Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.     

Time dependence of near-infrared spectra of photodissociated hemoglobin and myoglobin

The near-infrared charge-transfer transitions at approximately 760 nm in photodissociated hemoglobin and myoglobin display very different time dependences. In photodissociated myoglobin at room temperature the transition has fully relaxed to its deoxymyoglobin value by 10 ns. In photodissociated hemoglobin, the transition is shifted by 6 nm to longer wavelengths at 10 ns. It relaxes about halfway back to the deoxyhemoglobin value by about 100 ns but subsequently changes very slowly out to about 100 microseconds when the signal intensity becomes too small to follow any further. The intensity of this transition, present in only five-coordinate hemes, is found to follow the same time dependence as the wavelength change. Consequently, there appears to be a correlation between a structural property of the heme (as inferred from the wavelength of the charge-transfer transition) and a functional property (the CO recombination) of the protein (as inferred from the intensity of the transition). Possible origins for this correlation are considered.     

Picosecond transient absorption study of photodissociated carboxy hemoglobin and myoglobin.

The optical transient absorption spectra at 30 ps and 6.5 ns after photolysis are compared for both carboxy hemoglobin (HbCO) and carboxy myoglobin (MbCO). Both 355- and 532-nm excitation pulses were used. In all cases the shapes of the optical difference spectra thus generated are stationary over the complete time-scale studied. The photolysis spectra for MbCO are not significantly different from the equilibrium difference spectra generated on the same picosecond spectrometer when measured to an accuracy of +/- 0.5 nm. In addition, spectral parameters for delegated HbCO generated on the same spectrometer but detected by two different techniques, either by a Vidicon detector or point by point with photomultiplier tubes, are reported; the results are different from some of the previously reported picosecond experiments.     

The structural dynamics of myoglobin

Conformational fluctuations in proteins were initially invoked to explain the observation that diffusion of small ligands through the matrix is a global phenomenon. Small globular proteins contain internal cavities that play a role not only in matrix dynamics but also in controlling function, tracing a pathway for the diffusion of the ligand to and from the active site. This is the main point addressed in this Review, which presents pertinent information obtained on myoglobin (Mb). Mb, a simple globular heme protein which binds reversibly oxygen and other ligands. The bond between the heme Fe(II) and gaseous ligands can be photodissociated by a laser pulse, generating a non-equilibrium population of protein structures that relaxes on a picosecond to millisecond time range. This process is associated with migration of the ligand to internal cavities of the protein, which are known to bind xenon. Some of the results obtained by laser photolysis, molecular dynamics simulations, and X-ray diffraction of intermediate states of wild-type and mutant myoglobins are summarized. The extended relaxation of the globin moiety directly observed by Laue crystallography reflects re-equilibration among conformational substates known to play an essential role in controlling protein function.     

Structural dynamics of myoglobin

Conformational fluctuations have been invoked to explain the observation that the diffusion of small ligands through a protein is a global phenomenon, as suggested (for example) by the oxygen induced fluorescence quenching of buried tryptophans. In enzymes processing large substrates, a channel to the catalytic site is often seen in the crystal structure; on the other hand in small globular proteins, it is not known if the cavities identified in the interior space are important in controlling their function by defining specific pathways in the diffusion to the active site. This point is addressed in this paper, which reports some relevant results obtained on myoglobin, the hydrogen atom of molecular biology. Protein conformational relaxations have been extensively investigated with myoglobin because the photosensivity of the adduct with CO, O2 and NO allows us to follow events related to the migration of the ligand through the matrix. Results obtained by laser photolysis, molecular dynamics simulations, X-ray diffraction of intermediate states of wt type and mutant myoglobins are briefly summarized. Crystallographic data on the photochemical intermediate of a new triple mutant of sperm whale myoglobin (Mb-YQR) show, for the first time, the photolyzed CO* sitting in one of the Xe-binding cavities, removed from the heme group. These results support the viewpoint that pre-existing 'packing defects' in the protein interior play a major role in controlling the dynamics of ligand binding, including oxygen, and thereby acquire a survival value.     

Time-resolved resonance Raman study on ultrafast structural relaxation and vibrational cooling of photodissociated carbonmonoxy myoglobin

A localized small structural change is converted to a higher order conformational change of protein and extends to a mesoscopic scale to induce a physiological function. To understand such features of protein, ultrafast dynamics of myoglobin (Mb) following photolysis of carbon monoxide were investigated. Recent results are summarized here with a stress on structural and vibrational energy relaxation. The core expansion of heme takes place within 2 ps but the out of plane displacement of the heme iron and the accompanying protein conformational change occur in 10 and 100 s of the picosecond regimes, respectively. Unexpectedly, it was found from UV resonance Raman spectra that Trp7 in the N-terminal region and Tyr151 in the C-terminal region undergo appreciable structural changes upon ligand binding-dissociation while Tyr104, Tyr146, and Trp14 do not. Because of the communication between the movements of these surface residues and the heme iron, the rate of spectral change of the iron-histidine (Fe- His) stretching band after CO photodissociation is influenced by the viscosity of solvent. Temporal changes of the anti-Stokes Raman intensity demonstrated immediate generation of vibrationally excited heme upon photodissociation and its decay with a time constant of 1-2 ps.     

Molecular dynamics simulation of hydration in myoglobin

This study was carried out to evaluate the stability of the 89 bound water molecules that were observed in the neutron diffraction study of CO myoglobin. The myoglobin structure derived from the neutron analysis was used as the starting point in the molecular dynamics simulation using the software package CHARMM. After solvation of the protein, energy minimization and equilibration of the system, 50 ps of Newtonian dynamics was performed. This data showed that only 4 water molecules are continously bound during the length of this simulation while the other solvent molecules exhibit considerable mobility and are breaking and reforming hydrogen bonds with the protein. At any instant during the simulation, 73 of the hydration sites observed in the neutron structure are occupied by water. © 1995 Wiley-Liss, Inc.     

Toward an understanding of the role of dynamics on enzymatic catalysis in lactate dehydrogenase

The motions of key residues at the substrate binding site of lactate dehydrogenase (LDH) were probed on the 10 ns to 10 ms time scale using laser-induced temperature-jump relaxation spectroscopy employing both UV fluorescence and isotope-edited IR absorption spectroscopy as structural probes. The dynamics of the mobile loop, which closes over the active site and is important for catalysis and binding, were characterized by studies of the inhibitor oxamate binding to the LDH/NADH binary complex monitoring the changes in emission of bound NADH. The bound NAD-pyruvate adduct, whose pyruvate moiety likely interacts with the same residues that interact with pyruvate in its ternary complex with LDH, served as a probe for any relative motions of active site residues against the substrate. The frequencies of its C=O stretch and -COO(-) antisymmetric stretch shift substantially should any relative motion of the polar moieties at the active site (His-195, Asp-168, Arg-109, and Arg-171) occur. The dynamics associated with loop closure are observed to involve several steps with motions from 1 to 300 microms. Apart from the "melting" of a few residues on the protein's surface, no kinetics were observed on any time scale in experiments of the bound NAD-pyr adduct although the measurements were made with a high degree of accuracy, even for final temperatures close to the unfolding transition of the protein. This is contrary to simple physical considerations and models. These results show that, once a productive protein/substrate complex is formed, the binding pocket is very rigid with very little, if any, motion apart from the mobile loop. The results also show that loop opening involves concomitant movement of the substrate out of the binding pocket.     

On the role of myoglobin in muscle respiration

The presence of myoglobin in red muscle tissue has a marked effect on its respiration because it combines reversibly with oxygen and hence gives rise to facilitated diffusion. In this paper we consider the role of myoglobin in facilitating oxygen diffusion and give quantitative results for the oxygen concentration within a typical muscle fibre. Simple expressions are derived for the critical metabolism for the onset of oxygen debt and the growth and size of the region in oxygen debt when the muscle metabolism exceeds this critical value.The general principle, enunciated by Murray &; Wyman (1971), that the macromolecule, myoglobin here, can only function as a carrier if it is unsaturated in some region of the system is again shown to hold.A singular perturbation procedure is used to analyze the model, the effect of which is to reduce the mathematical problem to that of trivially solving a quadratic algebraic equation for the oxygen concentration in the muscle fibre. Physically one condition which causes this phenomenon to be singular in the mathematical sense is that the relaxation times of the myoglobin-oxygen reaction are small compared with the diffusion time of the myoglobin-oxygen complex.     

Structural dynamics of liganded myoglobin.

X-ray crystallography can reveal the magnitudes and principal directions of the mean-square displacements of every atom in a protein. This structural information is complementary to the temporal information obtainable by spectroscopic techniques such as nuclear magnetic resonance. Determination of the temperature dependence of the mean-square displacements makes it possible to separate large conformational motions from simple thermal vibrations. The contribution of crystal lattice disorder to the overall apparent displacement can be estimated by Mössbauer spectroscopy. This technique has been applied to high resolution x-ray diffraction data from sperm whale myoglobin in its Met iron and oxy cobalt forms. Both crystal structures display regions of large conformational motions, particularly at the chain termini and in the region of the proximal histidine. Overall, the mean-square displacement increases with increasing distance from the center of gravity of the molecule. Some regions of the heme pocket in oxy cobalt myoglobin are more rigid than the corresponding regions in Met myoglobin.     

Cavities and packing defects in the structural dynamics of myoglobin

Small globular proteins contain internal cavities and packing defects that reduce thermodynamic stability but seem to play a role in controlling function by defining pathways for the diffusion of the ligand/substrate to the active site. In the case of myoglobin (Mb), a prototype for structure–function relationship studies, the photosensitivity of the adduct of the reduced protein with CO, O₂ and NO allows events related to the migration of the ligand through the matrix to be followed. The crystal structures of intermediate states of wild-type (wt) and mutant Mbs show the photolysed CO to be located either in the distal heme pocket (primary docking site) or in one of two alternative cavities (secondary docking sites) corresponding to packing defects accessible to an atom of xenon. These results convey the general picture that pre-existing internal cavities are involved in controlling the dynamics and reactivity of the reactions of Mb with O₂ and other ligands, including NO.     

The role of myoglobin in retarding oxygen depletion in anoxic heart

The present study explores the role of myoglobin (Mb) in retarding the development of anoxia in the perfused working rat heart. We examine this phenomenon by analyzing the behavior and the kinetics of Mb oxygenation and cytochrome aa3 (cytaa3) redoxation. Absorbance changes, measured at wavelength pairs specific to Mb and cytaa3, show parallelism between the Mb oxygenation status and the redox states of cytaa3. Induction of anoxia leads to early and accelerated Mb deoxygenation whereas cytaa3 reduction marks a slight delay and its rate is twice slower than that of Mb. Then, when Mb is desatured above 50%, the cytaa3 reduction becomes accelerated. With the reoxygenated perfusion following the anoxia, the rate of Mb reoxygenation is twice faster than that of the cytaa3 reoxidation. When the oxygen-binding function of Mb, in situ in the heart, is abolished by treatment with sodium nitrite (NaNO2), the redox kinetics of cytaa3 show significant perturbations. Induction of anoxia leads to a precocious and accelerated reduction of cytaa3, compared to the same anoxic heart before the treatment. At reoxygenation, the reoxidation rate of cytaa3 decreases significantly, compared to that before the treatment. Similarly, in the nitrite treated heart, the phosphocreatine (PCr) level decreases to 60% of the control, whereas the inorganic phosphate (Pi) level increases to 300%. ATP concentration, however, remains constant. We conclude from these results that Mb may support mitochondrial respiration at the critical levels of the myocardial O2 supply.     

Comparison of the dynamics of myoglobin in different crystal forms.

Crystals have been grown of "sperm whale" myoglobin produced in Escherichia coli from a synthetic gene and the structure has been solved to 1.9 A resolution. Because of a remaining initiator methionine, this protein crystallizes in a different space group from native sperm whale myoglobin. The three-dimensional structure of the synthetic protein is essentially identical to the native sperm whale protein. However, the crystallographic B-factors for parts of the molecule are quite different in the two crystal forms, and provide a measure of the effect of different packing constraints on the flexibility of the protein. The effect of the packing forces is to reduce the mobility of the protein in the regions of contact and thereby introduce differences in mobilities between the two crystal forms. Discrepancies between mobilities calculated from molecular dynamics simulations and crystallography can be reduced by considering the data from both crystal forms.     

The role of the individual in social dynamics

The mathematical theories of social dynamics developed previously are deterministic and leave no room for the effects of single “exceptional” individuals. They all, however, lead to the existence of instability points and threshold phenomena. It is shown that in the neighborhood of such instability points, exceptional individuals, who appear rarely, can appreciablyadvance orretard the moment at which the instability is reached and at which a sudden change in the society occurs. Such individuals, however, do not eitherprevent orcause the instability, or the change, to occur. The indeterminacy introduced by “rare” individuals into the time course of social change is inversely proportional to the rate of social change.     

The photoprotective role of carotenoids in higher plants

Carotenoids have two important roles in photosynthetic organisms. First, they act as accessory light-harvesting pigments, effectively extending the range of light absorbed by the photosynthetic apparatus. Secondly, they perform an essential photoprotective role by quenching triplet state chlorophyll molecules and scavenging singlet oxygen and other toxic oxygen species formed within the chloroplast. Only recently an additional, novel, protective role has been proposed for the carotenoid zeaxanthin, involving the dissipation of harmful excess excitation energy under stress conditions. Zeaxanthin may be formed through de novo synthesis in response to long-term environmental stress, and through the rapid enzymic de-epoxidation of the carotenoid violaxanthin (the xanthophyll cycle) in response to short-term alterations in the plant's light environment. Interspecific differences occur in the ability of plants and algae to produce zeaxanthin under stress conditions, and hence the ability to photoprotect the photosynthetic apparatus through this means varies from species to species. The ability of a plant to respond to light-mediated environmental stress by producing zeaxanthin may therefore affect, at least in part, the ability of that plant to inhabit or colonise certain habitats (e.g. sun or shade conditions).     

Molecular dynamics simulations of heme reorientational motions in myoglobin.

Molecular dynamics simulations of 2-ns duration were performed on carbonmonoxymyoglobin and deoxymyoglobin in vacuo to study the reorientational dynamics of the heme group. The heme in both simulations undergoes reorientations of approximately 5 degrees amplitude on a subpicosecond time scale, which produce a rapid initial decay in the reorientational correlation function to about 0.99. The heme also experiences infrequent changes in average orientation of approximately 10 degrees amplitude, which lead to a larger slow decay of the reorientational correlation function over a period of hundreds of picoseconds. The simulations have not converged with respect to these infrequent transitions. However, an estimate of the order parameter for rapid internal motions of the heme from those orientations which are sampled by the simulations suggests that the subnanosecond orientational dynamics of the heme accounts for at least 30% of the unresolved initial anisotropy decay observed in the nanosecond time-resolved optical absorption experiments on myoglobin reported by Ansari et al. in a companion paper (Ansari, A., C.M. Jones, E.R. Henry, J. Hofrichter, and W.A. Eaton. 1992. Biophys. J. 64:852-868.). A more complete sampling of the accessible heme orientations would most likely increase this fraction further. The simulation of the liganded molecule also suggests that the conformational dynamics of the CO ligand may contribute significantly to discrepancies between the ligand conformation as probed by x-ray diffraction and by infrared-optical photoselection experiments. The protein back-bone explores multiple conformations during the simulations, with the largest structural changes appearing in the E and F helices, which are in contact with the heme. The variations in the heme orientation correlate with the conformational dynamics of the protein on a time scale of hundreds of picoseconds, suggesting that the heme orientation may provide a useful probe of dynamical processes in the protein.     

The effect of ligand dynamics on heme electronic transition band III in myoglobin.

Band III is a near-infrared electronic transition at ~13,000 cm(-1) in heme proteins that has been studied extensively as a marker of protein conformational relaxation after photodissociation of the heme-bound ligand. To examine the influence of the heme pocket structure and ligand dynamics on band III, we have studied carbon monoxide recombination in a variety of myoglobin mutants after photolysis at 3 K using Fourier transform infrared temperature-derivative spectroscopy with monitoring in three spectral ranges, (1) band III, the mid-infrared region of (2) the heme-bound CO, and (3) the photodissociated CO. Here we present data on mutant myoglobins V68F and L29W, which both exhibit pronounced ligand movements at low temperature. From spectral and kinetic analyses in the mid-infrared, a small number of photoproduct populations can be distinguished, differing in their distal heme pocket conformations and/or CO locations. We have decomposed band III into its individual photoproduct contributions. Each photoproduct state exhibits a different "kinetic hole-burning" (KHB) effect, a coupling of the activation enthalpy for rebinding to the position of band III. The analysis reveals that the heme pocket structure and the photodissociated CO markedly affect the band III transition. A strong kinetic hole-burning effect results only when the CO ligand resides in the docking site on top of the heme group. Migration of CO away from the heme group leads to an overall blue shift of band III. Consequently, band III can be used as a sensitive tool to study ligand dynamics after photodissociation in heme proteins.