Dynamics of heme iron in crystals of metmyoglobin and deoxymyoglobin

Storage of human biospecimens: selection of the optimal storage temperature

Millions of biological samples are currently kept at low tempertures in cryobanks/biorepositories for long-term storage. The quality of the biospecimen when thawed, however, is not only determined by processing of the biospecimen but the storage conditions as well. The overall objective of this article is to describe the scientific basis for selecting a storage temperature for a biospecimen based on current scientific understanding. To that end, this article reviews some physical basics of the temperature, nucleation, and ice crystal growth present in biological samples stored at low temperatures (-20°C to -196°C), and our current understanding of the role of temperature on the activity of degradative molecules present in biospecimens. The scientific literature relevant to the stability of specific biomarkers in human fluid, cell, and tissue biospecimens is also summarized for the range of temperatures between -20°C to -196°C. These studies demonstrate the importance of storage temperature on the stability of critical biomarkers for fluid, cell, and tissue biospecimens.

The dynamics of the non-heme iron in bacterial reaction centers from Rhodobacter sphaeroides

We investigate the dynamical properties of the non-heme iron (NHFe) in His-tagged photosynthetic bacterial reaction centers (RCs) isolated from Rhodobacter (Rb.) sphaeroides. Mössbauer spectroscopy and nuclear inelastic scattering of synchrotron radiation (NIS) were applied to monitor the arrangement and flexibility of the NHFe binding site. In His-tagged RCs, NHFe was stabilized only in a high spin ferrous state. Its hyperfine parameters (IS=1.06±0.01mm/s and QS=2.12±0.01mm/s), and Debye temperature (θ(D0)~167K) are comparable to those detected for the high spin state of NHFe in non-His-tagged RCs. For the first time, pure vibrational modes characteristic of NHFe in a high spin ferrous state are revealed. The vibrational density of states (DOS) shows some maxima between 22 and 33meV, 33 and 42meV, and 53 and 60meV and a very sharp one at 44.5meV. In addition, we observe a large contribution of vibrational modes at low energies. This iron atom is directly connected to the protein matrix via all its ligands, and it is therefore extremely sensitive to the collective motions of the RC protein core. A comparison of the DOS spectra of His-tagged and non-His-tagged RCs from Rb. sphaeroides shows that in the latter case the spectrum was overlapped by the vibrations of the heme iron of residual cytochrome c(2), and a low spin state of NHFe in addition to its high spin one. This enabled us to pin-point vibrations characteristic for the low spin state of NHFe.

Resilience of the iron environment in heme proteins

Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.

Protein dynamical transition does not require protein structure

Terahertz time domain spectroscopy shows that the protein dynamical transition, the rapid increase in protein dynamics occurring at approximately 200 K, needs neither tertiary nor secondary structure. Further, short chain alanine studies find a dynamical transition down to penta-alanine, with no transition observed for di-alanine or tri-alanine. These results reveal the temperature dependence arises strictly from the side-chain interaction with the solvent. The lack of a transition for shorter chain peptides may indicate a qualitative change in this interaction occurs at a specific peptide chain length.

The role of dynamics in enzyme activity

Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.

Vibrational dynamics of myoglobin determined by the phonon-assisted Mössbauer effect

The phonon-assisted Mössbauer effect is used to determine the partial phonon density of states of the iron within the active center of deoxymyoglobin, carboxymyoglobin, and dry and wet metmyoglobin between 40 and 300 K. Between 0 and 1 meV the iron density of states increases quadratically with the energy, as in a Debye solid. Mean sound velocities are extracted from this slope. Between 1 and 3 meV a nearly quadratic "Debye-like" increase follows due to the similar strength of intermolecular and intramolecular forces. Above 3 meV, optical vibrations are characteristic for the iron-ligand conformation. The overall mean square displacements of the heme iron atom obtained from the density of states agree well with the values of Mössbauer absorption experiments below 180 K. In the physiological temperature regime the data confirm the existence of harmonic vibrations in addition to the protein specific dynamics measured by Mössbauer absorption. In the Debye energy regime the mean square displacement of the iron is in agreement with that of the hydrogens measured by incoherent neutron scattering demonstrating the global character of these modes. At higher energies the vibration of the heavy iron atom at 33 meV in metmyoglobin is as large as that of the lightweight hydrogens at that energy. A freeze dried, rehydrated (h=0.38 g H2O/g protein) metmyoglobin sample shows an excess of states above the Debye law between 1 and 3 meV, similar to neutron scattering experiments. The room temperature density of states below 3 meV exhibit an increase of the density compared to the low temperature data, which can be interpreted as mode softening.

Intramolecular dynamics and conformational transition in proteins studied by biophysical labelling methods. Common and specific features of proteins from thermophylic micro-organisms

A general survey is carried out on the theoretical grounds for methods of spin, luminescence and Mössbauer labels, as well as their application in the study of protein intramolecular dynamics. When combined, these methods allow the protein dynamics to be investigated within a wide range of correlation times (tau c = 10(2) - 10(-10) s) and amplitudes. The purposeful application of the methods to various proteins at different temperatures (30-330 K), water content, substrate addition, etc., revealed a number of dynamical processes and conformational transitions in proteins. The experiments indicated correlations between the local segmental mobility of protein globules in a nanosecond temporal scale and biochemical reactions, such as long-distance electron transfer, hydrolysis and photoreactions. The biophysical labelling methods results were analysed together with the data on dynamics obtained using complementary physico-chemical methods and theoretical calculations. Special emphasis is given to recent results on proteins from thermophylic micro-organisms. The mechanisms of protein intramolecular dynamics and their role in the stability and functions of proteins and enzymes are discussed.

Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics

The activity and dynamics of a simple, single subunit enzyme, the xylanase from Thermotoga maritima strain Fj SS3B.1 have been measured under similar conditions, from -70 to +10 degrees C. The internal motions of the enzyme, as evidenced by neutron scattering, undergo a sharp transition within this temperature range; they show no evidence for picosecond-timescale anharmonic behaviour (e.g. local diffusive motions or jumps between alternative conformations) at temperatures below -50 degrees C, whereas these motions are strongly activated at higher temperatures. The activity follows Arrhenius behaviour over the whole of the temperature range investigated, -70 to +10 degrees C. The results indicate that a temperature range exists over which the enzyme rate-limiting step is independent of fast anharmonic dynamics.

Backbone motions in a crystalline protein from field-dependent 2H-NMR relaxation and line-shape analysis

We have used 2H-nmr to study backbone dynamics of the 2H-labeled, slowly exchanging amide sites of fully hydrated, crystalline hen egg white lysozyme. Order parameters are determined from the residual quadrupole coupling and values increase from S2 = 0.85 at 290 K to S2 = 0.94 at 200 K. Dynamical rates are determined from spin-lattice relaxation at three nmr frequencies (38.8, 61.5, and 76.7 MHz). The approach used here is thus distinct from solution nmr studies where dynamical amplitudes and rates are both determined from relaxation measurements. At temperatures below 250 K, relaxation is independent of the nmr frequency indicating that backbone motions are fast compared to the nmr frequencies. However, as the temperature is increased above 250 K, relaxation is significantly more efficient at the lowest frequency, which shows, in addition, the presence of motions that are slow compared to the nmr frequencies. Using the values of S2 determined from the residual quadrupole coupling and a model-free relaxation formalism that allows for fast and slow internal motions, we conclude that these slow motions have correlation times in the range of 0.1 to 1.0 microsecond and are effectively frozen out at 250 K where fast motions of the amide planes with approximately 15 ps effective correlation times and 9 degrees rms amplitudes dominate relaxation. The fast internal motions increase slightly in amplitude as the temperature rises toward 290 K, but the correlation time, as is also observed in solution nmr studies of RNase H, is approximately constant. These findings are consistent with hypotheses of dynamic glass transitions in hydrated proteins arising from temperature-dependent damping of harmonic modes of motion above the transition point.

Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability

We study the fluctuations of native proteins by exact enumeration using the HP lattice model. The model fluctuations increase with temperature. We observe a low-temperature point, below which large fluctuations are frozen out. This prediction is consistent with the observation by Tilton et al. [R. F. Tilton, Jr., J. C. Dewan, and G. A. Petsko, Biochemistry 31, 2469 (1992)], that the thermal motions of ribonuclease A increase sharply above about 200 K. We also explore protein "flexibility" as defined by Debye-Waller-like factors and solvent accessibilities of core residues to hydrogen exchange. We find that proteins having greater stability tend to have fewer large fluctuations, and hence lower flexibilities. If flexibility is necessary for enzyme catalysis, this could explain why proteins from thermophilic organisms, which are exceptionally stable, may be catalytically inactive at normal temperatures.

The denaturation and degradation of stable enzymes at high temperatures

Now that enzymes are available that are stable above 100 degrees C it is possible to investigate conformational stability at this temperature, and also the effect of high-temperature degradative reactions in functioning enzymes and the inter-relationship between degradation and denaturation. The conformational stability of proteins depends upon stabilizing forces arising from a large number of weak interactions, which are opposed by an almost equally large destabilizing force due mostly to conformational entropy. The difference between these, the net free energy of stabilization, is relatively small, equivalent to a few interactions. The enhanced stability of very stable proteins can be achieved by an additional stabilizing force which is again equivalent to only a few stabilizing interactions. There is currently no strong evidence that any particular interaction (e.g. hydrogen bonds, hydrophobic interactions) plays a more important role in proteins that are stable at 100 degrees C than in those stable at 50 degrees C, or that the structures of very stable proteins are systematically different from those of less stable proteins. The major degradative mechanisms are deamidation of asparagine and glutamine, and succinamide formation at aspartate and glutamate leading to peptide bond hydrolysis. In addition to being temperature-dependent, these reactions are strongly dependent upon the conformational freedom of the susceptible amino acid residues. Evidence is accumulating which suggests that even at 100 degrees C deamidation and succinamide formation proceed slowly or not at all in conformationally intact (native) enzymes. Whether this is the case at higher temperatures is not yet clear, so it is not known whether denaturation of degradation will set the upper limit of stability for enzymes.

Mössbauer spectroscopy on nonequilibrium states of myoglobin: a study of r-t relaxation

A frozen solution of 57Fe-enriched metmyoglobin was irradiated by x rays at 77 K. Mössbauer spectra showed a reduction of Fe(III) high spin by thermalized electrons and a production of a metastable Fe(II) low spin myoglobin complex with H2O at its sixth coordination site. The relaxation of the intermediate was investigated by Mössbauer spectroscopy as a function of temperature and time. The relaxation process starts above 140 K and is fully completed at approximately 200 K. At temperatures between 140 and 200 K, the relaxation lasts for hours and is nonexponential in time. Up to 180 K, the process can be described satisfactorily by a gamma distribution of activation enthalpies with an Arrhenius relation for the rate coefficient. The temperature and time dependence of the Mössbauer parameters indicates structural changes in the active center of the protein as early as 109 K that continue for several hours at higher temperatures. Above 180 K, structural rearrangements involving the whole protein molecule lead to a shift and narrowing of the barrier height distribution.

Structure and dynamics of the water around myoglobin

The interplay between simulations at various levels of hydration and experimental observables has led to a picture of the role of solvent in thermodynamics and dynamics of protein systems. One of the most studied protein-solvent systems is myoglobin, which serves as a paradigm for the development of structure-function relationships in many biophysical studies. We review here some aspects of the solvation of myoglobin and the resulting implications. In particular, recent theoretical and simulation studies unify much of the diverse set of experimental results on water near proteins.

The effect of low temperatures on enzyme activity

The stability of two enzymes from extreme thermophiles (glutamate dehydrogenase from Thermococcales strain AN1 and beta-glucosidase from Caldocellum saccharolyticum expressed in Escherichia coli) has been exploited to allow measurement of activity over a 175 degrees C temperature range, from +90 degrees C to -85 degrees C for the glutamate dehydrogenase and from +90 degrees C to -70 degrees C for the beta-glucosidase. The Arrhenius plots of these enzymes, and those for two mesophilic enzymes (glutamate dehydrogenase from bovine liver and beta-galactosidase from Escherichia coli), exhibit no downward deflection corresponding to the glass transition, found by biophysical measurements of several non-enzymic mesophilic proteins at about -65 degrees C and reflecting a sharp decrease in protein flexibility as the overall motion of groups of atoms ceases.

The low-temperature heat capacity of solid proteins

Several harmonic models of protein fluctuations are used to calculate the heat capacity. They get the spectral density of conformational modes from inelastic neutron scattering, normal mode calculations, or macroscopic elasticity (Debye model). It is assumed that the low-frequency spectral density depends only weakly on temperature and protein species. The Debye model predicts temperatures below which modes are primarily in their ground states: 10 and 80 K for the lattice and conformational modes, respectively. The models differ most below 100 K. The mode calculations yield the most accurate predictions, though all three models are within twofold of the data. The heat capacity has the power law form aTb for T less than 30 K. The experimental b's of proteins are 1.6-1.8, and the theoretical, 1.1-1.3. One possible explanation for the discrepancy is the occurrence of transitions between discrete conformations. All of the models approach the measured data in the range 100-200 K. They are very similar above 200 K, where the heat capacity includes significant contributions from bond stretching and bending. This masks the possible anharmonic behavior of the conformational modes. Hydration substantially increases the heat capacity above 200 K. This effect seems to be a consequence of conformational transitions that have higher energy than the ones seen with low hydration. The analysis also predicts that denaturation with constant hydration produces a negligible increase of heat capacity. The larger increment in solution arises from the different hydration of the folded and unfolded states, and is responsible for the existence of cold denaturation. This phenomenon is thus predicted not to occur when the hydration is constant.

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.

Hemoglobin dynamics in rat erythrocytes investigated by Mössbauer spectroscopy

Rats have been enriched in 57Fe and erythrocytes were isolated from the blood. Mössbauer absorption spectroscopy on the hemoglobin of these erythrocytes has shown rather similar dynamics as found earlier in crystals of myoglobin, in frozen solutions of human hemoglobin and in a number of other proteins. The results strongly indicate that the motion of the heme and presumably some part of the F-helix is mainly influenced by the average viscosity of the sample determined by a network of hydrogen bridges and other weak interactions. Extrapolations of Mössbauer results from protein crystals to proteins in their physiological surroundings seem to be suitable for heme proteins.

Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data

Molecular dynamics is used to probe the atomic motions of the carboxy-myoglobin protein as a function of temperature. Simulations of 150 picoseconds in length are carried out on the protein at 20, 60, 100, 180, 220, 240, 260, 280, 300, 320 and 340 K. The simulations attempt to mimic neutron scattering experiments very closely by including a partial hydration shell around the protein. Theoretical elastic, quasielastic and inelastic neutron scattering data are derived from the trajectories and directly compared with experiment. Compared to experiment, the simulation-derived elastic scattering curves show a decrease in intensity as a function of the scattering wavevector, q2. The inelastic and quasielastic spectra show that the inelastic peak is shifted to lower frequency than the experimental value, while quasielastic behavior is in good agreement with experiment. This suggests that the theoretical model is too flexible in the harmonic limit (low temperature), but accurately reproduces high-temperature behavior. Time correlation functions of the intermediate scattering function are determined. At low temperature there is one fast decay process, and at high temperatures there is an additional slow relaxation process that is due to quasielastic scattering. The average atomic fluctuations show that the protein behaves harmonically at low temperatures. At approximately 210 K, a glass-like transition in atomic fluctuations is seen. Above the transition temperature, the atomic fluctuations exhibit both harmonic and anharmonic behavior. Comparison of protein mobility behavior with experiment indicate the fluctuations derived from simulations are larger in the harmonic region. However, the anharmonic region agrees very well with experiment. The anharmonicity is large at all temperatures, with a gradual monotonic increase from 0.5 at 20 K to greater than 0.7 at 340 K without a noticeable change at the glass transition temperature. Heavy-atom dihedral transitions are monitored as a function of temperature. Trends in the type of dihedral transitions that occur with temperature are clearly visible. Dihedral transitions involving backbone atoms occur only above the glass transition temperature. The overall protein behavior results suggest that at low temperatures there is purely vibrational motion with one fast decay process, and above the glass transition temperature there is more anharmonic motion with a fast and a slower relaxation process occurring simultaneously.(ABSTRACT TRUNCATED AT 400 WORDS)

Molecular cloning, structure and expression of the yeast proliferating cell nuclear antigen gene

The budding yeast Saccharomyces cerevisiae is proving to be an useful and accurate model for eukaryotic DNA replication. It contains both DNA polymerase alpha (I) and delta (III). Recently, proliferating cell nuclear antigen (PCNA), which in mammalian cells is an auxiliary subunit of DNA polymerase delta and is essential for in vitro leading strand SV40 DNA replication, was purified from yeast. We have now cloned the gene for yeast PCNA (POL30). The gene codes for an essential protein of 29 kDa, which shows 35% homology with human PCNA. Cell cycle expression studies, using synchronized cells, show that expression of both the PCNA (POL30) and the DNA polymerase delta (POL3, or CDC2) genes of yeast are regulated in an identical fashion to that of the DNA polymerase alpha (POL1) gene. Thus, steady state mRNA levels increase 10-100-fold in late G1 phase, peak in early S-phase, and decrease to low levels in late S-phase. In addition, in meiosis mRNA levels increase prior to initiation of premeiotic DNA synthesis.

Temperature dependence of cytochrome photooxidation and conformational dynamics of Chromatium reaction center complexes

A temperature dependence of multiheme cytochrome c oxidation induced by a laser pulse was studied in photosynthetic reaction center preparations from Chromatium minutissimum. Absorbance changes and kinetic characteristics of the reaction were measured under redox conditions where one or all of the hemes of the cytochrome subunit are chemically reduced (E h =+300 mV or E h =-20 to -60 mV respectively). In the first case photooxidation is inhibited at temperatures lower than 190-200 K with the rate constant of the photooxidation reaction being practically independent on temperature over the range of 300 to 190 K (k=2.2×10(5) s(-1)). Under reductive conditions (E h =-20 to -60 mV) lowering the temperature to 190-200 K causes the reaction to slow from k=8.3×10(5) s(-1) to 2.1×10(4) s(-1). Under further cooling down to the liquid nitrogen temperature, the reaction rate changes negligibly. The absorption amplitude decreases by 30-40% on lowering the temperature. A new physical mechanism of the observed critical effects of temperature on the rate and absorption amplitude of the multiheme cytochrome c oxidation reaction is proposed. The mechanism suggests a close interrelation between conformational mobility of the protein and elementary electron tunneling act. The effect of "freezing" conformational motion is described in terms of a local diffusion along a random rough potential.

On the mechanism of ligand binding to myoglobin. The role of structural fluctuations

The association reaction of CO and O2 with heme is expected to reflect the differences in the electronic structures of the two ligands. CO binding should be controlled by a high spin/low spin transition while oxygen binding is spin-allowed. Dioxygen should thus bind substantially faster than CO. The experimental association rates of the two ligands are, however, almost identical. We propose that the reaction is triggered in both cases by a fast structural intermediate which allows the CO molecule to bind adiabatically. A suitable structural transition has been identified recently by inelastic neutron scattering.

Dynamical transition of myoglobin revealed by inelastic neutron scattering

Structural fluctuations in proteins on the picosecond timescale have been studied in considerable detail by theoretical methods such as molecular dynamics simulation, but there exist very few experimental data with which to test the conclusions. We have used the technique of inelastic neutron scattering to investigate atomic motion in hydrated myoglobin over the temperature range 4-350 K and on the molecular dynamics timescale 0.1-100 ps. At temperatures below 180 K myoglobin behaves as a harmonic solid, with essentially only vibrational motion. Above 180 K there is a striking dynamic transition arising from the excitation of nonvibrational motion, which we interpret as corresponding to torsional jumps between states of different energy, with a mean energy asymmetry of 12 kJ mol-1. This extra mobility is reflected in a strong temperature dependence of the mean-square atomic displacements, a phenomenon previously observed specifically for the heme iron by Mössbauer spectroscopy, but on a much slower timescale (10(-7) s). It also correlates with a glass-like transition in the hydration shell of myoglobin and with the temperature-dependence of ligand-binding rates at the heme iron, as monitored by flash photolysis. In contrast, the crystal structure of myoglobin determined down to 80 K shows no significant structural transition. The dynamical behaviour we find for myoglobin (and other globular proteins) suggests a coupling of fast local motions to slower collective motions, which is a characteristic feature of other dense glass-forming systems.

Protein and protein-bound water dynamics studied by Rayleigh scattering of Mössbauer radiation (RSMR)

In all contemporary models of enzyme catalysis, the functional activity of enzymes is directly associated with the dynamic properties of proteins (see Blumenfeld, 1977; Chernavaskaya & Chernavskii, 1977; Volkenstein, 1975; Austinet al.1975; Shaitan & Rubin, 1985; Ansariet al.1985). This has recently led to a much greater interest in the dynamical properties of proteins.

Structural disorder in proteins. A comparison of myoglobin and erythrocruorin

The refinement of X-ray structural data gives the mean square displacements, (chi 2), at each position in the protein molecule. In order to get information on the significance of such values different refinement methods have been compared. The metmyoglobin structure was determined at 300 K and (chi 2)-values were obtained with the restrained refinement procedure in reciprocal space of Konnert and Hendrickson. A comparison with the results of Frauenfelder et al. was used for an error estimation. The inclusion of surface bound water increases the accuracy of the results but does not change the general picture. For erythrocruorin (CTT3) a refinement was performed in reciprocal space and compared with a refinement in real space performed earlier. The (chi 2)-values obtained from both procedures are similar although the reciprocal space refinement gives results which are physically more reasonable. A comparison of the disorder in myoglobin and erythrocruorin showed that the structural similarity results in a similarity in the disorder. Contacts of molecules in the crystal do not dominate the disorder although they locally influence (chi 2)-values. CTT3 shows large disorder in the heme region in contrast to myoglobin. The differences in the rigidity of the F-helix can be correlated with the oxygen affinities supporting models for O2 binding developed by Frauenfelder et al.

Do vibrational spectroscopies uniquely describe protein dynamics? The case for myoglobin

We develop a quasi-harmonic description of protein dynamics and apply this description to the anomalous Mössbauer, infrared, x-ray diffraction, and EXAFS (extended x-ray absorption fine structure spectroscopy) data that are available for myoglobin (Mb) and its interactions with carbon monoxide (CO). In the quasi-harmonic approximation the dynamical parameters derived from these spectroscopic data are relevant in the calculation of reaction rates, and we give a quantitative description of the nonexponential kinetics of Mb-CO binding observed at low temperatures. All these data have previously been interpreted in terms of the more complex conformational substates model for protein dynamics. We point out several problems with this model and propose experiments that can provide detailed tests of the quasi-harmonic theory proposed here.

Protein states and proteinquakes

After photodissociation of carbon monoxide bound to myoglobin, the protein relaxes to the deoxy equilibrium structure in a quake-like motion. Investigation of the proteinquake and of related intramolecular equilibrium motions shows that states and motions have a hierarchical glass-like structure.

Determination of the second order doppler shift of iron in myoglobin by Mössbauer spectroscopy

We have performed Mössbauer absorption experiments on a sample of deoxygenated myoglobin crystals from 5 K to 280 K. With two series of measurements, one with the source and sample at the same temperature and the other with the source always at 298 K, we are able to extract information from the second-order Doppler effect in the sample. Simple models consistent with a description of myoglobin with low lying electronic states which are thermally populated above 40 K indicate that the Debye temperature of myoglobin is 220 K, in agreement with measurements using the Lamb-Mössbauer factor. The second-order Doppler effect is proportional to the square of the velocity of the motion. We are unable to see any indication of protein specific motion from the second-order Doppler effect, thereby indicating that protein specific motions are relatively slow.

A consistent picture of protein dynamics

Information about the protein dynamics of myoglobin obtained by x-ray and Mössbauer investigations is analyzed and compared with computer simulations. Computer simulations give correct amplitudes of mean-square displacements but fail in the description of the time dependence of motions. Our model describes protein dynamics at physiological temperatures as an overdamped diffusion-like motion in a restricted space. The fluctuations occur around the average conformation determined by x-ray structure analysis. The gain in entropy drives the molecule into the transition state and, in this way, accounts for its flexibility.

Theory of Mössbauer spectra of proteins fluctuating between conformational substates

Mössbauer spectra of 57Fe in proteins fluctuating between different conformational substates are evaluated by means of a two-sided Padée approximation, which can reproduce the low and high frequency dependence of the spectral line shape I(omega) to any desired accuracy. The dynamics of the atom is modeled as Brownian motion in a multiminimum potential and described by a Fokker-Planck equation. The Mössbauer spectrum is expanded in terms of Lorentzian contributions, which can be attributed separately to fluctuations between conformational substates (potential minima) and to relaxation within the substates. In the limit of closely spaced substates, the Mössbauer spectra can be accounted for by an effective diffusion coefficient with Arrhenius-type temperature dependence. We demonstrate that the observed temperature dependence of Mössbauer spectra of proteins [Parak, F., Knapp, E.W. & Kucheida, D. (1982) J. Mol. Biol. 161, 177-194] can be accounted for by stochastic motion in a multiminimum potential.

Magnetosome dynamics in magnetotactic bacteria

Diffusive motions of the magnetosomes (enveloped Fe3O4 particles) in the magnetotactic bacterium Aquaspirillum magnetotacticum result in a very broad-line Mössbauer spectrum (T approximately 100 mm/s) above freezing temperatures. The line width increases with increasing temperature. The data are analyzed using a bounded diffusion model to yield the rotational and translational motions of the magnetosomes as well as the effective viscosity of the material surrounding the magnetosomes. The results are [theta 2] l/2 less than 1.5 degrees and [x2] 1/2 less than 8.4 A for the rotational and translational motions, respectively, implying that the particles are fixed in whole cells. The effective viscosity is 10 cP at 295 K and increases with decreasing temperature. Additional Fe3+ material in the cell is shown to be associated with the magnetosomes. Fe2+ material in the cell appears to be associated with the cell envelope.