMed1996

Vibrational dephasing of long- and short-lived primary donor excited states in mutant reaction centers of Rhodobacter sphaeroides.

Femtosecond spectroscopy was used to study vibrational dynamics in the first singlet excited state (P*) of the primary donor of bacterial reaction centers (RC)in which primary electron transfer dynamics have been altered by single amino acid modifications. We studied intracytoplasmic RC-only membranes containing Rhodobacter sphaeroides wild-type RCs and RCs bearing mutations in the vicinity of P, where Tyr M210 was modified to His, Leu, and Trp and where Phe L181 was modified to Tyr. These mutations do not change the frequencies of the main low-frequency activated modes, which is consistent with a description in which these modes involve extended regions of the protein. Electron transfer in FL181Y, YM210H, and wild-type RCs at 10 K occurs in approximately 1 ps or less, and damping of the coherences occurs simultaneously with the decay of the P* excited state. These results, and a comparison with YM210L RCs, show that in wild-type RCs the damping is primarily determined by the depletion of P* and not by vibrational dephasing induced by interactions with the bath or nonharmonic coupling. In the YM210L and W mutants, electron transfer occurs on a time scale of hundreds of picoseconds at 10 K. Analysis of the longer-lasting vibrational dynamics in these mutants sets a new lower limit for the intrinsic vibrational dephasing time of 1.2 ps for some modes, but of approximately 2 ps for most activated modes.

Electron Transport↗
PubMed1994

Coherent nuclear dynamics at room temperature in bacterial reaction centers.

A room-temperature study is reported of the femtosecond spectral evolution of the stimulated emission band of the primary electron-transfer precursor P* in bacterial photosynthesis. The study was performed with membranes of the antenna-deficient RCO1 mutant of Rhodobacter sphaeroides. A time-dependent red shift, reflecting nuclear motion out of the Franck-Condon region of the excited state, is resolved. Analysis of oscillatory features persisting for > 1 ps in the kinetics revealed main frequencies of the activated motions at 30, 84, 145, and 192 cm-1. The oscillations occur on the time scale of primary electron transfer. Our results set a lower limit for the vibrational dephasing time in P* that is not compatible with the usual assumption in theoretical treatments of complete vibrational relaxation prior to electron transfer, even at room temperature.

Bacteriochlorophylls↗