Picosecond transient absorption study of photodissociated carboxy hemoglobin and myoglobin

Femtosecond X-ray spectroscopy of haem proteins

We discuss our recently reported femtosecond (fs) X-ray emission spectroscopy results on the ligand dissociation and recombination in nitrosylmyoglobin (MbNO) in the context of previous studies on ferrous haem proteins. We also present a preliminary account of femtosecond X-ray absorption studies on MbNO, pointing to the presence of more than one species formed upon photolysis.

Adiabatic Ligand Binding in Heme Proteins: Ultrafast Kinetics of Methionine Rebinding in Ferrous Cytochrome c

The dynamics of methionine geminate recombination following photodissociation in ferrous cytochrome c is investigated over a broad temperature range. The kinetic response, above the solvent glass transition ( T_g), is nearly monoexponential and displays a weak temperature dependence. Below T_g, the rebinding kinetics are nonexponential and can be explained using a quenched distribution of enthalpic rebinding barriers, arising from a relatively narrow distribution of heme out-of-plane displacements. The Arrhenius prefactor of this (Δ S = 2) reaction is ∼10¹¹ s^-1, which is similar to what has been found for the (Δ S = 1) NO binding reaction in heme proteins. This observation, along with other examples of ultrafast CO binding, provides strong evidence that ligand binding to heme is an adiabatic reaction with a spin-independent prefactor. In order to simultaneously account for the adiabatic nature of the reaction as well as the temperature dependence of both ultrafast CO and methionine geminate rebinding, it is proposed that a spin triplet state intersects and strongly couples to the reactant ( S = 2) and product ( S = 0) state surfaces in the transition state region along the reaction coordinate. It is also suggested that the nature of the intersecting triplet state and the reaction path may depend upon the proximity of the photolyzed ligand relative to the iron atom. At temperatures below ∼60 K, the kinetic data suggest that there is either an unexpected retardation of the heme photoproduct relaxation or that heavy atom quantum mechanical tunneling becomes significant.

Internal water and microsecond dynamics in myoglobin

Myoglobin (Mb) binds diatomic ligands, like O₂, CO, and NO, in a cavity that is only transiently accessible. Crystallography and molecular simulations show that the ligands can migrate through an extensive network of transiently connected cavities but disagree on the locations and occupancy of internal hydration sites. Here, we use water ²H and ¹⁷O magnetic relaxation dispersion (MRD) to characterize the internal water molecules in Mb under physiological conditions. We find that equine carbonmonoxy Mb contains 4.5 ± 1.0 ordered internal water molecules with a mean survival time of 5.6 ± 0.5 μs at 25 °C. The likely locations of these water molecules are the four polar hydration sites, including one of the xenon-binding cavities, that are fully occupied in all high-resolution crystal structures of equine Mb. The finding that water escapes from these sites, located 17–31 Å apart in the protein, on the same μs time scale suggests a global exchange mechanism. We propose that this mechanism involves transient penetration of the protein by H-bonded water chains. Such a mechanism could play a functional role by eliminating trapped ligands. In addition, the MRD results indicate that 2 or 3 of the 11 histidine residues of equine Mb undergo intramolecular hydrogen exchange on a μs time scale.

Ligand migration in myoglobin: a combined study of computer simulation and x-ray crystallography

A ligand-migration mechanism of myoglobin was studied by a multidisciplinary approach that used x-ray crystallography and molecular dynamics simulation. The former revealed the structural changes of the protein along with the ligand migration, and the latter provided the statistical ensemble of protein conformations around the thermal average. We developed a novel computational method, homogeneous ensemble displacement, and generated the conformational ensemble of ligand-detached species from that of ligand-bound species. The thermally averaged ligand-protein interaction was illustrated in terms of the potential of mean force. Although the structural changes were small, the presence of the ligand molecule in the protein matrix significantly affected the 3D scalar field of the potential of mean force, in accordance with the self-opening model proposed in the previous x-ray study.

Cytochrome c552 Mutants: Structure and Dynamics at the Active Site Probed by Multidimensional NMR and Vibration Echo Spectroscopy

Spectrally resolved infrared stimulated vibrational echo experiments are used to measure the vibrational dephasing of a CO ligand bound to the heme cofactor in two mutated forms of the cytochrome c552 from Hydrogenobacter thermophilus. The first mutant (Ht-M61A) is characterized by a single mutation of Met61 to an Ala (Ht-M61A), while the second variant is doubly modified to have Gln64 replaced by an Asn in addition to the M61A mutation (Ht-M61A/Q64N). Multidimensional NMR experiments determined that the geometry of residue 64 in the two mutants is consistent with a non-hydrogen-bonding and hydrogen-bonding interaction with the CO ligand for Ht-M61A and Ht-M61A/Q64N, respectively. The vibrational echo experiments reveal that the shortest time scale vibrational dephasing of the CO is faster in the Ht-M61A/Q64N mutant than that in Ht-M61A. Longer time scale dynamics, measured as spectral diffusion, are unchanged by the Q64N modification. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to confirm that the dynamical difference induced by the Q64N mutation is primarily an increase in the fast (hundreds of femtoseconds) frequency fluctuations, while the slower (tens of picoseconds) dynamics are nearly unaffected. We conclude that the faster dynamics in Ht-M61A/Q64N are due to the location of Asn64, which is a hydrogen bond donor, above the heme-bound CO. A similar difference in CO ligand dynamics has been observed in the comparison of the CO derivative of myoglobin (MbCO) and its H64V variant, which is caused by the difference in axial residue interactions with the CO ligand. The results suggest a general trend for rapid ligand vibrational dynamics in the presence of a hydrogen bond donor.

Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy

Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.

Dynamics of hemoglobin in human erythrocytes and in solution: influence of viscosity studied by ultrafast vibrational echo experiments

Ultrafast spectrally resolved stimulated vibrational echo experiments are used to measure the vibrational dephasing of the CO stretching mode of hemoglobin-CO (HbCO) inside living human erythrocytes (red blood cells), in liquid solutions, and in a glassy matrix. A method is presented to overcome the adverse impact on the vibrational echo signal from the strong light scattering caused by the cells. The results from the cytoplasmic HbCO are compared to experiments on aqueous HbCO samples prepared in different buffers, solutions containing low and high concentrations of glycerol, and in a solid trehalose matrix. Measurements are also presented that provide an accurate determination of the viscosity at the very high Hb concentration that is found inside the cells. It is demonstrated that the dynamics of the protein, as sensed by the CO ligand, are the same inside the erythrocytes and in aqueous solution and are independent of the viscosity. In solutions that are predominantly glycerol, the dynamics are modified somewhat but are still independent of viscosity. The experiments in trehalose give the dynamics at infinite viscosity and are used to separate the viscosity-dependent dynamics from the viscosity-independent dynamics. Although the HbCO dynamics are the same in the red blood cell and in the equivalent aqueous solutions, differences in the absorption spectra show that the distribution of a protein's equilibrium substates is sensitive to small pH differences.

Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction

A time-resolved Laue X-ray diffraction technique has been used to explore protein relaxation and ligand migration at room temperature following photolysis of a single crystal of carbon monoxymyoglobin. The CO ligand is photodissociated by a 7.5 ns laser pulse, and the subsequent structural changes are probed by 150 ps or 1 micros X-ray pulses at 14 laser/X-ray delay times, ranging from 1 ns to 1.9 ms. Very fast heme and protein relaxation involving the E and F helices is evident from the data at a 1 ns time delay. The photodissociated CO molecules are detected at two locations: at a distal pocket docking site and at the Xe 1 binding site in the proximal pocket. The population by CO of the primary, distal site peaks at a 1 ns time delay and decays to half the peak value in 70 ns. The secondary, proximal docking site reaches its highest occupancy of 20% at approximately 100 ns and has a half-life of approximately 10 micros. At approximately 100 ns, all CO molecules are accounted for within the protein: in one of these two docking sites or bound to the heme. Thereafter, the CO molecules migrate to the solvent from which they rebind to deoxymyoglobin in a bimolecular process with a second-order rate coefficient of 4.5 x 10(5) M(-1) s(-1). Our results also demonstrate that structural changes as small as 0.2 A and populations of CO docking sites of 10% can be detected by time-resolved X-ray diffraction.

Fast protein dynamics probed with infrared vibrational echo experiments

IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T(1.3), that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electric field-coupling mechanism is tested by observing differences in the temperature dependence of the pure dephasing of Mb-CO mutations.

Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography

The biological activity of macromolecules is accompanied by rapid structural changes. The photosensitivity of the carbon monoxide complex of myoglobin was used at the European Synchrotron Radiation Facility to obtain pulsed, Laue x-ray diffraction data with nanosecond time resolution during the process of heme and protein relaxation after carbon monoxide photodissociation and during rebinding. These time-resolved experiments reveal the structures of myoglobin photoproducts, provide a structural foundation to spectroscopic results and molecular dynamics calculations, and demonstrate that time-resolved macromolecular crystallography can elucidate the structural bases of biochemical mechanisms on the nanosecond time scale.

Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K

Myoglobin's reversible binding of oxygen is a model for studies of protein control of ligand binding and discrimination. Protein relaxation and geminate ligand rebinding subsequent to ligand photodissociation have been studied extensively by a variety of techniques. The ps to ns time scales for these processes are still much shorter than the ms time resolution of X-ray diffraction experiments, but it may be possible to trap these intermediates at low temperatures. We report here an X-ray diffraction investigation of structural changes induced by photolysis of carbonmonoxy myoglobin crystals at 40 K. Our results provide a structural basis for the interpretation of ambient and low temperature spectroscopic observations and molecular dynamics simulations of the ligand photodissociation and binding processes in haem proteins.

Conformational relaxation and ligand binding in myoglobin

Absorption spectroscopy with nanosecond time resolution shows that myoglobin undergoes conformational relaxation on the same time scale as geminate rebinding of carbon monoxide. Ligand rebinding following photodissociation of the heme-CO complex was measured from the amplitude of the average difference spectrum, while conformational changes were measured from changes in the detailed shape of the Soret spectra of the deoxyhemes. Experiments in which the solvent viscosity was varied between 1 and 300 cP and the temperature between 268 and 308 K were analyzed by fitting the multiwavelength kinetic data with both empirical and molecular models. Novel numerical techniques were employed in fitting the data, including the use of singular value decomposition to remove the effects of temperature and solvent on the spectra and of a Monte Carlo method to overcome the multiple minimum problem in searching parameter space. The molecular model is the minimal model that incorporates all of the major features of myoglobin kinetics at ambient temperatures, including a fast and slow rebinding conformation and two geminate states for each conformation. The results of fitting the kinetic data with this model indicate that the geminate-rebinding rates for the two conformations differ by at least a factor of 100. The differences between the spectra of the two conformations generated from the fits are similar to the differences between those of the R and T conformations of hemoglobin. In modeling the data, the dependence of the rates on temperature and viscosity was parametrized using a modification of Kramers theory which includes the contributions of both protein and solvent to the friction. The rate of the transition from the fast to the slow rebinding conformation is found to be inversely proportional to the viscosity when the viscosity exceeds about 30 cP and nearly viscosity independent at low viscosity. The viscosity dependence at high viscosities suggests that the two conformations differ by the global displacement of protein atoms on the proximal side of the heme observed by X-ray crystallography. We suggest that the conformational change observed in our experiments corresponds to the final portion of the nonexponential conformational relaxation recently observed by Anfinrud and co-workers, which begins on a picosecond time scale. Furthermore, extrapolation of our data to temperatures near that of the solvent glass transition suggests that this conformational relaxation may very well be the one postulated by Frauenfelder and co-workers to explain the decrease in the rate of geminate rebinding with increasing temperature above 180 K.

Photoselection in polarized photolysis experiments on heme proteins

Polarized photolysis experiments have been performed on the carbon monoxide complex of myoglobin to assess the effects of photoselection on the kinetics of ligand rebinding and to investigate the reorientational dynamics of the heme plane. The results are analyzed in terms of the optical theory developed in the preceding paper by Ansari and Szabo. Changes in optical density arising from rotational diffusion of the photoselected population produce large deviations from the true geminate ligand rebinding curves if measurements are made with only a single polarization. The apparent ligand rebinding curves are significantly distorted even at photolysis levels greater than 90%. These deviations are eliminated by obtaining isotropically-averaged optical densities from measurements using both parallel and perpendicular polarizations of the probe pulse. These experiments also yield the optical anisotropy, which gives a novel method for accurately determining the degree of photolysis, as well as important information on the reorientational dynamics of the heme plane. The correlation time for the overall rotational diffusion of the molecule is obtained from the decay of the anisotropy. The anisotropy prior to rotational diffusion is lower than that predicted for a rigidly attached, perfectly circular absorber, corresponding to an apparent order parameter of S = 0.95 +/- 0.02. Polarized absorption data on single crystals suggest that the decreased anisotropy results more from internal motions of the heme plane which take place on time scales shorter than the duration of the laser pulse (10 ns) than from out-of-plane polarized transitions.

Evidence for a band III analogue in the near-infrared absorption spectra of cytochrome c oxidase

Ground state near-infrared absorption spectra of fully reduced unliganded and fully reduced CO (a2+ CuA+ a3(2+)-CO CuB+) cytochrome c oxidase were investigated. Flash-photolysis time-resolved absorption difference spectra of the mixed-valence (a3+ CuA2+ a3(2+)-CO CuB+) and the fully reduced CO complexes were also studied. A band near 785 nm (epsilon approximately 50 M-1cm-1) was observed in the fully reduced unliganded enzyme and the CO photoproducts. The time-resolved 785 nm band disappeared on the same timescale (t1/2 approximately 7 ms) as CO recombined with cytochrome a3(2+). This band, which is attributed to the unliganded five coordinate ferrous cytochrome a3(2+), has some characteristics of band III in deoxy-hemoglobin and deoxy-myoglobin. A second band was observed at approximately 710 nm (epsilon approximately 80 M-1cm-1) in the fully reduced unliganded and the fully reduced CO complexes. This band, which we assign to the low spin ferrous cytochrome a, appears to be affected by the ligation state at the cytochrome a3(2+) site.

Ligand binding and protein relaxation in heme proteins: a room temperature analysis of NO geminate recombination

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.

Direct observation of global protein motion in hemoglobin and myoglobin on picosecond time scales

Picosecond phase-grating spectroscopy is highly sensitive to density changes and provides a new holographic approach to the study of protein dynamics. Photodissociation of carbon monoxide from heme proteins induces a well-defined transition from a ligated to a deoxy structure that is important to hemoglobin and myoglobin functionality. Grating spectroscopy was used to observe protein-driven density waves on a picosecond time scale after carbon monoxide dissociation. This result demonstrates that global tertiary structure changes of proteins occur on an extremely fast time scale and provides new insight into the biomechanics of deterministic protein motion.

Subpicosecond resonance Raman spectroscopy of carbonmonoxy- and oxyhemoglobin

In this paper we present the resonance Raman spectrum of the carbonmonoxy- (HbCO) and oxyhemoglobin (HbO2) photointermediates on a 800-900 fs timescale. In the case of HbCO, the frequencies of the so-called core-size markers (1500-1650 cm-1) are characteristic of a deoxylike photoproduct in a high spin state (S = 2) with a partially domed heme. The spectrum of the HbO2 photointermediate, on the other hand, is different, and may be characteristic of an excited-state species. These results are discussed in terms of a reaction scheme previously presented by Petrich, J. W., C. Poyart, and J. L. Martin (1988. Biochemistry. 27:4049-4060) and compared with those obtained in the literature on a 30-40 ps timescale. In both molecules a distinct downshift of the v4 mode was observed with respect to the equilibrium value, which is indicative of an elevated temperature of the heme after photodissociation.

A possible new control mechanism suggested by resonance Raman spectra from a deep ocean fish hemoglobin

The rattail fish, Coryphaenoides armatus, lives at ocean depths of 3000 m. As an adaptation for pumping oxygen into the swim bladder against the extreme pressures at the ocean bottom, the hemoglobin from this fish at low pH exhibits an extraordinarily low affinity for ligands. In this study, continuous wave and time-resolved Raman techniques are used to probe the binding site in this hemoglobin. The findings show an association between the low-affinity material and a highly strained heme-proximal histidine linkage. The transient Raman studies reveal differences in the protein structural dynamics at pH 6 and 8. The emerging picture derived from both this and earlier studies is that in vertebrate hemoglobins the heme-proximal histidine linkage represents a key channel through which species- and solution-dependent variations in the globin are communicated both statically and dynamically to the heme to produce an extensive range of ligand binding properties. Also presented is a new model that relates both intensity and frequency of the resonance Raman band involving the iron-proximal histidine stretching mode to specific protein controlled structural degrees of freedom. There emerges from this model a mechanism whereby modifications in the proximal heme pocket can further reduce the affinity of an already highly strained T state structure of hemoglobin.

Reactions of excited triplet states of metal substituted myoglobin with dioxygen and quinone

The triplet state absorption and phosphorescence of Zn and Pd derivatives of myoglobin were compared. Both metal derivatives exhibit long triplet state lifetimes at room temperature, but whereas the Pd derivative showed exponential decay and an isosbestic point in the transient absorption spectra, the decay of the Zn derivative was nonsingle exponential and the transient absorption spectra showed evidence of more than one excited state species. No difference was seen in triplet quenching by oxygen for either derivative, indicating that differences in the polypeptide chain between the two derivatives are not large enough to affect oxygen penetrability. Quenching was also observed by anthraquinone sulfonate. In this case, the possibility of long-range transfer by an exchange mechanism is considered.

Applications of ultrafast laser spectroscopy for the study of biological systems

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.