Linkage of functional and structural heterogeneity in proteins: dynamic hole burning in carboxymyoglobin

Heme geometry in the 10 K photoproduct from sperm whale carbonmonoxymyoglobin

We have measured the Soret band of the photoproduct obtained by complete photolysis of sperm whale carbonmonoxymyoglobin at 10 K. The experimental spectrum has been modeled with an analytical expression that takes into account the homogeneous bandwidth, the coupling of the electronic transition with both high and low frequency vibrational modes, and the effects of static conformational heterogeneity. The comparison with deoxymyoglobin at low temperature reveals three main differences. In the photoproduct, the Soret band is shifted to red. The band is less asymmetric, and an enhanced coupling to the heme vibrational mode at 674 cm-1 is observed. These differences reflect incomplete relaxation of the active site after ligand dissociation. The smaller band asymmetry of the photoproduct can be explained by a smaller displacement of the iron atom from the mean porphyrin plane, in quantitative agreement with the X-ray structure analysis. The enhanced vibrational coupling is attributed to a subtle heme distortion from the planar geometry that is barely detectable in the X-ray structure.

Ligand binding and protein dynamics in cupredoxins

Type 1 copper sites bind nitric oxide (NO) in a photolabile complex. We have studied the NO binding properties of the type 1 copper sites in two cupredoxins, azurin and halocyanin, by measuring the temperature dependence of the ligand binding equilibria and the kinetics of the association reaction after photodissociation over a wide range of temperature (80-280 K) and time (10(-6)-10(2) s). In both proteins, we find nonexponential kinetics below 200 K that do not depend on the NO concentration. Consequently, this process is interpreted as geminate recombination. In azurin, the rebinding can be modeled with the Arrhenius law using a single pre-exponential factor of 10(8.3) s-1 and a Gaussian distribution of enthalpy barriers centered at 22 kJ/mol with a width [full width at half-maximum (FWHM)] of 11 kJ/mol. In halocyanin, a more complex behavior is observed. About 97% of the rebinding population can also be characterized by a Gaussian distribution of enthalpy barriers at 12 kJ/mol with a width of 6.0 kJ/mol (FWHM). The pre-exponential of this population is 1.6 x 10(12) s-1 at 100 K. After the majority population has rebound, a power-law phase that can be modeled with a gamma-distribution of enthalpy barriers is observed. Between 120 and 180 K, an additional feature that can be interpreted as a relaxation of the barrier distribution toward higher barriers shows up in the kinetics. Above 200 K, a slower, exponential rebinding appears in both cupredoxins. Since the kinetics depend on the NO concentration, this process is identified as bimolecular rebinding.(ABSTRACT TRUNCATED AT 250 WORDS)

Protein reaction kinetics in a room-temperature glass

Protein reaction kinetics in aqueous solution at room temperature are often simplified by the thermal averaging of conformational substates. These substates exhibit widely varying reaction rates that are usually exposed by trapping in a glass at low temperature. Here, it is shown that the solvent viscosity, rather than the low temperature, is primarily responsible for the trapping. This was demonstrated by placement of myoglobin in a glass at room temperature and subsequent observation of inhomogeneous reaction kinetics. The high solvent viscosity slowed the rate of crossing the energy barriers that separated the substates and also suppressed any change in the average protein conformation after ligand dissociation.

Thermal fluctuations between conformational substates of the Fe(2+)-HisF8 linkage in deoxymyoglobin probed by the Raman active Fe-N epsilon (HisF8) stretching vibration

We have measured the VFe-His Raman band of horse heart deoxymyoglobin dissolved in an aqueous solution as a function of temperature between 10 and 300 K. The minimal model to which these data can be fitted in a statistically significant and physically meaningful way comprises four different Lorentzian bands with frequencies at 197, 209, 218, and 226 cm-1, and a Gaussian band at 240 cm-1, which exhibit halfwidths between 10 and 12.5 cm-1. All these parameters were assumed to be independent of temperature. The temperature dependence of the apparent total band shape's frequency is attributed to an intensity redistribution of the subbands at omega 1 = 209 cm-1, omega 2 = 218 cm-1, and omega 3 = 226 cm-1, which are assigned to Fe-N epsilon (HisF8) stretching modes in different conformational substrates of the Fe-HisF8 linkage. They comprise different out-of-plane displacements of the heme iron. The two remaining bands at 197 and 240 cm-1 result from porphyrin modes. Their intensity ratio is nearly temperature independent. The intensity ratio I3/I2 of the vFe-His subbands exhibits a van't Hoff behavior between 150 and 300 K, bending over in a region between 150 and 80 K, and remains constant between 80 and 10 K, whereas I2/I1 shows a maximum at 170 K and approaches a constant value at 80 K. These data can be fitted by a modified van't Hoff expression, which accounts for the freezing into a non-equilibrium distribution of substates below a distinct temperature Tf and also for the linear temperature dependence of the specific heat of proteins. The latter leads to a temperature dependence of the entropic and enthalpic differences between conformational substates. The fits to the intensity ratios of the vFe-His subbands yield a freezing temperature of Tf = 117 K and a transition region of delta T = 55 K. In comparison we have utilized the above thermodynamic model to reanalyze earlier data on the temperature dependence of the ratio Ao/A1 of two subbands underlying the infrared absorption band of the CO stretching vibration in CO-ligated myoglobin (A. Ansari, J. Berendzen, D. Braunstein, B. R. Cowen, H. Frauenfelder, M. K. Kong, I. E. T. Iben, J. Johnson, P. Ormos, T. B. Sauke, R. Scholl, A. Schulte, P. J. Steinbach, R. D. Vittitow, and R. D. Young, 1987, Biophys. Chem. 26:237-335). This yields thermodynamic parameters, in particular the freezing temperature (Tf = 231 K) and the width of the transition region (AT =8 K), which are significantly different from the corresponding parameters obtained from the above vFe-His data, but very close to values describing the transition of protein bound water from a liquid into an amorphous state. These findings and earlier reported data on the temperature dependence exhibited by the Soret absorption bands of various deoxy and carbonmonoxymyoglobins led us to the conclusion that the fluctuations between conformational substates of the heme environment in carbonmonoxymyoglobin are strongly coupled to motions within the hydration shell, whereas the thermal motions between the substates of the Fe-HisF8 linkage in deoxymyoglobin proceed on an energy landscape that is mainly determined by the intrinsic properties of the protein. The latter differ from protein fluctuations monitored by Mossbauer experiments ondeoxymyoglobin crystals which exhibit a strong coupling to the protein bound water and most probably reflect a higher tier in the hierarchical arrangement of substates and equilibrium fluctuations.

Ligand binding to heme proteins. V. Light-induced relaxation in proximal mutants L89I and H97F of carbonmonoxymyoglobin

We have studied the proximal mutants L89I and H97F of MbCO with FTIR and temperature-derivative spectroscopy at temperatures between 10 and 160 K. The mutations give rise only to minor alterations of the stretch spectra of the bound and photodissociated CO ligand. The most pronounced difference is a larger population in the A3 substate at approximately 1930 cm-1 in the mutants. The barrier distributions, as determined by temperature-derivative spectroscopy, are very similar to native MbCO after short illumination. Extended illumination leads to substantial increases of the rebinding barriers in native MbCO and the proximal mutants. A larger fraction of light-relaxed states is found in the proximal mutants, implying that the conformational energy landscape has been modified to more easily allow light-induced transitions. These and other spectroscopic data imply that the large changes in the binding properties are brought about by a light-induced conformational relaxation involving the structure at the heme iron. Similarities with spectral hole-burning studies and physical models are discussed.

Correlation of carbon monoxide association rates and the position of absorption band III in hemoproteins

We have examined the absorbance of a charge-transfer transition near 760 nm, known as band III, in several hemoproteins and heme complexes. The band III position correlates with the rate of carbon monoxide binding to the heme. A band III present at 760 nm indicates an unfavorable geometry of the heme for carbon monoxide binding; a red-shift of the band III to 765 nm indicates a less-constrained geometry of the heme as evidenced by higher carbon monoxide association rates. The band III position correlates well with the Raman frequency of the Fe-His(F8) bond as suggested previously for normal hemoglobin A [Sassaroli, M. & Rousseau, D. L. (1987) Biochemistry 26, 3092-3098]. Aplysia myoglobin and the chimeric heme protein kinase FixL from Bradyrhizobium japonicum, hemoproteins with an apolar residue in place of the highly conserved polar histidine E7, do not fit the relationship between the band III position and the rate of binding of carbon monoxide to the heme. With these few exceptions, the measurement of band III appears to be a practical means to probe the stretch frequency of the Fe-His(F8) bond.

Ligand binding to heme proteins: the effect of light on ligand binding in myoglobin

Extended illumination slows the rebinding of CO to myoglobin after photodissociation at cryogenic temperatures. Two types of models have been put forward to explain the effect: motions of the CO within the heme pocket or conformational transitions of the protein. To resolve this ambiguity, we have studied the effect of extended illumination on ligand binding to horse and sperm whale myoglobin (hMb and swMb) with temperature-derivative spectroscopy, monitoring the reaction in the CO stretch bands in the infrared and the conformation-sensitive band III near 760 nm. The experiments show that the stretch frequency of the photodissociated CO does not change upon illumination, implying that the slowing of the CO rebinding is caused by conformational relaxation of Mb from the bound state toward the deoxy structure. The light-induced relaxation (LIR) depends on the number of photons absorbed but not on the light intensity or duration separately. LIR occurs on photon absorption in either the bound or photodissociated state and depends on the temperature at which the MbCO is illuminated. The LIR proceeds in jumps through a small number of conformational substates. The effective barrier for rebinding increases with each step. The substates populated are similar to those found in the thermally-induced relaxation (TIR) that is observed above 160 K. LIR depends markedly on the structural details; it differs for swMbCO and hMbCO and even for the three A substates of swMbCO. Pronounced differences exist between the effects in MbCO and MbO2. The similarity of LIR and TIR leads to a revised model for ligand binding to swMbCO and hMbCO, in which the relaxation is crucial for the escape of the ligand from the pocket, as was first suggested by Friedman [Friedman, J. M. (1985) Science 228, 1273-1280].

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.

The transition from inhomogeneous to homogeneous kinetics in CO binding to myoglobin

Heme proteins react inhomogeneously with ligands at cryogenic temperatures and homogeneously at room temperature. We have identified and characterized a transition from inhomogeneous to homogeneous behavior at intermediate temperatures in the time dependence of CO binding to horse myoglobin. The turnover is attributed to a functionally important tertiary protein relaxation process during which the barrier increases dynamically. This is verified by a combination of theory and multipulse measurements. A likely biological significance of this effect is in the autocatalysis of the ligand release process.

Structural heterogeneity of the Fe(2+)-N epsilon (HisF8) bond in various hemoglobin and myoglobin derivatives probed by the Raman-active iron histidine stretching mode

We have examined the Fe(2+)-N epsilon (HisF8) complex in hemoglobin A (HbA) by measuring the band profile of its Raman-active nu Fe-His stretching mode at pH 6.4, 7.0, and 8.0 using the 441-nm line of a HeCd laser. A line shape analysis revealed that the band can be decomposed into five different sublines at omega 1 = 195 cm-1, omega 2 = 203 cm-1, omega 3 = 212 cm-1, omega 4 = 218 cm-1, and omega 5 = 226 cm-1. To identify these to the contributions from the different subunits we have reanalyzed the nu Fe-His band of the HbA hybrids alpha(Fe)2 beta(Co)2 and alpha(Co)2 beta(Fe)2 reported earlier by Rousseau and Friedman (D. Rousseau and J. M. Friedman. 1988. In Biological Application on Raman Spectroscopy. T. G. Spiro, editor, 133-216). Moreover we have reanalyzed other Raman bands from the literature, namely the nu Fe-His band of the isolated hemoglobin subunits alpha SH- and beta SH-HbA, various hemoglobin mutants (i.e., Hb(TyrC7 alpha-->Phe), Hb(TyrC7 alpha-->His), Hb M-Boston and Hb M-Iwate), N-ethylmaleimide-des(Arg141 alpha) hemoglobin (NES-des(Arg141 alpha)HbA) and photolyzed carbonmonoxide hemoglobin (Hb*CO) measured 25 ps and 10 ns after photolysis. These molecules are known to exist in different quaternary states. All bands can be decomposed into a set of sublines exhibiting frequencies which are nearly identical to those found for deoxyhemoglobin A. Additional sublines were found to contribute to the nu Fe-His band of NES-des(Arg141 alpha) HbA and the Hb*CO species. The peak frequencies of the bands are determined by the most intensive sublines. Moreover we have measured the nu Fe-His band of deoxyHbA at 10 K in an aqueous solution and in a 80% glycerol/water mixture. Its subline composition at this temperature depends on the solvent and parallels that of more R-like hemoglobin derivatives. We have also measured the optical charge transfer band III of deoxyHbA at room temperature and found, that at least three subbands are required to fit its asymmetric band shape. This corroborates the findings on the nu Fe-His band in that it is indicative of a heterogeneity of the Fe(2+)-N epsilon(HisF8) bond. Finally we measured the nu Fe-His band of horse heart deoxyMb at different temperatures and decomposed it into three different sublines. In accordance with what was obtained for HbA their intensities rather than their frequencies are temperature-dependent. By comparison with VFe-His bands of some Mb mutants (i.e., Mb(His E7.->Gly) and Mb(HisE7__*Met) we suggest that these sublines may be attributed to different conformations of the heme pocket. Our data show, that the V Fe-His band is governed by at least two different coordinates x and y determining its frequency and intensity, respectively. While the former can be assigned to the tilt angle theta between the Fe2+-NJ(HisF8) bond and the heme normal and/or to the displacement delta of the iron from the heme plane, variations in the intensity may be caused by changes of the azimuthal angle phi formed by the projection of the proximal imidazole and the N(l)-Fe2+-N(III) line of the heme. The sublines are therefore interpreted as resulting from different conformational substates of the Fe2+-N(HisFa) complex which differ in terms of x (theta and/or delta). Each of them may further be subdivided in sub-substates with respect to the coordinate y (theta). Quaternary and tertiary transitions of the protein alter the population of these substates thus giving rise to a redistribution of the VFe-HiS sublines which shifts the corresponding peak frequency to higher values.

Dynamics of protein relaxation in site-specific mutants of human myoglobin

We have recently reported spectroscopic evidence for structural relaxation of myoglobin (Mb) following photodissociation of MbCO [Lambright, D. G., Balasubramanian, S., & Boxer, S. G. (1991) Chem. Phys. 158, 249-260]. In this paper we report measurements for a series of single amino acid mutants of human myoglobin on the distal side of the heme pocket (positions 45, 64, and 68) in order to examine specific structural determinants involved in this conformational relaxation and to determine the nature of the coupling between relaxation and the functional process of ligand binding. The kinetics of ligand binding and conformational relaxation were monitored by transient absorption spectroscopy in the Soret spectral region, and the results are analyzed using a four-state ligand binding model. Two principal results emerge: (1) amino acid substitutions in the distal heme pocket affect the kinetics of the nonequilibrium conformational relaxation and (2) the rate of ligand escape from the protein matrix is not significantly perturbed by the distal heme pocket mutations.

Functional consequences of mutations at the allosteric interface in hetero- and homo-hemoglobin tetramers

A seminal difference exists between the two types of chains that constitute the tetrameric hemoglobin in vertebrates. While alpha chains associate weakly into dimers, beta chains self-associate into tightly assembled tetramers. While heterotetramers bind ligands cooperatively with moderate affinity, homotetramers bind ligands with high affinity and without cooperativity. These characteristics lead to the conclusion that the beta 4 tetramer is frozen in a quaternary R-state resembling that of liganded HbA. X-ray diffraction studies of the liganded beta 4 tetramers and molecular modeling calculations revealed several differences relative to the native heterotetramer at the "allosteric" interface (alpha 1 beta 2 in HbA) and possibly at the origin of a large instability of the hypothetical deoxy T-state of the beta 4 tetramer. We have studied natural and artificial Hb mutants at different sites in the beta chains responsible for the T-state conformation in deoxy HbA with the view of restoring a low ligand affinity with heme-heme interaction in homotetramers. Functional studies have been performed for oxygen equilibrium binding and kinetics after flash photolysis of CO for both hetero- and homotetramers. Our conclusion is that the "allosteric" interface is so precisely tailored for maintaining the assembly between alpha beta dimers that any change in the side chains of beta 40 (C6), beta 99 (G1), and beta 101 (G3) involved in the interface results in increased R-state behavior. In the homotetramer, the mutations at these sites lead to the destabilization of the beta 4 hemoglobin and the formation of lower affinity noncooperative monomers.

CO recombination to human myoglobin mutants in glycerol-water solutions

The kinetics of CO recombination to site-specific mutants of human myoglobin have been studied by flash photolysis in the temperature range 250-320 K on the nanosecond to second time scale in 75% glycerol at pH 7. The mutants were constructed to examine specific proposals concerning the roles of Lys 45, Asp 60, and Val 68 in the ligand binding process. It is found that ligand recombination is nonexponential for all the mutants and that both the geminate amplitude and rate show large variations. The results are interpreted in terms of specific models connecting the dynamics and structure. It is shown that removal of the charged group at position 45 does not substantially affect the barrier height for escape or entry of the ligand; therefore the breakage of the salt bridge linking Lys 45, Asp 60, and a heme propionate is ruled out as the rate-determining barrier for this process. On the other hand, it is found that the escape barrier decreases roughly as size of the residue at position 68 increases, in the order Ala > Val > Asn > Leu. The residue at position 68 is also a major contributor to the final barrier to rebinding, but the barrier height shows no correlation with residue size and is more dependent on the stereochemistry of the residue. A molecular mechanism for ligand binding that is consistent with the results is discussed, and supporting evidence for this mechanism is examined.

Vibronic energy map and excited state vibrational characteristics of magnesium myoglobin determined by energy-selective fluorescence

The vibrational frequencies of the singlet excited state of Mg-substituted myoglobin and relative absorption probabilities were determined by fluorescence line-narrowing spectroscopy. These spectra contain information on the structure of the excited state species, and the availability of vibrationally resolved spectra from excited state biomolecules should aid in elucidating their structure and reactivity.

Conformational substates in azurin

Azurin is a small blue copper protein in the electron transfer chain of denitrifying bacteria. It forms a photolabile complex with nitric oxide (NO) at low temperatures. We studied the temperature dependence of the ligand binding equilibrium and the kinetics of the association reaction after photodissociation over a wide range of temperature (80-280 K) and time (10(-6)-10(2) s). The nonexponential rebinding below 200 K is independent of the NO concentration and is interpreted as internal recombination. The rebinding can be modeled with the Arrhenius law by using a single preexponential factor of 6.3 x 10(8) s-1 and a Gaussian distribution of enthalpy barriers centered at 23 kJ/mol with a width of 11 kJ/mol. Above 200 K, a slower, exponential rebinding process appears. The dependence of the kinetics on the NO concentration characterizes this reaction as bimolecular rebinding. The binding kinetics of NO to azurin show impressive analogies to the binding of carbon monoxide to myoglobin. We conclude that conformational substates occur not only in heme proteins but also in proteins with different active sites and secondary structures.

Spectroscopic evidence for conformational relaxation in myoglobin

The time and temperature dependencies of the line area (M0) and position (M1) of band III at approximately 760 nm have been measured with Fourier-transform infrared spectroscopy in deoxymyoglobin (Mb) and continuously photolyzed carbon monoxide myoglobin (MbCO). Below 200 K, the area of band III in the photoproduct Mb* increases with time even on time scales of hours. This behavior indicates changes in the distribution of activation enthalpy barriers for ligand rebinding under extended illumination. The band position of Mb* shifts to higher wavenumbers with increasing temperature up to 100 K owing to kinetic hole burning; the same protein coordinate that controls the position of band III also determines the rebinding barrier height. The shift ceases above 100 K, implying that more than one protein coordinate affects the height of the rebinding barrier. Above 160 K, the line position in Mb* shifts again and coalesces with the value of Mb for temperatures above 200 K. The shift is accompanied by an increase of the line area, reflecting a slowing of rebinding kinetics. Both effects are explained in the framework of the model introduced by Steinbach et al. [(1991) Biochemistry 30, 3988-4001]. Above approximately 160 K, the conformational relaxation Mb*----Mb simultaneously shifts the line position of band III and increases the enthalpy barrier for ligand rebinding. Furthermore, equilibrium fluctuations lead to an averaging of the band position and the rebinding enthalpy.

pH-induced conformational changes of the Fe(2+)-N epsilon (His F8) linkage in deoxyhemoglobin trout IV detected by the Raman active Fe(2+)-N epsilon (His F8) stretching mode

To investigate heme-protein coupling via the Fe(2+)-N epsilon (His F8) linkage we have measured the profile of the Raman band due to the Fe(2+)-N epsilon (His F8) stretching mode (nu Fe-His) of deoxyHb-trout IV and deoxyHbA at various pH between 6.0 and 9.0. Our data establish that the band of this mode is composed of five different sublines. In deoxyHb-trout IV, three of these sublines were assigned to distinct conformations of the alpha-subunit (omega alpha 1 = 202 cm-1, omega alpha 2 = 211 cm-1, omega alpha 3 = 217 cm-1) and the other two to distinct conformations of the beta-subunit (omega beta 1 = 223 cm-1 and omega beta 2 = 228 cm-1). Human deoxyHbA exhibits two alpha-chain sublines at omega alpha 1 = 203 cm-1, omega alpha 2 = 212 cm-1 and two beta-chain sublines at omega beta 1 = 217 cm-1 and omega beta 2 = 225 cm-1. These results reveal that each subunit exists in different conformations. The intensities of the nu Fe-His sublines in deoxyHb-trout IV exhibit a significant pH dependence, whereas the intensities of the corresponding sublines in the deoxyHbA spectrum are independent on pH. This finding suggests that the structural basis of the Bohr effect is different in deoxyHbA and deoxyHb-trout IV. To analyse the pH dependence of the deoxyHb-trout IV sublines we have applied a titration model describing the intensity of each nu Fe-His subline as an incoherent superposition of the intensities from sub-sublines with the same frequency but differing intrinsic intensities due to the different protonation states of the respective subunit. The molar fractions of these protonation states are determined by the corresponding Bohr groups (i.e., pK alpha 1 = pK alpha 2 = 8.5, pK beta 1 = 7.5, pK beta 2 = 7.4) and pH. Hence, the intensities of these sublines reflect the pH dependence of the molar fractions of the involved protonation states. Fitting this model to the pH-dependent line intensities yields a good reproduction of the experimental data. To elucidate the structural basis of the observed results we have employed models proposed by Bangchoroenpaurpong, O., K. T. Schomaker, and P. M. Champion. (1984. J. Am. Chem. Soc. 106:5688-5698) and Friedman, J. M., B. F. Campbell, and R. W. Noble. (1990. Biophys. Chem. 37:43-59) which describe the coupling between the sigma *orbitals of the Fe2+-NJ(His F8) bond and the phi * orbitals of the pyrrole nitrogens in terms of the tilt angle theta between its Fe2+-N,(HisF8)-bond and the heme normal and the azimuthal angle phi between the Fe2+-N.(His F8) projection on the heme and the N1-N3 axis.Our results indicate that each subconformation reflected by different frequencies of the VFe His-subline is related to different tilt angles theta, whereas the pH-induced intensity variations of each VFe His subline of the deoxy Hb trout IV spectrum are caused by changes of the azimuthal angle phi.

The energy landscapes and motions of proteins

Recent experiments, advances in theory, and analogies to other complex systems such as glasses and spin glasses yield insight into protein dynamics. The basis of the understanding is the observation that the energy landscape is complex: Proteins can assume a large number of nearly isoenergetic conformations (conformational substates). The concepts that emerge from studies of the conformational substates and the motions between them permit a quantitative discussion of one simple reaction, the binding of small ligands such as carbon monoxide to myoglobin.

Picosecond study of the near infrared absorption band of hemoglobin after photolysis of carbonmonoxyhemoglobin

Picosecond absorption spectroscopy is used to examine the position and band shape of the near infrared absorption band of hemoglobin as a function of time after the photodissociation of CO from carbonmonoxyhemoglobin. For the earliest delay time probed, 35 ps, the peak of the transient spectrum is at 765 nm, red shifted by 6 nm from that characteristic of equilibrium deoxyhemoglobin. No evolution in either the peak position or band shape is observed for time delays up to 60 ns. In addition, the position and shape of the spectrum are independent of photolysis energies ranging from 15 microJ/pulse to 150 microJ/pulse, spanning conditions under which the photon/heme ratio is varied from 0.01 to 2.0. This indicates that the geometry in the heme group is unrelaxed and that equilibration of the surrounding protein structure occurs on a time scale longer than 60 ns.

Protein dynamics: comparison of simulations with inelastic neutron scattering experiments

To deepen our understanding of the principles determining the folding and functioning of globular proteins the determination of their three-dimensional structures must be supplemented with the characterization of their internal motions. Although dynamical events in proteins occur on time-scale ranging from femtoseconds to at least seconds, the physical properties of globular proteins are such that picosecond (ps) time-scale motions make a particularly important contribution to the internal fluctuations of the atoms from their mean positions.

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.

Active site conformation in myoglobin as determined by X-ray absorption spectroscopy

X-ray absorption fine structure experiments were performed to study structural and dynamic aspects of the active site of various forms of myoglobin. The structures determined for deoxyMb, MbCO, and MbO2 are consistent with the structure established by X-ray absorption fine structure experiment and X-ray crystallography. The first shell of ferrous MbNO determined contains 5 nitrogens located at 2.02 A and a short NO bond length of 1.76 A. This study focuses on the change of the XAFS Debye-Waller factor with temperature, which is a measure of thermal and static disorder. It was found that the changes of Debye-Waller factor with temperature for the Mb proteins, except deoxyMb, are consistent with a simple Einstein model, in which a single frequency was assumed for the bond stretching modes. In contrast, the temperature dependence of deoxyMb cannot be fitted to the Einstein model and a large disorder was found at low temperatures, which indicates the existence of conformational substates of the active site.

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.

Conformational substates and motions in myoglobin. External influences on structure and dynamics

Myoglobin, a simppe dioxygen-storage protein, is a good laboratory for the investigation of the connection between protein structure, dynamics, and function. Fourier-transform infrared spectroscopy on carbon-monoxymyoglobin (MbCO) shows three major CO bands. These bands are excellent probes for the investigation of the structure-function relationship. They have different CO binding kinetics and their CO dipoles form different angles with respect to the heme normal, implying that MbCO exists in three major conformational substates, A0, A1, and A3. The entropies and enthalpies of these substates depend on temperature above approximately 180 K and are influenced by pH, solvent, and pressure. These results suggest that even a protein as simple as Mb can assume a small number of clearly different structures that perform the same function, but with different rates. Moreover, protein structure and dynamics depend strongly on the interaction of the protein with its environment.

O2 and CO reactions with heme proteins: quantum yields and geminate recombination on picosecond time scales

Picosecond time-resolved absorption spectroscopy and low-temperature studies have been undertaken in order to understand the nature of the intrinsic quantum yields and geminate recombination of carbon monoxide and oxygen to hemoglobin and myoglobin. We find that the photoproduct yields at 40 ps and long times (minutes) after photolysis at 8 K are similar; however, the yield of oxygen photoproducts is 0.4 +/- 0.1 while the yield of carbon monoxide photoproducts is 1.0 +/- 0.1 for both myoglobin and hemoglobin. Measurements in the Soret, near-infrared, and far-IR are used to quantitate the photoproduct yields. These results call into question previous cryogenic kinetic studies of O2 recombination. Significant subnanosecond geminate recombination is observed in oxyhemoglobin down to 150 K, while below 100 K this geminate recombination disappears. The lower photoproduct yields for oxyheme protein complexes can be attributed to both subnanosecond and subpicosecond recombination events which are ligand and protein dynamics dependent.

E.p.r. studies of photolysis of nitrosyl haemoglobin at low temperatures

Photolysis of HbNO has been studied from 6.2 K to 15.5 K by electron spin resonance during and after continuous illumination. Non-exponential kinetics of both dissociation and reassociation of NO was observed. The prolonged illumination separates the fast and slow ligands. This picture is consistent with NO tunnelling from two sites at different distances from the bound position. This result is obtained using a model of a sum of two exponentials or of conformational substates.

Inhomogeneous broadening in spectral bands of carbonmonoxymyoglobin. The connection between spectral and functional heterogeneity

The rebinding kinetics of CO to myoglobin after flash photolysis is nonexponential in time below approximately 180 K; the kinetics is governed by a distribution of enthalpic barriers. This distribution results from inhomogeneities in the protein conformation, referred to as conformational substates. Hole-burning experiments on the Soret and IR CO-stretch bands test the assumption that an inhomogeneous distribution of conformational substates results in inhomogeneously broadened spectra. CO was slowly photolyzed at different wavelengths in the Soret band at 10 K. Both the Soret band and the CO-stretch band A1, centered at 1,945 cm-1, shift during photolysis, demonstrating that different wavelengths excite different parts of the distributed population. We have also done kinetic hole-burning experiments by measuring peak shifts in the Soret and A1 bands as the CO molecules rebind. The shifts indicate that the spectral and enthalpic distributions are correlated. In the A1 band, the spectral and enthalpic distributions are highly correlated while in the Soret the correlation is weak. From the peak shifts in the spectral and kinetic hole-burning experiments the inhomogeneous broadening is estimated to be approximately 15% of the total width in the Soret band and approximately 60% in A1. We have previously measured the tilt angle alpha between the bound CO and the heme normal (Ormos, P., D. Braunstein, H. Frauenfelder, M. K. Hong, S.-L. Lin, T. B. Sauke, and R. D. Young. 1988. Proc. Natl. Acad. Sci. USA. 85:8492-8496) and observed a wave number dependence of the tilt angles within the CO-stretch A bands. Thus the spectral and enthalpic distributions of the A bands are coupled to a heterogeneity of the structure.

Temperature-derivative spectroscopy: a tool for protein dynamics

A relaxation method that measures the derivative of a population with respect to temperature is introduced and used to study the recombination of CO to sperm whale myoglobin after a photolyzing flash. Measurement of the geminate process in the infrared CO-stretch bands shows distributed activation enthalpies with different distributions for each band, transitions between two bands that correspond to photolyzed ligands, and kinetic hole burning. The data are well described by gaussian enthalpy distributions; the results match and complement those of isothermal methods. The temperature-derivative technique is further used to explore the recombination of CO from outside the heme pocket.

Reactive line-shape narrowing in low-temperature inhomogeneous geminate recombination of CO to myoglobin

The temporal shift in the near-IR absorption peak of myoglobin (Mb) following flash photolysis of MbCO at cryogenic temperatures appears to be due largely to an inhomogeneous reactive process rather than to relaxation. This conclusion, which follows from a new analysis of the experimental data, is based on the following three points: First, at very low temperatures (60 K) a transient line-narrowing effect can be detected. Second, there is a universal, temperature-independent, correlation between spectral shift and survival probability in the rebinding kinetics, and third, the same quantitative model which accounts for rebinding accounts semiquantitatively for the temporal shift in the peak. A fit to the model indicates that the inhomogeneous broadening of the near-IR peak in myoglobin is 15-20% of the total width. The same rebinding process which governs the loss of intensity of this peak is therefore most likely responsible for the shift in its center wavelength.