Heme protein dynamics revealed by geminate nitric oxide recombination in mutants of iron and cobalt 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.

Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11

In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH (e.g., pH 3.1-6.1) and concentration (e.g., 1-50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged (e.g., [M]+, [M - 2H + NH4]+, [M - H + Na]+ and [M - H + K]+) and doubly charged (e.g., [M + H]2+, [M - H + NH4]2+, [M + Na]2+ and [M + K]2+) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity (e.g., number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges (e.g., NH4 +, Na+ and K+ vs. H+). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge (i.e., a CE50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H]3+, [2M - H + NH4]3+, [2M + Na]3+ and [2M + K]3+, respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species.

Femtosecond X-ray emission study of the spin cross-over dynamics in haem proteins

In haemoglobin the change from the low-spin (LS) hexacoordinated haem to the high spin (HS, S = 2) pentacoordinated domed deoxy-myoglobin (deoxyMb) form upon ligand detachment from the haem and the reverse process upon ligand binding are what ultimately drives the respiratory function. Here we probe them in the case of Myoglobin-NO (MbNO) using element- and spin-sensitive femtosecond Fe K_α and K_β X-ray emission spectroscopy at an X-ray free-electron laser (FEL). We find that the change from the LS (S = 1/2) MbNO to the HS haem occurs in ~800 fs, and that it proceeds via an intermediate (S = 1) spin state. We also show that upon NO recombination, the return to the planar MbNO ground state is an electronic relaxation from HS to LS taking place in ~30 ps. Thus, the entire ligand dissociation-recombination cycle in MbNO is a spin cross-over followed by a reverse spin cross-over process.

The change from low-spin hexacoordinated to high-spin pentacoordinated domed form in heam upon ligand detachment and the reverse process underlie the respiratory function. The authors, using femtosecond time-resolved X-ray emission spectroscopy, capture the transient states connecting the two forms in myoglobin-NO upon NO photoinduced detachment.

Effect of Single-Point Mutations on Nitric Oxide Rebinding and the Thermodynamic Stability of Myoglobin

The effect of single amino acid mutations on the rebinding dynamics of nitrogen monoxide (NO) to myoglobin is investigated using reactive molecular dynamics simulations. In particular, mutations of residues surrounding the heme-active site (Leu29, His64, Val68) were considered. Consistent with experiments, all mutations studied here have a significant effect on the kinetics of the NO-rebinding process, which consists of a rapid (several 10 ps) and a slow (100s of ps) time scale. For all modifications considered, the time scales and rebinding fractions agree to within a few percents with results from experiments by adjusting one single, physically meaningful, conformationally averaged quantity: the asymptotic energy separation between the NO-bound (²A) and photodissociated (⁴A) states. It is furthermore shown that the thermodynamic stability of wild-type versus mutant Mb for the ligand-free and ligand-bound variants of the protein can be described by the same computational model. Therefore, ligand kinetics and thermodynamics are related in a direct fashion akin to Φ-value analysis, which establishes a relationship between protein folding rates and thermal stability of proteins.

Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase

The rebinding kinetics of NO after photodissociation from microperoxidase (Mp-9) is studied in different solvent environments. In mixed glycerol/water (G/W) mixtures the dissociating ligand rebinds with a yield close to 1 due to the cavities formed by the solvent whereas in pure water the ligand can diffuse into the solvent after photodissociation. In the G/W mixture, only geminate rebinding on the sub-picosecond and 5 ps time scales was found and the rebinding fraction is unity which compares well with available experiments. Contrary to that, simulations in pure water find two time scales – ~10 ps and ~200 ps - indicating that both, geminate rebinding and rebinding after diffusion of NO in the surrounding water contribute. The rebinding fraction is around 0.63 within 1 ns which is in stark contrast with experiment. Including ions (Na and Cl) at 0.15 M concentration in water leads to rebinding kinetics tending to that in the glycerol/water mixture and yields agreement with experiments. The effect of temperature is also probed and found to be non-negligible. The present simulations suggest that NO rebinding in Mp is primarily driven by thermal fluctuations which is consistent with recent resonance Raman spectroscopy experiments and simulations on MbNO.

Rebinding dynamics of NO to microperoxidase-8 probed by time-resolved vibrational spectroscopy

Femtosecond vibrational spectroscopy was used to probe the rebinding kinetics of NO to microperoxidase-8 (Mp), an ideal model system for the active site of ligand-binding heme proteins, including myoglobin and hemoglobin, after the photodeligation of MpNO in glycerol/water (G/W) solutions at 294 K. The geminate rebinding (GR) of NO to Mp in viscous solutions was highly efficient and ultrafast and negligibly dependent on the solution viscosity, which was adjusted by changing the glycerol content from 65% to 90% by volume in G/W mixtures. The kinetics of the GR of NO to Mp in viscous solutions was well represented by an exponential function with a time constant of ca. 11 ps. Although the kinetic traces of the GR of NO to Mp in solutions with three different viscosities (18, 81, and 252 cP) almost overlap, they show a slight difference early in the decay process. The kinetic traces were also described by the diffusion-controlled reaction theory with a Coulomb potential. Since the ligand is deligated in a neutral form, an ionic pair of NO(-) and Mp(+) may be produced before forming the Mp-NO bond by an electron transfer from Mp to NO as the deligated NO is sufficiently near to the Fe atom of Mp. The strong reactivity between NO and ferrous heme may arise from the Coulomb interaction between the reacting pair, which is consistent with the harpooning mechanism for NO binding to heme.

NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy

Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein's function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼ 200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump-probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.

Reactivity and dynamics of H2S, NO, and O2 interacting with hemoglobins from Lucina pectinata

Hemoglobin HbI from the clam Lucina pectinata is involved in H2S transport, whereas homologous heme protein HbII/III is involved in O2 metabolism. Despite similar tertiary structures, HbI and HbII/III exhibit very different reactivity toward heme ligands H2S, O2, and NO. To investigate this reactivity at the heme level, we measured the dynamics of ligand interaction by time-resolved absorption spectroscopy in the picosecond to nanosecond time range. We demonstrated that H2S can be photodissociated from both ferric and ferrous HbI. H2S geminately rebinds to ferric and ferrous out-of-plane iron with time constants (τgem) of 12 and 165 ps, respectively, with very different proportions of photodissociated H2S exiting the protein (24% in ferric and 80% in ferrous HbI). The Gln(E7)His mutation considerably changes H2S dynamics in ferric HbI, indicating the role of Gln(E7) in controling H2S reactivity. In ferric HbI, the rate of diffusion of H2S from the solvent into the heme pocket (kentry) is 0.30 μM(-1) s(-1). For the HbII/III-O2 complex, we observed mainly a six-coordinate vibrationally excited heme-O2 complex with O2 still bound to the iron. This explains the low yield of O2 photodissociation and low koff from HbII/III, compared with those of HbI and Mb. Both isoforms behave very differently with regard to NO and O2 dynamics. Whereas the amplitude of geminate rebinding of O2 to HbI (38.5%) is similar to that of myoglobin (34.5%) in spite of different distal heme sites, it appears to be much larger for HbII/III (77%). The distal Tyr(B10) side chain present in HbII/III increases the energy barrier for ligand escape and participates in the stabilization of bound O2 and NO.

Site-specific difference 2D-IR spectroscopy of bacteriorhodopsin

We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.

Investigations of vibrational coherence in the low-frequency region of ferric heme proteins

Femtosecond coherence spectroscopy is applied to a series of ferric heme protein samples. The low-frequency vibrational spectra that are revealed show dominant oscillations near 40 cm(-1). MbCN is taken as a typical example of a histidine-ligated, six-coordinate, ferric heme and a comprehensive spectroscopic analysis is carried out. The results of this analysis reveal a new heme photoproduct species, absorbing near 418 nm, which is consistent with the photolysis of the His(93) axial ligand. The photoproduct undergoes subsequent rebinding/recovery with a time constant of approximately 4 ps. The photoproduct lineshapes are consistent with a photolysis quantum yield of 75-100%, although the observation of a relatively strong six-coordinate heme coherence near 252 cm(-1) (assigned to nu(9) in the MbCN Raman spectrum) suggests that the 75% lower limit is much more likely. The phase and amplitude excitation profiles of the low-frequency mode at 40 cm(-1) suggest that this mode is strongly coupled to the MbCN photoproduct species and it is assigned to the doming mode of the transient penta-coordinated material. The absolute phase of the 40 cm(-1) mode is found to be pi/2 on the red side of 418 nm and it jumps to 3pi/2 as excitation is tuned to the blue side of 418 nm. The absolute phase of the 40 cm(-1) signal is not explained by the standard theory for resonant impulsive stimulated Raman scattering. New mechanisms that give a dominant momentum impulse to the resonant wavepacket, rather than a coordinate displacement, are discussed. The possibilities of heme iron atom recoil after photolysis, as well as ultrafast nonradiative decay, are explored as potential ways to generate the strong momentum impulse needed to understand the phase properties of the 40 cm(-1) mode.

Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates

We present temperature-dependent kinetic measurements of ultrafast diatomic ligand binding to the "bare" protoheme (L(1)-FePPIX-L(2), where L(1) = H(2)O or 2-methyl imidazole and L(2) = CO or NO). We found that the binding of CO is temperature-dependent and nonexponential over many decades in time, whereas the binding of NO is exponential and temperature-independent. The nonexponential nature of CO binding to protoheme, as well as its relaxation above the solvent glass transition, mimics the kinetics of CO binding to myoglobin (Mb) but on faster time scales. This demonstrates that the nonexponential kinetic response observed for Mb is not necessarily due to the presence of protein conformational substates but rather is an inherent property of the solvated heme. The nonexponential kinetic data were analyzed by using a linear coupling model with a distribution of enthalpic barriers that fluctuate on slower time scales than the heme-CO recombination time. Below the solvent glass transition (T(g) approximately 180 K), the average enthalpic rebinding barrier for H(2)O-PPIX-CO was found to be approximately 1 kJ/mol. Above T(g), the barrier relaxes and is approximately 6 kJ/mol at 290 K. Values for the first two moments of the heme doming coordinate distribution extracted from the kinetic data suggest significant anharmonicity above T(g). In contrast to Mb, the protoheme shows no indication of the presence of "distal" enthalpic barriers. Moreover, the wide range of Arrhenius prefactors (10(9) to 10(11) s(-1)) observed for CO binding to heme under differing conditions suggests that entropic barriers may be an important source of control in this class of biochemical reactions.

Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c

The bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 +/- 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins.

Hydrophobic Distal Pocket Affects NO−Heme Geminate Recombination Dynamics in Dehaloperoxidase and H64V Myoglobin

The recombination dynamics of NO with dehaloperoxidase (DHP) from Amphitrite ornata following photolysis were measured by femtosecond time-resolved absorption spectroscopy. Singular value decomposition (SVD) analysis reveals two important basis spectra. The first SVD basis spectrum reports on the population of photolyzed NO molecules and has the appearance of the equilibrium difference spectrum between the deoxy and NO forms of DHP. The first basis time course has two kinetic components with time constants of tau(11) approximately 9 ps and tau(12) approximately 50 ps that correspond to geminate recombination. The fast geminate process tau(11) arises from a contact pair with the heme iron in a bound state with S = 3/2 spin. The slow geminate process tau(12) corresponds to the recombination from a more remote docking site >3 A from the heme iron with the greater barrier corresponding to a S = 5/2 spin state. The second SVD basis spectrum represents a time-dependent Soret band shift indicative of heme photophysical processes and protein relaxation with time constants of tau(21) approximately 3 ps and tau(22) approximately 17 ps, respectively. A comparison between the more rapid rate constant of the slow geminate phase in DHP-NO and horse heart myoglobin (HHMbNO) or sperm whale myoglobin (SWMbNO) suggests that protein interactions with photolyzed NO are weaker in DHP than in the wild-type MbNOs, consistent with the hydrophobic distal pocket of DHP. The slower protein relaxation rate tau(22) in DHP-NO relative to HHMbNO implies less effective trapping in the docking site of the distal pocket and is consistent with a greater yield for the fast geminate process. The trends observed for DHP-NO also hold for the H64V mutant of SWMb (H64V MbNO), consistent with a more hydrophobic distal pocket for that protein as well. We examine the influence of solution viscosity on NO recombination by varying the glycerol content in the range from 0% to 90% (v/v). The dominant effect of increasing viscosity is the increase of the rate of the slow geminate process, tau(12), coupled with a population decrease of the slow geminate component. Both phenomena are similar to the effect of viscosity on wild-type Mb due to slowing of protein relaxation resulting from an increased solution viscosity and protein surface dehydration.

Role of Heme Iron Coordination and Protein Structure in the Dynamics and Geminate Rebinding of Nitric Oxide to the H93G Myoglobin Mutant

The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman time-resolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases ( approximately 10 and approximately 100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes.

Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mus of total simulation time) for the rebinding of NO to myoglobin. The unbound surface (Fe...NO) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

The Position 68(E11) Side Chain in Myoglobin Regulates Ligand Capture, Bond Formation with Heme Iron, and Internal Movement into the Xenon Cavities

After photodissociation, ligand rebinding to myoglobin exhibits complex kinetic patterns associated with multiple first-order geminate recombination processes occurring within the protein and a simpler bimolecular phase representing second-order ligand rebinding from the solvent. A smooth transition from cryogenic-like to solution phase properties can be obtained by using a combination of sol-gel encapsulation, addition of glycerol as a bathing medium, and temperature tuning (-15 --> 65 degrees C). This approach was applied to a series of double mutants, myoglobin CO (H64L/V68X, where X = Ala, Val, Leu, Asn, and Phe), which were designed to examine the contributions of the position 68(E11) side chain to the appearance and disappearance of internal rebinding phases in the absence of steric and polar interactions with the distal histidine. Based on the effects of viscosity, temperature, and the stereochemistry of the E11 side chain, the three major phases, B --> A, C --> A, and D --> A, can be assigned, respectively, to ligand rebinding from the following: (i) the distal heme pocket, (ii) the xenon cavities prior to large amplitude side chain conformational relaxation, and (iii) the xenon cavities after significant conformational relaxation of the position 68(E11) side chain. The relative amplitudes of the B --> A and C --> A phases depend markedly on the size and shape of the E11 side chain, which regulates sterically both ligand return to the heme iron atom and ligand migration to the xenon cavities. The internal xenon cavities provide a transient docking site that allows side chain relaxations and the entry of water into the vacated distal pocket, which in turn slows ligand recombination markedly.

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model

Geminate CO rebinding in myoglobin is studied for two viscous solvents, trehalose and sol-gel (bathed in 100% glycerol) at several temperatures. Mutations in key distal hemepocket residues are used to eliminate or enhance specific relaxation modes. The time-resolved data are analyzed with a modified Agmon-Hopfield model which is capable of providing excellent fits in cases where a single relaxation mode is dominant. Using this approach, we determine the relaxation rate constants of specific functionally important modes, obtaining also their Arrhenius activation energies. We find a hierarchy of distal pocket modes controlling the rebinding kinetics. The "heme access mode" (HAM) is responsible for the major slow-down in rebinding. It is a solvent-coupled cooperative mode which restricts ligand return from the xenon cavities. Bulky side-chains, like those His64 and Trp29 (in the L29W mutant), operate like overdamped pendulums which move over and block the binding site. They may be either unslaved (His64) or moderately slaved (Trp29) to the solvent. Small side-chain relaxations, most notably of leucines, are revealed in some mutants (V68L, V68A). They are conjectured to facilitate inter-cavity ligand motion. When all relaxations are arrested (H64L in trehalose), we observe pure inhomogeneous kinetics with no temperature dependence, suggesting that proximal relaxation is not a factor on the investigated timescale.

Human myoglobin recognition of oxygen: dynamics of the energy landscape

Femtosecond to nanosecond dynamics of O(2) rebinding to human WT myoglobin and its mutants, V68F and I107F, have been studied by using transient absorption. The results are compared with NO rebinding. Even though the immediate environment around the heme binding site is changed by the mutations, the picosecond geminate rebinding of oxygen is at most minimally affected. On the other hand, the V68F (E11) mutation causes drastic differences in rebinding on the nanosecond time scale, whereas the effect of the I107F (G8) mutation remains relatively small within our 10-ns time window. Unlike traditional homogeneous kinetics and molecular dynamics collisional simulations, we propose a "bifurcation model" for populations of directed and undirected dynamics on the ultrafast time scale, reflecting the distribution of initial protein conformations. The major mutation effect occurs on the time scale on which global protein conformational change is possible, consistent with transitions between the conformations of directed and undirected population playing a role in the O(2) binding. We discuss the relevance of these findings to the bimolecular function of the protein.

Ligand Dynamics in Myoglobin: Calculation of Infrared Spectra for Photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Time-resolved visible and infrared study of the cyano complexes of myoglobin and of hemoglobin I from Lucina pectinata

The dynamics of the ferric CN complexes of the heme proteins Myoglobin and Hemoglobin I from the clam Lucina pectinata upon Soret band excitation is monitored using infrared and broad band visible pump-probe spectroscopy. The transient response in the UV-vis spectral region does not depend on the heme pocket environment and is very similar to that known for ferrous proteins. The main feature is an instantaneous, broad, short-lived absorption signal that develops into a narrower red-shifted Soret band. Significant transient absorption is also observed in the 360-390 nm range. At all probe wavelengths the signal decays to zero with a longest time constant of 3.6 ps. The infrared data on MbCN reveal a bleaching of the C triple bond N stretch vibration of the heme-bound ligand, and the formation of a five-times weaker transient absorption band, 28 cm(-1) lower in energy, within the time resolution of the experiment. The MbC triple bond N stretch vibration provides a direct measure for the return of population to the ligated electronic (and vibrational) ground state with a 3-4 ps time constant. In addition, the CN-stretch frequency is sensitive to the excitation of low frequency heme modes, and yields independent information about vibrational cooling, which occurs on the same timescale.

Measurements of the photodissociation quantum yields of MbNO and MbO(2) and the vibrational relaxation of the six-coordinate heme species

The (t approximately 0) photodissociation quantum yields (Y(0)) of MbNO and MbO(2) are measured to be 50 +/- 5 and 28 +/- 6%, respectively, using MbCO (Y(0) = 100%) as a reference. When photolysis does not take place, we find that a significant portion of the photon energy contributes to heating of the residual six-coordinate heme (MbNO and MbO(2)). The time constant for vibrational relaxation of the six-coordinate ligand-bound heme is found to be close to 1 ps for both samples. The MbO(2) sample also shows a approximately 4-ps optical response that is assigned to a rapid phase (25-30% amplitude) of O(2) geminate rebinding. We observe no additional geminate recombination in the MbO(2) sample out to 120 ps. In contrast, the MbNO sample displays significant geminate recombination over the first 120 ps, which can be adequately fit with two exponentials whose amplitudes and time constants appear to depend weakly on the pump wavelength. This more complex kinetic behavior conceivably arises due to heating of the photodissociated heme and its effect on the geminate recombination as the system cools. Overall, the data are consistent with a hypothesis that distortions along the iron-ligand bending coordinate play a key role in the photodissociation process. The transient formation of an unphotolyzable FeO(2) side-on binding geometry is suggested to be responsible for the lowered quantum yield of MbO(2) relative to MbNO.

The leghemoglobin proximal heme pocket directs oxygen dissociation and stabilizes bound heme

Sperm whale myoglobin (Mb) and soybean leghemoglobin (Lba) are two small, monomeric hemoglobins that share a common globin fold but differ widely in many other aspects. Lba has a much higher affinity for most ligands, and the two proteins use different distal and proximal heme pocket regulatory mechanisms to control ligand binding. Removal of the constraint provided by covalent attachment of the proximal histidine to the F-helices of these proteins decreases oxygen affinity in Lba and increases oxygen affinity in Mb, mainly because of changes in oxygen dissociation rate constants. Hence, Mb and Lba use covalent constraints in opposite ways to regulate ligand binding. Swapping the F-helices of the two proteins brings about similar effects, highlighting the importance of this helix in proximal heme pocket regulation of ligand binding. The F7 residue in Mb is capable of weaving a hydrogen-bonding network that holds the proximal histidine in a fixed orientation. On the contrary, the F7 residue in Lba lacks this property and allows the proximal histidine to assume a conformation favorable for higher ligand binding affinity. Geminate recombination studies indicate that heme iron reactivity on picosecond timescales is not the dominant cause for the effects observed in each mutation. Results also indicate that in Lba the proximal and distal pocket mutations probably influence ligand binding independently. These results are discussed in the context of current hypotheses for proximal heme pocket structure and function.

Control of nitric oxide dynamics by guanylate cyclase in its activated state

Soluble guanylate cyclase (sGC) is the target of nitric oxide (NO) released by nitric-oxide synthase in endothelial cells, inducing an increase of cGMP synthesis in response. This heterodimeric protein possesses a regulatory subunit carrying a heme where NO binding occurs, while the second subunit harbors the catalytic site. The binding of NO and the subsequent breaking of the bond between the proximal histidine and the heme-Fe(2+) are assumed to induce conformational changes, which are the origin of the catalytic activation. At the molecular level, the activation and deactivation mechanisms are unknown, as is the dynamics of NO once in the heme pocket. Using ultrafast time-resolved absorption spectroscopy, we measured the kinetics of NO rebinding to sGC after photodissociation. The main spectral transient in the Soret band does not match the equilibrium difference spectrum of NO-liganded minus unliganded sGC, and the geminate rebinding was found to be monoexponential and ultrafast (tau = 7.5 ps), with a relative amplitude close to unity (0.97). These characteristics, so far not observed in other hemoproteins, indicate that NO encounters a high energy barrier for escaping from the heme pocket once the His-Fe(2+) bond has been cleaved; this bond does not reform before NO recombination. The deactivation of isolated sGC cannot occur by only simple diffusion of NO from the heme; therefore, several allosteric states may be inferred, including a desensitized one, to induce NO release. Thus, besides the structural change leading to activation, a consequence of the decoupling of the proximal histidine may also be to induce a change of the heme pocket distal geometry, which raises the energy barrier for NO escape, optimizing the efficiency of NO trapping. The non-single exponential character of the NO picosecond rebinding coexists only with the presence of the protein structure surrounding the heme, and the single exponential rate observed in sGC is very likely to be due to a closed conformation of the heme pocket. Our results emphasize the physiological importance of NO geminate recombination in hemoproteins like nitric-oxide synthase and sGC and show that the protein structure controls NO dynamics in a manner adapted to their function. This control of ligand dynamics provides a regulation at molecular level in the function of these enzymes.

Mechanistic studies on the reversible binding of nitric oxide to metmyoglobin

The ferriheme protein metmyoglobin (metMb) in buffer solution at physiological pH 7.4 reversibly binds the biomessenger molecule nitric oxide to yield the nitrosyl adduct (metMb(NO)). The kinetics of the association and dissociation processes were investigated by both laser flash photolysis and stopped-flow kinetics techniques at ambient and high pressure, in three laboratories using several different sources of metMb. The activation parameters DeltaH, DeltaS, and DeltaV were calculated from the kinetic effects of varying temperature and hydrostatic pressure. For the "on" reaction of metMb plus NO, reasonable agreement was found between the various techniques with DeltaH(on), DeltaS(on), and DeltaV(on) determined to have the respective values approximately 65 kJ mol(-1), approximately 60 J mol(-1) K(-1), and approximately 20 cm(3) mol(-1). The large and positive DeltaS and DeltaV values are consistent with the operation of a limiting dissociative ligand substitution mechanism whereby dissociation of the H(2)O occupying the sixth distal coordination site of metMb must precede formation of the Fe-NO bond. While the activation enthalpies of the "off" reaction displayed reasonable agreement between the various techniques (ranging from 68 to 83 kJ mol(-1)), poorer agreement was found for the DeltaS(off) values. For this reason, the kinetics for the "off" reaction were determined more directly via NO trapping experiments, which gave the respective activation parameters DeltaH(off) = 76 kJ mol(-1), DeltaS(off) = approximately 41 J mol(-1) K(-1), and DeltaV(off) = 20 cm(3) mol(-1)), again consistent with a limiting dissociative mechanism. These results are discussed in reference to other investigations of the reactions of NO with both model systems and metalloproteins.

Syntheses and structural characterization of the (OCnOPor) capped porphyrins: Co(OC2OPor).CH2Cl2, Co(OC2OPor)(NO)out.0.46CHCl3, Co(OC3OPor).CHCl3, and Co(OC3OPor)(MeIm).3C7H8

The compounds Co(OC2OPor).CH2Cl2 (1), Co(OC2OPor)(NO)out.0.46CHCl3 (2), Co(OC3OPor).CHCl3 (3), and Co(OC3OPor)(MeIm).3C7H8 (4) (OC2OPor = 5,10,15,20-(benzene-1,2,4,5- tetrakis(2-phenyloxy)ethoxy)-2',2",2"',2""-tetraylporphyrinato dianion; OC3OPor = 5,10,15,20-(benzene-1,2,4,5-tetrakis(2- phenyloxy)propoxy)-2',2",2"',2""-tetraylporphyrinato dianion; MeIm = 1-methylimidazole), have been synthesized, and their structures have been determined by single-crystal X-ray diffraction methods at T = -120 degrees C: 1, a = 8.824(1) A, b = 16.674(1) A, c = 16.836(1) A, alpha = 104.453(1) degrees, beta = 92.752(1) degrees, gamma = 90.983(1) degrees, P1, Z = 2; 2, a = 9.019(1) A, b = 16.588(2) A, c = 16.909(2) A, alpha = 103.923(2) degrees, beta = 92.082(2) degrees, gamma = 93.583(2) degrees, P1, Z = 2; 3, a = 13.484(3) A, b = 14.404(3) A, c = 14.570(3) A, alpha = 105.508(3) degrees, beta = 100.678(3) degrees, gamma = 93.509(4) degrees, P1, Z = 2; 4, a = 16.490(1) A, b = 22.324(2) A, c = 17.257(1) A, b = 92.437(1) degrees, P2(1)/n, Z = 4. These compounds are the first structurally characterized Co-bound members of the OCnOPor ligand system. The NO ligand in 2 and the MeIm ligand in 4 bind asymmetrically and lead to several metrical changes in these porphyrins, e.g., variations in average porphyrin deviations and Co atom displacements relative to the porphyrinato N atoms and the mean porphyrin planes.

Dissociation and recombination between ligands and heme in a CO-sensing transcriptional activator CooA. A flash photolysis study

CooA from Rhodospirillum rubrum is a transcriptional activator in which a heme prosthetic group acts as a CO sensor and regulates the activity of the protein. In this study, the electronic relaxation of the heme, and the concurrent recombination between ligands and the heme at approximately 280 K were examined in an effort to understand the environment around the heme and the dynamics of the ligands. Upon photoexcitation of the reduced CooA at 400 nm, electronic relaxation of the heme occurred with time constants of 0.8 and 1.7 ps. The ligand rebinding was substantially completed with a time constant of 6.5 ps, followed by a slow relaxation process with a time constant of 173 ps. In the case of CO-bound CooA, relaxation of the excited heme occurred with two time constants, 1.1 and 2.4 ps, which were largely similar to those with reduced CooA. The subsequent CO recombination process was remarkably fast compared with that of other CO-bound heme proteins. It was well described as a biphasic geminate recombination process with time constants of 78 ps (60%) and 386 ps (30%). About 10% of the excited heme remained unligated at 1.9 ns. The dynamics of rebinding of CO thus will help us to understand how the physiologically relevant diatomic molecule approaches the heme binding site in CooA with picosecond resolution.