Fast reactions in carbon monoxide binding to heme proteins

Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources

Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.

Ligand binding to heme proteins: a comparison of cytochrome c variants with globins

We have studied the binding of carbon monoxide (CO) in mutants of Cyt c having its methionine at position 80 replaced by alanine, aspartate, and arginine, so that the sixth coordination is available for ligand binding. We have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy to examine interactions of the heme-bound and photolyzed CO (and also nitric oxide, NO) in the small heme pocket created by the mutations. By using FTIR temperature derivative spectroscopy (TDS) and nanosecond flash photolysis, the enthalpy barrier distributions for CO rebinding were determined. In flash photolysis experiments, the majority of ligands rebind to the heme iron on picosecond time scales so that only the high-barrier tail of the distributions is visible on the nanosecond scale. By continuous wave excitation prior to TDS characterization of the barriers, however, each Cyt c molecule is photoexcited multiple times and complete photodissociation can be achieved, which likely arises from a rotation of the CO within the heme pocket so that the oxygen faces the heme iron. Apparently, reorientation prior to rebinding constitutes an additional and significant contribution to the rebinding barrier. Our experiments reveal that the compact, rigid structure of Cyt c offers no alternative binding sites for photodissociated ligands in the protein matrix. A comparison of ligand binding in these Cyt c mutants and hemoglobins underscores the importance of internal ligand docking sites and ligand migration routes for conveying a ligand binding function to heme proteins.

Local structure and dynamics of hemeproteins by X-ray absorption near edge structure spectroscopy

X-ray absorption near edge structure (XANES) spectroscopy is a synchrotron radiation technique sensitive to the local structure and dynamics around the metal site of a heme containing protein. Advances in detection techniques and theoretical/computational platforms in the last 15 years allowed the use of XANES as a quantitative probe of the key structural determinants driving functional changes, both in a concerted way with protein crystallography and EXAFS (extended X-ray absorption fine structure), or as a stand-alone method to apply in the crystal state as well as in solution. Moreover, the local dynamics of the heme site has been deeply investigated, on one hand, coupling XANES to classical photolysis experiments at cryogenic temperatures; on the other hand, the intrinsic property of the synchrotron radiation to induce radiolysis events, has been exploited to investigate specific cryotrapped intermediates, using X-rays both as a pump and a probe. Insights on the XANES method and some specific examples are presented to illustrate these topics.

Reactivity of coordinatively unsaturated iron complexes towards carbon monoxide: to bind or not to bind?

An overview of the reactivity of coordinatively unsaturated iron complexes (in most cases Fe(II)) towards carbon monoxide is presented. Unsaturated iron complexes are known with coordination numbers (CN) of two to five adopting linear or slightly bent (CN = 2), trigonal (CN = 3), tetrahedral, square planar or trigonal pyramidal (CN = 4), and square-pyramidal or trigonal-bipyramidal geometries (CN = 5), respectively. The binding of CO depends strongly on the number and the nature of co-ligands (overall ligand field strength), the charge of the complex, the complex geometry, and the spin state of the unsaturated metal center. In many cases, CO addition to high-spin iron complexes takes place with concomitant spin state changes forming compounds in the lowest possible spin state, i.e., with S = 0. In several other cases, however, the addition of CO is reversible or is even totally rejected altogether for either thermodynamic or kinetic reasons. In the case of the latter such reactions are termed "spin-blocked" or "spin forbidden".

Picosecond resonance Raman spectroscopic evidence for excited-state spin conversion in carbonmonoxy-hemoglobin photolysis

The structure of the carbonmonoxy-hemoglobin (COHb) photoproduct has been studied on the picosecond time scale with resonance Raman spectroscopy, by tightly focusing the 30-ps pulses of a synchronously pumped mode-locked cavitydumped dye laser on a jet stream of COHb solution. The spectrum of the photoproduct is similar to that of deoxy Hb, but the frequencies 1603 cm(-1) (depolarized), 1552 cm(-1) (anomalously polarized), and 1542 cm(-1) (depolarized) are 2-4 cm(-1) lower than those of deoxy Hb. Similar low frequencies are observed for a species believed to be the bis-tetrahydrofuran adduct of Fe(II) octaethylporphyrin, containing in-plane high-spin Fe(II). These results indicate that in the COHb photoproduct the Fe(II) is already high-spin but is closer to the heme plane than in deoxy Hb. Photodissociation from a quintet ligand-field excited state of COHb is suggested. The frequency shifts relative to deoxy Hb persist when the laser pulses are lengthened to 20 ns. The apparently slow relaxation to the fully out-of-plane heme conformation of deoxy Hb is suggested to be associated with change of the globin tertiary structure.

High-spin diimine complexes of iron(II) reject binding of carbon monoxide: theoretical analysis of thermodynamic factors inhibiting or favoring spin-crossover

A new series of Fe(II) complexes, FeCl2[N(R)=C(Me)C(Me)=N(R)], containing diimine ligands with hemilabile sidearms R (R = CH2(CH2)2NMe2, 1, CH2(CH2)2OMe, 2, CH2(CH2)2SMe), 3) were synthesized. The crystal structure of 1 showed 6-coordination where both amine arms were attached, whereas 2 was a 5-coordinate 16e species with one methoxy arm dangling free. Extensive attempts were made to bind CO to these species to synthesize precursors for dihydrogen complexes but were unsuccessful. Reaction of 1 with 1 or 2 equiv of AgOTf under CO atmosphere resulted in isolation of only a 6-coordinate bis(triflate)-containing product [Fe[N(R)=C(Me)C(Me)=N(R)](OTf)2] (R = CH2(CH2)2NMe2), 5. Reaction of 5-coordinate 2 with AgSbF6 under CO did not give a CO adduct but afforded instead a dicationic dinuclear complex [Fe[N(R)=C(Me)C(Me)=N(R)](mu-Cl)]2[SbF6]2 (R = CH2(CH2)2OMe), 4, containing a weakly bound SbF6. Thus coordination of hard-donor anions to iron was favored over CO binding. The unexpected rejection of binding of CO is rationalized by the iron being in a high-spin state in this system and energetically incapable of spin crossover to a low-spin state. Theoretical calculations on CO interaction with Fe(II) centers in spin states S = 0, 1, and 2 for both the 16e complexes and their CO adducts aid further understanding of this problem. They show that interaction of CO with a high-spin 5-coordinate Fe model diimine complex is essentially thermoneutral but is exergonic by about 48 kcal/mol to a comparable but low-spin diphosphine fragment. Spin crossover is thus disfavored thermodynamically rather than kinetically (e.g. a "spin block" effect); i.e., the ligand field strengths of the primarily N-donor groups are apparently insufficient to give a low-spin CO adduct.

Kinetic barriers to the folding of horse cytochrome C in the reduced state

To determine the kinetic barrier in the folding of horse cytochrome c, a CO-liganded derivative of cytochrome c, called carbonmonoxycytochrome c, has been prepared by exploiting the thermodynamic reversibility of ferrocytochrome c unfolding induced by guanidinium hydrochloride (GdnHCl), pH 7. The CO binding properties of unfolded ferrocytochrome c, studied by 13C NMR and optical spectroscopy, are remarkably similar to those of native myoglobin and isolated chains of human hemoglobin. Equilibrium unfolding transitions of ferrocytochrome c in the presence and the absence of CO observed by both excitation energy transfer from the lone tryptophan to the ferrous heme and far-UV circular dichroism (CD) indicate no accumulation of structural intermediates to a detectable level. Values of thermodynamic parameters obtained by two-state analysis of fluorescence transitions are DeltaG(H2O) = 11.65(+/-1.13) kcal x mol(-1) and C(m) = 3.9(+/-0.1) M GdnHCl in the presence of CO, and DeltaG(H2O)=19.3(+/-0.5) kcal x mol(-1) and C(m) = 5.1(+/-0.1) M GdnHCl in the absence of CO, indicating destabilization of ferrocytochrome c by approximately 7.65 kcal x mol(-1) due to CO binding. The native states of ferrocytochrome c and carbonmonoxycytochrome c are nearly identical in terms of structure and conformation except for the Fe2+-M80 --> Fe2+-CO replacement. Folding and unfolding kinetics as a function of GdnHCl, studied by stopped-flow fluorescence, are significantly different for the two proteins. Both refold fast, but carbonmonoxycytochrome c refolds 2-fold faster (tau = 1092 micros at 10 degrees C) than ferrocytochrome c. Linear extrapolation of the folding rates to the ordinate of the chevron plot projects this value of tau to 407 micros. The unfolding rate of the former in water, estimated by extrapolation, is faster by more than 10 orders of magnitude. Significant differences are also observed in rate-denaturant gradients in the chevron. Formation and disruption of the Fe2+-M80 coordination contact clearly impose high-energy kinetic barriers to folding and unfolding of ferrocytochrome c. The unfolding barrier due to the Fe2+-M80 bond provides sufficient kinetic stability to the native state of ferrocytochrome c to perform its physiological function as an electron donor.

Inhomogeneous broadening and kinetic carbon monoxide isotope effects in low-temperature carbon monoxide recombination with myoglobin and hemoglobin

We have analyzed the non-exponential kinetics, the temperature variation, and the CO isotope effects of the CO recombination reactions with myoglobin and single-chain hemoglobin. The analysis rests on multiphonon quantum-mechanical chemical-rate theory combined with static inhomogeneous broadening of either the reorganization free energy or the reaction Gibbs free energy. The simplest specific model which can account for all the data contains an inhomogeneous distribution function of width 0.2-0.3 eV, independent of temperature down to the tunnel transition at about 20 K, two discrete nuclear coordinates of low vibrational frequency (60-150 cm-1) representing iron-heme and CO bending motion, the CO stretching motion of frequency about 2000 cm-1, and additional inhomogeneous broadening of the protein and CO bending configuration below the tunnel transition temperature. The model appears somewhat involved but in return provides corresponding insight in the dynamics of this important class of processes.

Recombination of carbon monoxide to ferrous horseradish peroxidase types A and C

The recombination of carbon monoxide to isoenzymes A2 and C of horseradish peroxidase (HRP) was studied as a function of temperature (2 to 320 K) and pH (5 to 8.3) with flash photolysis and infrared difference absorption. At low temperatures three geminate recombination processes are observed. One of these internal processes, denoted by I*, is exponential in time with a rate coefficient that deviates strongly from an Arrhenius behavior below 100 K, implying phonon-assisted tunneling. The two other processes, denoted by I, are non-exponential in time and related to different carbonyl isomers, as shown by the infrared difference spectra. The existence of three internal processes indicates that HRP differs considerably from myoglobin where only one internal process, I, is seen. Moreover, the internal processes in HRP are faster than process I in myoglobin. At 300 K, only one recombination process from the solvent is observed and it is very slow (lambda s approximately 1 s-1 at 1 atm CO (1 atm = 101,325 Pa)), much slower than the corresponding association process in myoglobin. Since process I is fast, but binding from the solvent is slow, the barrier at the heme cannot be responsible for the small association rate. The infrared absorption difference spectra of the amide I/II bands indicate that photolysis and recombination trigger a two-step structural change. The slow recombination rate at 300 K can thus be explained by the large Gibbs energy of the conformational transition that is necessary to let CO move into the heme pocket. The partition coefficient for the CO in the heme pocket and the solvent is extremely small, while bond formation with the heme iron occurs in less than 100 nanoseconds.

Electron paramagnetic resonance- (EPR-) resolved kinetics of cryogenic nitric oxide recombination to cytochrome c oxidase and myoglobin

By the electron paramagnetic resonance (EPR) technique, recovery kinetics for nitric oxide (NO) to heme following cryogenic photolysis were studied for the nitrosylferrocytochrome a3 center in cytochrome c oxidase and for myoglobin. The recovery was nonexponential, as has been observed in previous cryogenic CO and O2 rebinding to heme systems. NO rebinding to heme a3 started near a temperature of 50 K and was related to a distribution of thermal activation energies. At the peak of the distribution the activation energy was 3.1 kcal/mol, and the preexponential in the recovery rate was 10(9.9) s-1. For recovery of NO back to the a3 heme, the activation energy was threefold less than that for CO where CO binds to nearby Cua3 following photolysis from heme a3, but was larger than the activation energy for CO, O2, and probably NO rebinding to myoglobin. NO ligand rebinding to myoglobin occurred at a temperature as low as 15 K and in a temperature regime where tunneling could occur. However, the rate of NO rebinding to myoglobin did increase with temperature in the 15-25 K range.

The reaction of cytochrome omicron in Escherichia coli with oxygen. Low-temperature kinetic and spectral studies

1. The reactions of cytochrome omicron in intact cells of aerobically grown Escherichia coli with O2 and CO have been studied at low temperature. 2. Flash photolysis of CO-liganded cells in the presence of O2 and at temperatures between -79 and -102 degrees C results in the oxidation of kinetically heterogeneous beta-type cytochromes (including cytochrome omicron), but not of cytochrome d. 3. The reaction of reduced cytochrome omicron with O2 involves O2 binding to give intermediate(s) with spectral characteristics similar to that of the reduced oxidase-CO complex. Observation in the alpha-region suggests that unexplained ligand dissociation accompanies the initial O2 binding. 4. At temperatures below -98 degrees C, an 'end point' in the reaction is reached; further reaction and oxidation of cytochrome omicron occurs on raising the temperature. 5. There is a linear relationship between the rate of formation of the oxygen compound and the O2 concentration up to 0.5 mM. The second-order constant for its formation (k+1) is 0.91 M-1.S-1 at -101 degrees C. The reaction is not readily reversible, the value of k-1 being 1.4 X 10(-5) S-1 and the kd 1.5 X 10(-5) M. 6. The energy of activation for this reaction at low temperatures is 29.9kJ (7.1 kcal)/mol. 7. The reaction with O2 is distinguished from that with CO by the markedly lower velocity and high photolytic reversibility of the latter. 8. Comparisons are drawn between the intermediate(s) in the O2 reaction of cytochrome omicron in E. coli and those identified in other bacteria and in the reaction of cytochrome aa3 with O2.