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Biomedical subjects

F Parak

Publications and source records attributed to F Parak.

At least 37 records · Page 2Linked to original sources
PubMed1992

The hydration shell of myoglobin.

The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 A2. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal water (R = 0.212). A reciprocal space refinement of the water and the protein coordinates has been performed. Monte Carlo calculations can be used to obtain information for crystallographically invisible parts of the unit cell and yield better coordinates for the visible part in the refinement.

Monte Carlo Method↗
PubMed1992

Spectral hole burning study of protoporphyrin IX substituted myoglobin.

Protoporphyrin IX substituted myoglobin reveals excellent hole burning properties. We investigated the frequency shift of persistent spectral holes under isotropic pressure conditions in a range from 0 to 2.4 MPa. In this range, the protein behaves like an elastic solid. The shift of the holes under pressure shows a remarkable frequency dependence from which the compressibility of the protein can be determined. The compressibility, in turn, allows for an estimation of the equilibrium volume fluctuations. Within the frame of the model used to interpret the pressure data, it is possible to determine the absorption frequency of the isolated chromophore and the associated solvent shift in the protein environment.

Animals↗
PubMed1987

Thermal expansion of a protein.

The thermal expansion of a protein, metmyoglobin, was investigated by analysis of the refined X-ray crystal structures at 80 and 255-300 K. On heating from 80 to 300 K, the volume occupied by myoglobin increases by approximately 3%. The linear thermal expansion coefficient is estimated to be 115 X 10(-6) K-1. This value is more than twice as large as that of liquid water but less than that of benzene. As the temperature is raised, the internal volume change does not come from the large, atom-sized internal cavities in the structure but from an increase in the small, subatomic free volumes between atoms. The largest expansion occurs in the region of the CD and GH corners; both these regions move away from the center of the protein. The remainder of the expansion results from the lengthening of contacts between segments of secondary structure.

Animals↗
PubMed1987

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.

Crystallography↗
PubMed1987

Low temperature X-ray investigation of structural distributions in myoglobin.

The results of X-ray structure analysis of metmyoglobin at 300 K, 185 K, 165 K, 115 K and 80 K are reported. The lattice vectors a and b decrease linearly with temperature while c shows non-linearity above 180 K, indicating some type of phase transition. Cooling does change the myoglobin structure but only within the structural distribution as determined by individual (chi 2)-values at room temperature. Two residues showed significant alternative positions for side-chains at higher temperatures while only one position is occupied at low temperatures. In the case of LEU 61 a jump between different positions of the side-chain reduces the potential barrier for the entrance of the O2 molecule to the heme pocket. The mean square displacements, (chi 2), of the individual residues decrease linearly with temperature in most cases, indicating a parabolic envelope for the potential responsible for motions. A separation of rotational and translational disorder of the entire molecule is discussed. Comparison with Mössbauer spectroscopy indicates that protein dynamics on a time scale faster than 10(-7) s is not simply a harmonic process. Extrapolation of the structural distributions to T = 0 K shows that a large zero point distribution of the myoglobin structure exists, thus proving that there is no absolute energy minimum for one well defined conformation.

Binding Sites↗
PubMed1985

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.

Animals↗
PubMed1984

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.

Computers↗
PubMed1983

Structural dynamics of human deoxyhemoglobin and hemochrome investigated by nuclear gamma resonance absorption (Mössbauer) spectroscopy.

Mössbauer spectra of human deoxyhemoglobin and hemochrome frozen solutions, selectively enriched with 57Fe in either the alpha chains or the beta chains, were measured from 4.2 to 250 K. The Lamb-Mössbauer factor, ln f = 4II2 [x2]gamma/lambda 2, was calculated from these spectra and gives the structural dynamics of the iron atom (heme). Large differences in the mean-squared displacement, [x2]gamma, of the heme between hemochrome and deoxyhemoglobin at temperatures above 210 K were observed, demonstrating that when iron is bound to a rigid part of the protein (i.e., distal histidine in hemochrome), motions of the heme are suppressed (i.e., the dynamics are decreased). Comparison of the motions of these two hemoglobins proves that molecular diffusion can be neglected in an analysis of the dynamics below approximately 250 K.

Hemeproteins↗
PubMed1982

Conformational substates in a protein: structure and dynamics of metmyoglobin at 80 K.

The crystal structure of sperm whale metmyoglobin has been determined at 80 K to a resolution of 2A. The overall structure at 80 K is similar to that at 300 K except that the volume is smaller. Refinement of the structure by the method of restrained least squares (current R = 0.175) permits the assignment of isotropic atomic mean-square displacements to all nonhydrogen atoms. Comparison with the values obtained earlier at 250-300 K indicates that the protein at 80 K is more rigid. The average experimentally determined Debye-Waller factor, B, for the protein is 14A2 at 300 K and 5A2 at 80 K. Plots of backbone mean-square displacement vs. temperature show a discontinuity of slope for at least one-third of all residues. This behavior is in good agreement with the temperature dependence of the mean-square displacement of the heme iron as measured by Mössbauer absorption. The magnitudes of the smallest mean-square displacements observed at 80 K indicate that intramolecular motions can be frozen out to a surprisingly large degree. Even at 80 K, however, some atoms in myoglobin still have mean-square displacements greater than 0.1A2, thus providing evidence for conformational substates.

Animals↗
PubMed1982

Electron paramagnetic resonance crystallography of bacterial catalase: g-Contour mapping method of analysis.

Single crystals of bacterial catalase from Micrococcus luteus have been examined by EPR at 77 K. X-ray perfect crystals gave a set of four prominent resonances in all three orthogonal planes which yielded eight heme direction cosine matrices to an accuracy of +/- 2 degrees as expected for the P4(2)2(1)2 space group and unit cell parameters previously determined. These matrices are related by D4 symmetry operation of the space group. There were additional weaker resonances only resolved in two or even one plane. A method of g-contour mapping was devised to solve for the orientations of hemes that give rise to these weaker resonances. Three additional sets of heme orientations, also following D4 symmetry, were determined. All of the above sites have the same principal g values, 2.0, 5.4, and 6.6. The EPR crystallographic results imply that several conformational substates may be trapped at 77 K.

Catalase↗