Dynamical properties of the hydration shell of fully deuterated myoglobin.

Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 H(2)O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 Å(-1) and a temperature range from 4 to 297 K. We used neutrons with a wavelength of λ αE 6 Å and an energy resolution of about 65 µeV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra caused by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjölander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time τ(0) in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time τ(1) in a nonbound state followed again by the oscillatory motions for τ(0) and so forth. We used the general formulation with no simplifications as τ(0)≫τ(1) or τ(1)≫τ(0). At room temperature, we obtained τ(0) αE 104 ps and τ(1) αE 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.

On the feasibility of nanocrystal imaging using intense and ultrashort X-ray pulses.

Structural studies of biological macromolecules are severely limited by radiation damage. Traditional crystallography curbs the effects of damage by spreading damage over many copies of the molecule of interest in the crystal. X-ray lasers offer an additional opportunity for limiting damage by out-running damage processes with ultrashort and very intense X-ray pulses. Such pulses may allow the imaging of single molecules, clusters, or nanoparticles. Coherent flash imaging will also open up new avenues for structural studies on nano- and microcrystalline substances. This paper addresses the theoretical potentials and limitations of nanocrystallography with extremely intense coherent X-ray pulses. We use urea nanocrystals as a model for generic biological substances and simulate the primary and secondary ionization dynamics in the crystalline sample. The results establish conditions for ultrafast single-shot nanocrystallography diffraction experiments as a function of X-ray fluence, pulse duration, and the size of nanocrystals. Nanocrystallography using ultrafast X-ray pulses has the potential to open up a new route in protein crystallography to solve atomic structures of many systems that remain inaccessible using conventional X-ray sources.

Protein dynamics of a beta-sheet protein.

Rhodnius prolixus Nitrophorin 4 (abbreviated NP4) is an almost pure beta-sheet heme protein. Its dynamics is investigated by X-ray structure determination at eight different temperatures from 122 to 304 K and by means of Mössbauer spectroscopy. A comparison of this beta-sheet protein with the pure alpha-helical protein myoglobin (abbreviated Mbmet) is performed. The mean square displacement derived from the Mössbauer spectra increases linearly with temperature below a characteristic temperature T(c). It is about 10 K larger than that of myoglobin. Above T(c) the mean square displacements increase dramatically. The Mössbauer spectra are analyzed by a two state model. The increased mean square displacements are caused by very slow motions occurring on a time scale faster than 140 ns. With respect to these motions NP4 shows the same protein specific modes as Mbmet. There is, however, a difference in the fast vibration regime. The B values found in the X-ray structures vary linearly over the entire temperature range. The mean square displacements in NP4 increase with slopes which are 60% larger than those observed for Mbmet. This indicates that nitrophorin has a larger structural distribution which makes it more flexible than myoglobin.

Synthesis and characterization of a dinuclear iron(II) spin crossover complex with wide hysteresis.

The magnetic properties and results from X-ray structure analysis for a new pair of iron(II) spin-crossover complexes [FeL1(meim) 2](meim) ( 1(meim)) and [Fe 2L2(meim) 4](meim) 4 ( 2(meim) 4), with L1 being a tetradentate N 2O 2 (2-) coordinating Schiff-base-like ligand [([3,3']-[1,2-phenylenebis(iminomethylidyne)]bis(2,4-pentane-dionato)(2-)N,N',O (2),O (2)'], L2 being an octadentate, dinucleating N 2O 2 (2-) coordinating Schiff-base-like ligand [3,3',3'',3''']-[1,2,4,5-phenylenetetra(iminomethylidyne)]tetra(2,4-pentanedionato)(2-) N, N', N'', N''', O (2), O (2) ', O (2) '', O (2) '''], and meim being N-methylimidazole, are discussed in this work. Crystalline samples of both complexes show a cooperative spin transition with an approximately 2-K-wide thermal hysteresis loop in the case of 1(meim) ( T 1/2 increase = 179 K and T 1/2 decrease = 177 K) and an approximately 21-K-wide thermal hysteresis loop in the case of dinuclear complex 2(meim) 4 ( T 1/2 increase= 199 K and T 1/2 decrease= 178 K). For a separately prepared powder sample of 2, a gradual spin transition with T 1/2 = 229 K is observed that was additionally followed by Mossbauer spectroscopy. The results from X-ray structure analysis give a deeper insight into the molecule packing in the crystal and, by this, help to explain the increase of cooperative interactions during the spin transition when going from the mononuclear to the dinuclear complex. Both compounds crystallize in the triclinic space group P1, and the X-ray structure was analyzed before and after the spin transition. The change of the spin state at the iron center is accompanied by a change of the O-Fe-O angle, the so-called bite of the equatorial ligand, from about 109 degrees in the high-spin state to 89 degrees in the low-spin state. The cooperative interactions responsible for the thermal hysteresis loop are due to elastic interactions between the complex molecules in both cases. However, due to the higher symmetry of the dinucleating ligand in 2(meim) 4, a 3D network of short contacts is formed, while for mononuclear complex 1(meim), a 2D layer of linked molecules is observed. The spin transition was additionally followed in solution using (1)H NMR spectroscopy for both complexes. In both cases, a gradual spin transition is observed, and the increase of cooperative interactions when going from the mononuclear to the dinuclear system is solely attributed to the extended network of intermolecular contacts.

Cooperative Iron(II) spin crossover complexes with N4O2 coordination sphere.

Two new spin crossover complexes [FeL(py)(2)] (1) and [FeL(DMAP)(2)] (2) with L being a tetradentate N(2)O(2)(2-) coordinating Schiff-base-like ligand [([3,3']-[1,2-phenylenebis(iminomethylidyne)]bis(2,4-pentanedionato)(2-)-N,N',O(2),O(2)'], py = pyridine and DMAP = p-dimethylaminopyridine have been investigated using temperature-dependent susceptibility and thermogravimetric and photomagnetic measurements as well as Mössbauer spectroscopy and X-ray structure analysis. Both complexes show a cooperative spin transition with an approximately 9 K wide thermal hysteresis loop in the case of 2 (T(1/2) upward arrow = 183 K and T(1/2) downward arrow = 174 K) and an approximately 2 K wide thermal hysteresis loop in the case of the pyridine diadduct 1 (T(1/2) upward arrow = 191 K and T(1/2) downward arrow = 189 K). The spin transition was additionally followed by different temperature-scanning calorimetry and Mössbauer spectroscopy for 2, and a good agreement for the transition temperatures obtained with the different methods was found. Results from X-ray structure analysis indicate that the cooperative interactions are due to elastic interactions in both compounds. They are more pronounced in the case of 2 with very short intermolecular iron-iron distances of 7.2 A and several intense C-C contacts. The change of the spin state at the iron center is accompanied by a change of the O-Fe-O angle, the so-called bit of the equatorial ligand, from 108 degrees in the high-spin state to 90 degrees in the low-spin state. The reflectivity measurements of both compounds give at low temperature indication that at the sample surface the light-induced excited spin state trapping (LIESST) effect occurs. In bulk condition using a SQUID magnetometer the complex 2 displays some photomagnetic properties with an photoexcitation level of 60% and a T(LIESST) value of 53 K.

The configuration of the Cu(2+) binding region in full-length human prion protein compared with the isolated octapeptide.

The cellular prion protein (PrP(C)) is a copper binding protein. The molecular features of the Cu(2+) binding sites have been investigated and characterized by spectroscopic experiments on PrP(C)-derived peptides and the correctly folded human full-length PrP(C) (hPrP-[23-231]). These experiments allowed us to distinguish two different configurations of copper binding. The different copper complexes depend on sequence context, buffer conditions and stoichiometry of copper. The combined information of spectroscopic data from our EXAFS, EPR and ENDOR experiments was used to create models for these two copper complexes. A large number of conformations of these models were calculated using molecular mechanics computations, and the simulated spectra of these structures were compared with our experimental data. Common features and differences of the copper binding motifs are discussed in this paper and it remains for future investigations to study whether different configurations are associated with different functional states of PrP(C).

The configuration of the Cu2+ binding region in full-length human prion protein.

The cellular prion protein (PrP(C)) is a Cu(2+) binding protein connected to the outer cell membrane. The molecular features of the Cu(2+) binding sites have been investigated and characterized by spectroscopic experiments on PrP(C)-derived peptides and the recombinant human full-length PrP(C )(hPrP-[23-231]). The hPrP-[23-231] was loaded with (63)Cu under slightly acidic (pH 6.0) or neutral conditions. The PrP(C)/Cu(2+)-complexes were investigated by extended X-ray absorption fine structure (EXAFS), electron paramagnetic resonance (EPR), and electron nuclear double resonance (ENDOR). For comparison, peptides from the copper-binding octarepeat domain were investigated in different environments. Molecular mechanics computations were used to select sterically possible peptide/Cu(2+) structures. The simulated EPR, ENDOR, and EXAFS spectra of these structures were compared with our experimental data. For a stoichiometry of two octarepeats per copper the resulting model has a square planar four nitrogen Cu(2+) coordination. Two nitrogens belong to imidazole rings of histidine residues. Further ligands are two deprotonated backbone amide nitrogens of the adjacent glycine residues and an axial oxygen of a water molecule. Our complex model differs significantly from those previously obtained for shorter peptides. Sequence context, buffer conditions and stoichiometry of copper show marked influence on the configuration of copper binding to PrP(C).

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.

Colloidal synthesis and characterization of tetrapod-shaped magnetic nanocrystals.

Tetrapod-shaped maghemite nanocrystals are synthesized by manipulating the decomposition of iron pentacarbonyl in a ternary surfactant mixture under mild thermal conditions. Adjustment of the reaction parameters allows for the systematic tuning of both the width and the length of the tetrapod arms, which grow preferentially along the 111 easy axis direction. Such degree of control leads to modulation of the magnetic behavior of the nanocrystals, which evolves systematically as their surface magnetization phase and shape anisotropy are progressively increased.

Targeting cancer cells: magnetic nanoparticles as drug carriers.

Magnetic drug targeting employing nanoparticles as carriers is a promising cancer treatment avoiding side effects of conventional chemotherapy. We used iron oxide nanoparticles covered by starch derivatives with phosphate groups which bound mitoxantrone as chemotherapeutikum. In this letter we show that a strong magnetic field gradient at the tumour location accumulates the nanoparticles. Electron microscope investigations show that the ferrofluids can be enriched in tumour tissue and tumour cells.

Ligand migration and protein fluctuations in myoglobin mutant L29W.

We have determined eight X-ray structures of myoglobin mutant L29W at various experimental conditions. In addition, infrared spectroscopic experiments are presented, which are discussed in the light of the X-ray structures. Two distinct conformations of the CO-ligated protein were identified, giving rise to two stretching bands of heme-bound CO. If L29W MbCO crystals are illuminated around 180 K, a deoxy species is formed. The CO molecules migrate to the proximal side of the heme and remain trapped in the so-called Xe1 cavity upon temperature decrease to 105 K. The structure of this photoproduct is almost identical to the equilibrium high-temperature deoxy Mb structure. If the temperature is cycled to increasingly higher values, CO recombination is observed. Three intermediate structures have been determined during the rebinding process. Efficient recombination occurs only above 180 K, the characteristic temperature for the onset of protein dynamics. Rebinding is remarkably slow because bulky residues His64 and Trp29 block important migration pathways of the CO molecule.

A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu(2+) complex.

Since high-intensity synchrotron radiation is available, "extended X-ray absorption fine structure" spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu(2+) complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.

Micellar environments induce structuring of the N-terminal tail of the prion protein.

In the physiological form, the prion protein is a glycoprotein tethered to the cell surface via a C-terminal glycosylphosphatidylinositol anchor, consisting of a largely alpha-helical globular C-terminal domain and an unstructured N-terminal portion. This unstructured part of the protein contains four successive octapeptide repeats, which were shown to bind up to four Cu(2+) ions in a cooperative manner. To mimic the location of the protein on the cell membrane and to analyze possible structuring effects of the lipid/water interface, the conformational preferences of a single octapeptide repeat and its tetrameric form, as well of the fragment 92-113, proposed as an additional copper binding site, were comparatively analyzed in aqueous and dodecylphosphocholine micellar solution as a membrane mimetic. While for the downstream fragment 92-113 no conformational effects were detectable in the presence of DPC micelles by CD and NMR, both the single octapeptide repeat and, in an even more pronounced manner, its tetrameric form are restricted into well-defined conformations. Because of the repetitive character of the rigid structural subdomain in the tetrarepeat molecule, the spatial arrangement of these identical motifs could not be resolved by NMR analysis. However, the polyvalent nature of the repetitive subunits leads to a remarkably enhanced interaction with the micelles, which is not detectably affected by copper complexation. These results strongly suggest interactions of the cellular form of PrP (PrP(c)) N-terminal tail with the cell membrane surface at least in the octapeptide repeat region with preorganization of these sequence portions for copper complexation. There are sufficient experimental facts known that support a physiological role of copper complexation by the octapeptide repeat region of PrP(c) such as a copper-buffering role of the PrP(c) protein on the extracellular surface.

Hydration structures in proteins and neutron diffraction experiment on dissimilatory sul te reductase D (DsrD).

Neutron crystallography can provide a substantial amount of information about the hydration of proteins. The hydration patterns of three proteins, whose structures have been solved at 1.5 or 1.6 A resolution using our BIX-type diffractometers, show interesting features. The water molecules adopt a variety of shapes in the neutron Fourier maps, revealing details of intermolecular hydrogen-bond formation and dynamics of hydration. In addition, the neutron diffraction study of a DNA-binding protein, dissimilatory sulfite reductase D (DsrD) is briefly described, and some preliminary results are presented. This topic is of interest because it is well known that hydrogen bonds play important roles in DNA-protein recognition.

Proteins in action: the physics of structural fluctuations and conformational changes.

Structural dynamics is essential for the biological function of proteins. Results from new experimental techniques should be compared with those from previous experiments in order to obtain a consistent picture of the physics of intramolecular fluctuations and conformational changes. The high intensity and time structure of synchrotron radiation have made possible time-resolved X-ray structure analysis and the determination of phonon density spectra through the Mössbauer effect. By combining results from Mössbauer absorption spectroscopy, incoherent neutron scattering, low-temperature crystallography and optical spectroscopy, a physical picture of protein dynamics emerges.

Hydrogen atoms in proteins: positions and dynamics.

Hydrogen atoms constitute about half of the atoms in proteins. Thus they contribute to the complex energy landscape of proteins [Frauenfelder, H., Sligar, S. G. & Wolynes, P. G. (1991) Science 254, 1598-1603]. Neutron crystal structure analysis was used to study the positions and mean-square displacements of hydrogen in myoglobin. A test of the reliability of calculated hydrogen atom coordinates by a comparison with our experimental results has been carried out. The result shows that >70% of the coordinates for hydrogen atoms that have a degree of freedom is predicted worse than 0.2 A. It is shown that the mean-square displacements of the hydrogen atoms obtained from the Debye-Waller factor can be divided into three classes. A comparison with the dynamic mean-square displacements calculated from the elastic intensities obtained from incoherent neutron scattering [Doster, W., Cusack, S. & Petry, W. (1989) Nature 337, 754-756] shows that mainly the side-chain hydrogen atoms contribute to dynamic displacements on a time scale faster than 100 ps.

A water network within a protein: temperature-dependent water ligation in H64V-metmyoglobin and relaxation to deoxymyoglobin.

The sperm whale myoglobin mutant H64V, where the distal histidine is mutated to valine, is known to be five coordinated in the ferric state at room temperature and physiological pH. A change of the ligation in this H64V-Mbmet has been observed by optical absorption spectroscopy as a function of temperature from 20 K to 300 K. Above the dynamical transition at about 180 K one observes the temperature-dependent equilibrium between five- and six-ligated heme. Below the dynamical transition the equilibrium is frozen-in at about 50% of six-coordinate molecules. The water ligation of the iron occurs at temperatures where protein-specific motions are present, as monitored by Mössbauer spectroscopy. The X-ray structures of H64V-Mbmet at 300 K and 110 K are reported with a resolution of 1.5 A and 1.3 A, respectively. The measurements at high resolutions are possible owing to crystallization in the space group P2(1), whereas all mutant myoglobins studies up to now have been carried out with crystals in the space group P6. The overall structure at both temperatures is very close to the native myoglobin. The binding of water at the sixth coordination site at lower temperatures is possible owing to a stabilizing water network extending from the protein surface to the active centre. The reduction of the H64V-Mbmet by electrons obtained by X-ray irradiation of the water-glycerol solvent at 85 K produces an intermediate low-spin state of the water-ligated molecules where Fe(II) retains the six-fold coordination. Mössbauer spectroscopy shows that the relaxation of the metastable low-spin state to high-spin H64V-Mbdeoxy with dissociation of the Fe(II)-H(2)O bond starts at about 115 K and is completed at about 170 K. Differences in the dynamics properties of the native and mutant myoglobin and the connection to the dynamical transition around 180 K are discussed.

Hydration in proteins observed by high-resolution neutron crystallography.

It is well known that water molecules surrounding a protein play important roles in maintaining its structural stability. Water molecules are known to participate in several physiological processes through the formation of hydrogen bonds. However, the hydration structures of most proteins are not known well at an atomic level at present because X-ray protein crystallography has difficulties to localize hydrogen atoms. In contrast, neutron crystallography has no problem in determining the position of hydrogens with high accuracy.1 In this article, the hydration structures of three proteins are described- myoglobin, wild-type rubredoxin, and a mutant rubredoxin-the structures of which were solved at 1.5- or 1.6-A resolution by neutron structure determination. These hydration patterns show fascinating features and the water molecules adopt a variety of shapes in the neutron Fourier maps, revealing details of intermolecular hydrogen bond formation and dynamics of hydration. Our results further show that there are strong relationships between these shapes and the water environments.

Myoglobin, a paradigm in the study of protein dynamics.

More than 40 years have passed since Kendrew determined the structure of sperm whale myoglobin. It gave us the first insight into the impressive architecture of an alpha helical protein folded via loops into a well ordered, nearly spherical molecule. As time progressed, thousands of new protein structures were published with increasing resolution. The myoglobin structure was also continuously improved and, three years ago, a resolution of 0.9 A was achieved. A wide variety of spectroscopic techniques have been applied to study the dynamics of this molecule and the electronic properties of the heme iron atom. Even nowadays, experiments on myoglobin are still of great interest for a number of reasons: Physical research cannot go into all details in a large number of systems. In semiconductor physics, most concepts were developed by investigating germanium and silicon and were subsequently used to understand more complicated semiconductor systems; myoglobin plays a similar role in molecular biophysics. Concepts like "energy landscape", "conformational substates", "dynamic transition", or "protein-specific motions" should be of general relevance for understanding the physics of biological macromolecules. In biology, functionally important processes often occur at conditions and time scales where physical experiments are extremely difficult and yield ambiguous results. Going to low temperatures often allows one to separate the different dynamic processes. Another helpful tool is molecular engineering. Specific alterations in the sequence of the protein open the possibility to modify reaction rates and to retard the kinetics.

Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP.

The temperature dependence of the mean square displacement of the (57)Fe nuclei due to motion faster than 100 ns are measured by temperature-dependent Mössbauer spectroscopy for oxidized and reduced HiPIPs from Ectothiorhodospira halophila, Chromatium vinosum WT and a Cys77Ser mutant. The behaviour is interpretable in the frame of the general model of protein dynamics distinguishing two temperature intervals. The character of harmonic and quasi-diffusional modes in HiPIPs is discussed. Dynamic information obtained from Mössbauer spectroscopy and Fe K-edge EXAFS are compared. Structure dynamics of the iron-sulfur cluster in the partially unfolded reduced HiPIP from C. vinosum was investigated by Mössbauer spectroscopy and EXAFS, indicating an intact metal centre and a protein backbone with a largely collapsed secondary structure. The role of the cofactor during protein folding is discussed. Differences in the dynamics between the native protein and the molten globule are found at physiological temperatures only. The structure and dynamic behaviour of the [Fe(4)S(4)]Cys(3)Ser cluster in the Cys77Ser mutant of the HiPIP from C. vinosum are analysed. The temperature dependence of electron relaxation in oxidized HiPIPs is investigated by Mössbauer spectroscopy and analysed theoretically, considering spin-spin and spin-lattice relaxation. The latter consists of contributions from direct phonon bottleneck and Orbach mechanisms. The data agree with former pulsed EPR results. Orbach relaxation is interpreted as due to transitions between electronic isomers of oxidized HiPIPs. With this interpretation, the energetic difference between both isomers equals the energy gap estimated from the temperature dependence of the Orbach relaxation.