Mössbauer effect in the study of structure dynamics

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.

A physical picture of protein dynamics and conformational changes

A physical model is reviewed which explains different aspects of protein dynamics consistently. At low temperatures, the molecules are frozen in conformational substates. Their average energy is 3/2RT. Solid-state vibrations occur on a time scale of femtoseconds to nanoseconds. Above a characteristic temperature, often called the dynamical transition temperature, slow modes of motions can be observed occurring on a time scale between about 140 and 1 ns. These motions are overdamped, quasidiffusive, and involve collective motions of segments of the size of an alpha-helix. Molecules performing these types of motion are in the "flexible state". This state is reached by thermal activation. It is shown that these motions are essential for conformational relaxation. Based on this picture, a new approach is proposed to understand conformational changes. It connects structural fluctuations and conformational transitions.

Reduced and oxidized cytochrome c4 exhibit differences in dynamics

The temperature-dependent dynamics of the fully reduced and fully oxidized forms of Pseudomonas stutzeri cytochrome c4 have been studied by Mössbauer spectroscopy. Prior to the dynamic analysis, an efficient labelling strategy has been developed for the expression of highly enriched (57)Fe recombinant cytochrome c4. Subsequently, the protein has been purified to apparent homogeneity. Mössbauer measurements were recorded in the temperature range 77-240 K for both protein forms. A detailed analysis of the high quality spectra is presented. Based on the information obtained from Mössbauer spectroscopy, similarities and differences between cytochrome c4, cytochrome c and HiPIP are discussed. The obtained results reveal that (a) cytochrome c4 exists in pure low spin electronic configuration in both oxidation states in the temperature range 77-240 K, (b) the heme pocket is more relaxed in cytochrome c4 than in cytochrome c, (c) the reduced cytochrome c4 is the most flexible at low temperatures, and (d) protein specific dynamics are most distinct in the oxidized protein.

Flexibility analysis of enzyme active sites by crystallographic temperature factors

Protein flexibility is inherent to protein structural behavior. Experimental evidence for protein flexibility is extensive both in solution and in the solid state. A major question is whether the flexibility observed in enzymes is simply an inherent property of proteins that must always be borne in mind or is essential for catalysis or substrate binding. The temperature factors or B-values, as determined crystallographically, are linearly related to the mean square displacement of an atom and give an indication of atomic flexibility in the crystalline state. In this paper, we describe the frequency distributions of the normalized B-factor (B'-factor) for the active site and non-active site residues in the selected 69 apo-enzymes. This analysis was performed over the entire sequences and for different structural subsets defined by the three-dimensional structure of proteins, as alpha-helices, beta-structures and coil conformation and buried and non-buried residues. The results show that in all cases, the active site residues predominantly occur in region of low B'-factor and the non-active site residues have a tendency to exist in the high B'-factor region. This observation suggests that the active site residues, in general, are less flexible than the non-active site residues and therefore the vibrational and the fast collective motions of the C(alpha) atoms of proteins appear not to have clear biological significance.

The dynamics of 57Fe nuclei in Fe(II)-DNA and [Fe(II)(1-methyl-2-mercaptoimidazole)2]-DNA condensates

Alcoholic solutions of FeCl(2) and Fe(II)(Hmmi)(2)Cl(2) (Hmmi=1-methyl-2-mercaptoimidazole) induce calf thymus DNA condensation from aqueous solutions buffered at pH 7.4. A 1:1 Fe(II)-(DNA monomer) stoichiometry is assumed. The (57)Fe Mössbauer hyperfine parameters suggest an octahedral coordination environment, severely distorted, in both Fe(II)-(DNA monomer) and [Fe(II)(Hmmi)(2)]-(DNA monomer) condensates. The dynamic properties of iron nuclei in freeze-dried samples were investigated by means of variable temperature (57)Fe Mössbauer spectroscopy. Mean square displacements, <x(2)>(T), were calculated, such as the effective vibrating mass and the Mössbauer lattice temperature of the solids. <x(2)> increases linearly with the temperature in the whole temperature range explored; the absolute values are typical for lattice or solid-state vibrations. Very similar values for the effective vibrating masses were extracted, suggesting comparable covalency of the bonding interaction between the metal atom and its ligands, while the Mössbauer lattice temperatures show a softening of the lattice for [Fe(II)(Hmmi)(2)]-(DNA monomer) with respect to Fe(II)-(DNA monomer) condensate.

The dynamics of (57)Fe nuclei in Fe(III)-DNA condensates

The dynamics of iron nuclei in the condensates obtained by interaction of Fe(III) with DNA, Fe(III)(DNA monomer)(2), have been investigated by variable temperature (57)Fe Mössbauer spectroscopy. Studies were effected on gel and freeze-dried samples, obtaining nearly coincident values of the parameters isomer shift and nuclear quadrupole splitting in T ranges 20-260 K. Functions ln(A(T)/A(77.3)) vs. T, here employed to investigate the dynamics of Fe nuclei, showed linear trends in the T ranges 20-150 and 150-260 K, respectively, the latter with larger slopes. Data coincided for gelled and freeze-dried specimens. No variation of delta or Delta E parameters occurred at the two T intervals, which suggests constancy of structure and bonding with the temperature changes. Functions <x(2)>(T) showed trends analogous to the corresponding functions determined for iron proteins, which were attributed to the occurrence of 'conformational substates'.

A synthetic picture of intramolecular dynamics of proteins. Towards a contemporary statistical theory of biochemical processes

An increasing body of experimental evidence indicates the slow character of internal dynamics of native proteins. The important consequence of this is that theories of chemical reactions, used hitherto, appear inadequate for description of most biochemical reactions. Construction of a contemporary, truly advanced statistical theory of biochemical processes will need simple but realistic models of microscopic dynamics of biomolecules. In this review, intended to be a contribution towards this direction, three topics are considered. First, an intentionally simplified picture of dynamics of native proteins which emerges from recent investigations is presented. Fast vibrational modes of motion, of periods varying from 10(-14) to 10(-11) s, are contrasted with purely stochastic conformational transitions. Significant evidence is adduced that the relaxation time spectrum of the latter spreads in the whole range from 10(-11) to 10(5) s or longer, and up to 10(-7) s it is practically quasi-continuous. Next, the essential ideas of the theory of reaction rates based on stochastic models of intramolecular dynamics are outlined. Special attention is paid to reactions involving molecules in the initial conformational substrates confirmed to the transition state, which is realized in actual experimental situations. And finally, the two best experimentally justified classes of models of conformational transition dynamics, symbolically referred to as "protein glass" and "protein machine", are described and applied to the interpretation of a few simple biochemical processes, perhaps the most important result reported is the demonstration of the possibility of predominance of the short initial condition-dependent stage of protein involved reactions over the main stage described by the standard kinetics. This initial stage, and not the latter, is expected to be responsible for the coupling of component reactions in the complete enzymatic cycles as well as more complex processes of biological free energy transduction.

Isolation and properties of PS II membrane fragments depleted of the non heme iron center

The functional properties and the content of non heme iron and cytochrome b559 were investigated by measuring flash induced transient changes of the relative fluorescence quantum yield and applying Mössbauer spectroscopy. It was found that untreated PS II membrane fragments contain a heterogeneous population of two types of non heme iron centers and about 2 cytochrome b559 per PS II. Twofold treatment of these samples with a recently described 'iron depletion' procedure (MacMillan, F., Lendzian, F., Renger, G. and Lubitz, W. (1995) Biochemistry 34, 3144-3156) leads to a complete loss (below the detection limit of Mössbauer spectroscopy) of the non heme iron center while more than 50% of the PS II complexes retain the functional integrity for light induced formation of the 'stable' radical pair Y(OX)(Z) P680Pheo Q(-.)(A). This sample type deprived of virtually all non heme iron in PS II provides a most suitable material for magnetic resonance studies that require an elimination of the interaction between Fe2+ and nearby radicals.

Distribution of the iron-heme displacement as resulting from myoglobin conformational substrates: an AOM approach to the interpretation of the EPR spectra

The electron paramagnetic resonance (EPR) low-temperature spectra of high spin ferric myoglobin samples in different solvent composition have been analyzed in terms of a distribution of the energy differences delta 1 and delta 2 for the iron low-lying electronic states. The widths of these distributions, which are found to be dependent on the solvent composition, have been correlated to the presence of a frozen ensemble of conformational substrates. A dedicated analysis based on the angular overlap method (AOM) has allowed us to work out a quantitative relationship between the delta 1 and delta 2 distributions and the spread of the iron-heme displacement; this being a structural parameter relevant for the biological functionality of the protein. The observed dependence of the iron-heme displacement distribution on the solvent composition is discussed.

Collective vibrations of an alpha-helix. A molecular dynamics study

The internal dynamics of a 20-residue polyalanine helix was investigated by molecular dynamics simulations. Special attention was paid to the collective vibrations of the helix backbone. The stretch and bend vibrations could be assigned unambiguously to oscillations with periods of 1.4 and 4.3 ps, respectively. The influence of the environment on the dynamics of the collective vibrations was studied by coupling the helix to a heat bath and by adding water molecules. In the presence of water, the stretch vibration becomes more strongly dampened, but still exists as a vibration , while the bend vibration becomes overdamped and degenerates into a relaxation process. The results are compared with available experimental data.