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We provide a direct demonstration of a "kinetic trap" mechanism in the proximal 5-coordinate heme-nitrosyl complex (5c-NO) of cytochrome c' from Alcaligenes xylosoxidans (AXCP) in which picosecond rebinding of the endogenous His ligand following heme-NO dissociation acts as a one-way gate for the release of proximal NO into solution. This demonstration is based upon picosecond transient absorption changes following NO photodissociation of the proximal 5c-NO AXCP complex. We have determined the absolute transient absorption spectrum of 4-coordinate ferrous heme to which NO rebinds with a time constant τ(NO) = 7 ps (k(NO) = 1.4 × 10(11) s(-1)) and shown that rebinding of the proximal histidine to the 4-coordinate heme takes place with a time constant τ(His) = 100 ± 10 ps (k(His) = 10(10) s(-1)) after the release of NO from the proximal heme pocket. This rapid His reattachment acts as a one-way gate for releasing proximal NO by precluding direct proximal NO rebinding once it has left the proximal heme pocket and requiring NO rebinding from solution to proceed via the distal heme face.

International audience; Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor that synthesizes cGMP upon NO activation. In synergy with the artificial allosteric effector BAY 41-2272 (a lead compound for drug design in cardiovascular treatment), sGC can also be activated by carbon monoxide (CO), but the structural basis for this synergistic effect are unknown. We recorded in the unusually broad time range from 1 ps to 1 s the dynamics of the interaction of CO binding to full length sGC, to the isolated sGC heme domain ß1(200) and to the homologous bacterial NO-sensor from Clostridium botulinum. By identifying all phases of CO binding in this full time range and characterizing how these phases are modified by BAY 41-2272, we show that this activator induces the same structural changes in both proteins. This result demonstrates that the BAY 41-2272 binding site resides in the ß1(200) sGC heme domain and is the same in sGC and in the NO-sensor from Clostridium botulinum. Cop. 2012 American Chemical Society.

The function of inducible NO synthase (WT iNOS) depends on the release of NO from the ferric heme before the enzyme is reduced. Key parameters controlling ligand dynamics include the distal and proximal heme pocket amino acids, as well as the inner solvent molecules. In this work, we tested how a point mutation in the distal heme side of WT iNOS affected the geminate rebinding of NO by ultrafast kinetics and molecular dynamics simulations. The mutation sequestered much of the photodissociated NO close to the heme compared to WT iNOS, with a main picosecond phase accounting for 78% of the rebinding to the arginine-bound Val346Ile protein. Consequently, the probability of NO release from Val346Ile decreased as compared to that from WT iNOS, provided the substrate binding site is filled. These data are rationalized by a steric effect of the Ile methyl group inducing events mediated by the substrate, transmitted via the propionates to the NO and the protein. This model is consistent with the role of the H-bonding network involving the heme, the substrate, and the BH4 cofactor in controlling NO release, with a key role of the heme propionates [Gautier et al. (2006) Nitric Oxide 15, 312]. These data support the effect of Val346Ile mutation in decreasing NO release and slowing down NO synthesis compared to WT iNOS determined by single turnover catalysis [Wang et al. (2004) J. Biol. Chem. 279, 19018].

International audience; Deactivation of the lowest excited triplet (pi,pi*) state, (3)(pi,pi*), of the cationic water-soluble Cu(II)-5,10,15,20-meso-tetrakis(4-N-methylpyridyl)porphyrin (CuTMpyP4) was studied by femtosecond transient absorption spectroscopy in three oxygen-containing solvents (Lewis bases) of various polarity, water, methanol, and dimethyl sulfoxide (DMSO). In all of these solvents, the (3)(pi,pi*) state depopulation follows biexponential kinetics. A majority of the (3)(pi,pi*) state population (similar to80%) deactivates very quickly with a time constant of about 1-2 ps to give rise to formation of an exciplex (CuTMpyP4)*-L between the porphyrin in its excited (d,d) state and a solvent molecule, L, the latter playing the role of porphyrin axial ligand. The exciplex lifetime is found to depend on the solvent dielectric constant E and increases from 7 ps in water (epsilon = 78.3) to 27 ps in methanol (epsilon = 32.7), through 23 ps in DMSO (epsilon = 46.5). A minor part of the initial (3)(pi,pi*) state population (similar to20%) deactivates to the ground state, without any detectable intermediate, with time constants of 25, 8, and 11 ps in water, DMSO, and methanol, respectively. These rather fast pathways (picosecond time scale) of excitation deactivation to the ground state are interpreted in terms of quenching influence of some low-lying intramolecular charge-transfer states that belong to four- and five-coordinate CuTMpyP4. A partitioning mechanism of (3)(pi,pi*) state CuTMpyP4 molecules into two populations decaying by different paths, that is, through exciplex formation and "directly" to the ground state, is proposed.

International audience; 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.

We have investigated ligand motions in the heme a3−CuB binuclear active site of cytochrome c oxidase by molecular dynamics simulations. The starting structural model is based on the two-subunit structure from the Paracoccus denitrificans enzyme and contains carbon monoxide (CO) bound to heme a3. Short (1 ps) trajectories of the enzyme were calculated, each initiated by the sudden breaking of the Fea3−CO bond. A comparison of two sets of calculations suggests a functional mechanistic role of the covalent bond between Tyr280 and His276, the latter being one of the three histidines coordinating the copper atom CuB. In particular, the presence of this bond enhances the coupling of the CO motion to the environment and confines motion of CO on the picosecond time scale to the region close to CuB. On the time scale of a few hundred femtoseconds after dissociation, the most important movement of CO consists of rotation over ∼90° and the most favorable position for binding to CuB appears to be occupied after 300−4...

Flow of excitation energy within the bacteriochlorin cofactor system of bacterial reaction centers has been studied by multicolor transient absorption spectroscopy using differently shaped excitation pulses of 30 fs, both at room temperature and at 15 K. This approach, which includes the analysis of free induction decay signals, helps to disentangle the processes of electronic dephasing, energy transfer, internal conversion, and nuclear motion, all taking place on the time scale of ∼100 fs. Part of the excitations (estimated at 80−90% at room temperature) flow via the scheme H* → B* → P+* → P-*, in which H* and B* represent excited bacteriopheophytin and bacteriochlorophyll monomers and P+* and P-* the upper and lower excited states of the bacteriochlorophyll dimer P, respectively. H* → B* takes less than 100 fs. B* → P+* (∼200 fs) energy transfer is a slower process than the internal conversion process within P* (50−100 fs) and therefore is rate limiting for P-* formation. At low temperature, electronic ...

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 be0.4, indicating that the pigments are excitonically coupled. After initial decay of this anisotropy in50 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.

Separation of the photophysical aspects of the sub-picosecond (sub-ps) time-resolved resonance Raman signal from contributions due to conformation has been achieved by comparing deoxyhemoglobin (Hb) in the T state with (carbonmonoxy)hemoglobin (HbCO), deoxy-P4 @CO) (all R state), and monomers deoxymyoglobin and (carbonmonoxy)myoglobin (MbCO) 104 consists of a tetramer of four P-subunits and shows no cooperativity). In all photolyzed species, Hb*(CO), Mb*(CO), and P4*(CO), the iron- histidine out-of-plane mode (YFe-His), indicative of heme doming, achieves 90% of its full intensity in 1 ps. The frequency of this mode (223-228 cm-') is shifted significantly relative to equilibrium deoxy- Hb (210-216 cm-') in the T state, but not with respect to either equilibrium deoxy-Mb or deoxy-/34. A correlation between the +12 cm-' bandshift of VFe-His and the -2 cm-' shift of the electron density marker band (~4 at 1370 cm-l) relative to T-state deoxy-Hb is shown to hold on all time scales, including the sub-picosecond time scale. Photolyzed Hb*(CO) consists of R-state or weakly interacting tetramers on the picosecond time scale and is shown to have properties similar to those of photolyzed Mb*(CO) and /34*(CO> on the picosecond time scale. These results establish that heme doming occurs as an ultrafast reaction to ligand dissociation and that heme doming is the primary event in the sequence of conformational changes leading to the cooperative R - T transition. In the oxygen transport protein hemoglobin, the formation or breakage of a single chemical bond between the heme iron and a diatomic ligand is transmitted to the protein and expressed in terms of intersubunit structural changes, which ultimately modify the binding affinity of all four heme irons in the protein. The X-ray crystal structure of hemoglobin shows that the heme iron is nearly coplanar with the heme in ligated hemoglobin and more than 0.4 A from the heme

The temporal evolution of the near-infrared stimulated emission band of the special pair excited state (P*) in the reaction center of Rhodobacter sphaeroides has been studied in intracytoplasmic membranes of the antenna-deficient RCO1 mutant at 10 K with a resolution of 30 fs. On the 100-fs time scale the emission band gradually shifts to longer wavelengths. After 150 fs the band shifts back to shorter wavelengths and continues to develop on the picosecond time scale in a damped oscillatory manner (most prominent fundamental frequencies around 15 cm-1 and at 92, 122, and 153 cm-1). These phenomena are shown to be due to low-frequency vibrational motions in the P* excited state that conserve their phase on the time scale of electron transfer. These results imply that the vibrational manifold of P* is not thermalized during the electron-transfer reaction in functional reaction centers. The initial Stokes shift dynamics are largely determined by the modes in the 90-160-cm-1 frequency range, which probably involve motions of several chromophores, including the bacteriopheophytin electron acceptor HL.

Ultrafast absorption spectroscopy is used to study heme-NO recombination at room temperature in aqueous buffer on time scales where the ligand cannot leave its cage environment. While a single barrier is observed for the cage recombination of NO with heme in the absence of globin, recombination in hemoglobin and myoglobin is nonexponential. Examination of hemoglobin with and without inositol hexaphosphate points to proximal constraints as important determinants of the geminate rebinding kinetics. Molecular dynamics simulations of myoglobin and heme-imidazole subsequent to ligand dissociation were used to investigate the transient behavior of the Fe-proximal histidine coordinate and its possible involvement in geminate recombination. The calculations, in the context of the absorption measurements, are used to formulate a distinction between nonexponential rebinding that results from multiple protein conformations (substates) present at equilibrium or from nonequilibrium relaxation of the protein triggered by a perturbation such as ligand dissociation. The importance of these two processes is expected to depend on the time scale of rebinding relative to equilibrium fluctuations and nonequilibrium relaxation. Since NO rebinding occurs on the picosecond time scale of the calculated myoglobin relaxation, a time-dependent barrier is likely to be an important factor in the observed nonexponential kinetics. The general implications of the present results for ligand binding in heme proteins and its time and temperature dependence are discussed. It appears likely that, at low temperatures, inhomogeneous protein populations play an important role and that as the temperature is raised, relaxation effects become significant as well.

The initial step of charge separation at 10 K has been monitored with 100-fs time resolution in reaction centers from Rhodopseudomonas viridis and Rhodobacter sphaeroides as well as in reaction centers from the latter species in which one of the two monomeric bacteriochlorophyll (B) molecules has been removed by treatment with borohydride. Upon excitation at 870 nm, the absorbance changes measured at several wavelengths in the near-infrared absorption bands of the pigments, and notably at the absorption maximum of the B molecule(s), give no indication of a detectable concentration of B-. Instead, the appearance of the cation radical of the dimeric primary electron donor (P) and of the bacteriopheophytin anion develops in concert with the decay of P*. An initial bleaching of the 850-nm band in reaction centers from Rho- dopseudomonas uiridis is consistent with an assignment of at least a large fraction of this band to the high-energy exciton component of P. Upon excitation of the B molecule(s) around 600 nm in the three types of reaction centers investigated, ultrafast energy transfer leads to the formation of P* in less than 100 fs. Under these conditions, a fast transient bleaching decaying with a 400-fs time constant is observed within the absorption band of B. This transient is also present upon preferential excitation of the bac- teriopheophytins in the reaction center of Rhodopseudomonas uiridis.