The X-ray absorption spectroscopy Debye-Waller factors of an iron compound and of met-myoglobin as a function of temperature

Protein dynamics can be characterized by the mean square displacements of the individual atoms of a molecule. This concept is extended to X-ray absorption spectroscopy (XAS) of proteins where the physical information in the Debye-Waller factor is in general neglected. In a first step, a procedure for the investigation of the temperature dependence of XAS spectra has been developed for a small iron compound. Subsequently, experiments have been performed on met-myoglobin. It is shown that the mean square displacements of XAS are smaller than those obtained by M?ssbauer spectroscopy and far smaller than crystallographic mean square displacements. This behavior is explained by the different sensitivity of the methods. XAS measures a relative mean square displacement between the absorbing and backscattering atoms only. A comparison with mean square displacements calculated from normal modes shows that static displacements contribute significantly. It becomes obvious that the atoms of the active center show a high correlation of their motions.     

Temperature dependence of the electronic absorption spectra of polynucleotides and their components]

The temperature dependence of UV-absorption spectra of solutions nucleic bases, nucleosides, nucleotides and metilated bases, uncapable of tautomerization has been studied. The nature of such dependence, its connection with hypochromic effect is discussed. It is shown that for some methods of investigating polynucleotides it is necessary to take into account the temperature changes spectra of monomers.     

Possible effects of the influence of dynamic disorder of biological systems on characteristics of intramolecular mobility, determined by Mossbauer spectroscopy]

A model for describing dynamic properties of proteins is proposed. The model involves the distribution over amplitudes and correlation times of intramolecular dynamics. It has been shown that distribution parameters and its temperature dependence have a great influence upon the values of experimental dynamic characteristics. Besides the discrepancy between the real and experimental temperature, dependence of characteristics on intramolecular dynamics can be observed.     

On peculiarities of temperature dependences of water spectra in the terahertz frequency domain

We analyzed spectra of light and heavy water at temperatures from 4 up to 50°C in a frequency range of 0.15 to 6.5 THz. It was shown that the amplitude of high-frequency relaxation absorption band with its maximum at 0.5 THz extends with increasing temperature and this temperature dependence for light water has a marked feature at 35–40°C as a sharp growth. This fact is noteworthy because this range corresponds to physiological values of a body temperature of the warm-blooded organisms. At the same time, the analogous temperature dependence for heavy water in the considered temperature range lacks this particular feature. Thus, the water with its properties differs significantly not only from other fluids, but also from its own isotopologues.     

Temperature dependent spectral changes of iron and nickel hemoglobins and their derivatives

Temperature dependent absolute and difference spectra for deoxy and oxy human hemoglobin, alpha and beta subunits, NiHbA, carboxypeptidase A treated deoxy HbA and NiHbA have been investigated. It is shown for the first time that the alpha subunits are mainly responsible for the temperature dependent spectral changes in the absorption spectra of Hb in the range from 0 degrees C to 40 degrees C. It has also been found that in the R state the spectral alterations caused by temperature variation are about 85% of those found for the T state of Hb. The value of following the temperature dependence of the porphyrin bands of hemoproteins, as a sensitive probe for subtle changes in the region of the heme, is demonstrated.     

Calorimetric study of the glass transition of denatured collagen

Temperature dependence of heat capacity of native and denatured collagen samples with different content of bound water (6 divided by 27%) has been studied by DSC method in the temperature range from -50 to 150 degrees C. Heat capacity of denatured samples demonstrates a jump of 0.50 J/g.grad. at temperature Tg, which depends on humidity of the sample. It has been shown that Tg value also depends on the heating rate and thermal history. Annealing at the temperature below Tg produces an additional maximum in the temperature dependence on heat capacity. The magnitude of this maximum, as well as the Tg value increase with the annealing time. It is concluded that these properties of heat capacity reflect glass transition in the denatured collagen.     

Computer simulation of temperature autostabilization: an analysis of the phenomenon

A mathematical model of the temperature autostabilization by microorganism populations in batch and continuous operation has been developed. It adequately describes the process of temperature autostabilization by Candida tropicalis yeast microorganisms on H-alkanes. The model analysis has permitted determination of the conditions for the existence of the phenomenon and an explanation of its basic factors, such as linear biomass growth and dependence of microorganisms growth velocity on heat transfer through reactor walls. The industrial application of this interesting phenomenon is discussed. Correspondence to: M. Kristapsons     

Characterization of the high-resolution ESR spectra of superoxide radical adducts of 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO) and 5,5-dimethyl-1-pyrroline N-oxide (DMPO). Analysis of conformational exchange

It has been previously reported that the spin trap 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO) can form stable radical adducts with superoxide radical. However, the presence of diastereomers of DEPMPO radical adducts and the appearance of superhyperfine structure complicates the interpretation of the ESR spectra. It has been suggested that the superhyperfine structure in the ESR spectrum of DEPMPO/^?OOH is a result of conformational exchange between conformers. The analysis of the temperature dependence of the ESR spectrum of DEPMPO/^?OOH and of its structural analog DMPO/^?OOH have demonstrated that both ESR spectra contain exchange effects resulting from conversion between two conformers. Computer simulation calculates a conformer lifetime on the order of 0.1?μs for DMPO/^?OOH at room temperature. However, temperature dependence of the ESR spectrum of DEPMPO/^?OOH suggests that superhyperfine structure does not depend on the conformational exchange. We have now found that the six-line ESR spectrum with superhyperfine structure should be assigned to a DEPMPO-superoxide-derived decomposition product. Therefore, ESR spectra previously assigned to DEPMPO/^?OOH contain not only the two diastereomers of DEPMPO/^?OOH but also the decomposition product, and these spectra should be simulated as a combination of four species: two conformers of the first diastereomer, one conformer of the second diastereomer and the superoxide-derived decomposition product. The presence of four species has been supported by the temperature dependence of the ESR spectra, nucleophilic synthesis of radical adducts, and isotopic substitution experiments. It is clear that to correctly interpret DEPMPO spin trapping of superoxide radicals, one must carefully consider formation of secondary radical adducts.     

Temperature dependence of protein dynamics: computer simulation analysis of neutron scattering properties

The temperature dependence of the internal dynamics of an isolated protein, bovine pancreatic trypsin inhibitor, is examined using normal mode analysis and molecular dynamics (MD) simulation. It is found that the protein exhibits marked anharmonic dynamics at temperatures of approximately 100-120 K, as evidenced by departure of the MD-derived average mean square displacement from that of the harmonic model. This activation of anharmonic dynamics is at lower temperatures than previously detected in proteins and is found in the absence of solvent molecules. The simulation data are also used to investigate neutron scattering properties. The effects are determined of instrumental energy resolution and of approximations commonly used to extract mean square displacement data from elastic scattering experiments. Both the presence of a distribution of mean square displacements in the protein and the use of the Gaussian approximation to the dynamic structure factor lead to quantified underestimation of the mean square displacement obtained.     

Characterization of the high-resolution ESR spectra of superoxide radical adducts of 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO) and 5,5-dimethyl-1-pyrroline N-oxide (DMPO). Analysis of conformational exchange

It has been previously reported that the spin trap 5-(diethoxyphosphoryl)-5-methyl-1-pyrroline N-oxide (DEPMPO) can form stable radical adducts with superoxide radical. However, the presence of diastereomers of DEPMPO radical adducts and the appearance of superhyperfine structure complicates the interpretation of the ESR spectra. It has been suggested that the superhyperfine structure in the ESR spectrum of DEPMPO/^⋅OOH is a result of conformational exchange between conformers. The analysis of the temperature dependence of the ESR spectrum of DEPMPO/^⋅OOH and of its structural analog DMPO/^⋅OOH have demonstrated that both ESR spectra contain exchange effects resulting from conversion between two conformers. Computer simulation calculates a conformer lifetime on the order of 0.1 μs for DMPO/^⋅OOH at room temperature. However, temperature dependence of the ESR spectrum of DEPMPO/^⋅OOH suggests that superhyperfine structure does not depend on the conformational exchange. We have now found that the six-line ESR spectrum with superhyperfine structure should be assigned to a DEPMPO-superoxide-derived decomposition product. Therefore, ESR spectra previously assigned to DEPMPO/^⋅OOH contain not only the two diastereomers of DEPMPO/^⋅OOH but also the decomposition product, and these spectra should be simulated as a combination of four species: two conformers of the first diastereomer, one conformer of the second diastereomer and the superoxide-derived decomposition product. The presence of four species has been supported by the temperature dependence of the ESR spectra, nucleophilic synthesis of radical adducts, and isotopic substitution experiments. It is clear that to correctly interpret DEPMPO spin trapping of superoxide radicals, one must carefully consider formation of secondary radical adducts.     

Protein dynamics of a β-sheet protein

Rhodnius prolixus Nitrophorin 4 (abbreviated NP4) is an almost pure β-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 β-sheet protein with the pure α-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.     

Mössbauer Effect in Hemoglobin and Some Iron-Containing Biological Compounds

The M?ssbauer effect in Fe(57) has been used to study the molecules, hemoglobin, O(2)-hemoglobin, CO(2)-hemoglobin, and CO-hemoglobin (within red cells) and the molecules, hemin and hematin (in the crystalline state). Quadrupole splittings and isomeric shifts observed in the M?ssbauer spectra of these molecules are tabulated. The temperature dependence of the quadrupole splitting and relative recoil-free fraction for hemoglobin with different ligands has been investigated. An estimate of the Debye-Waller factor in O(2)-hemoglobin at 5 degrees K is 0.83. An asymmetry in the quadrupole splitting observed in hemoglobin is attributed to a directional dependence of the recoil-free fraction which establishes the sign of the electric field gradient in the molecule and indicates that the lowest lying d orbital of the Fe atoms is |xy>. This asymmetry indicates that the iron atoms in hemoglobin are vibrating farther perpendicular to the heme planes than parallel to them, and, in fact, the ratio of the mean square displacements perpendicular and parallel to the heme planes in hemoglobin is approximately 5.5 at 5 degrees K. The temperature dependence of the quadrupole splitting in hemoglobin has been used to estimate a splitting between the lowest lying iron atom d orbitals of approximately 420 cm(-1).     

1H-n.m.r. study of the folding of ribonuclease 12-(beta-(3-pyridyl)-L-Ala) S-peptide (1-14)

The 1H-n.m.r. spectra (360 MHz) of 12-(beta-(3-pyridyl)-L-Ala) ribonuclease S-peptide (1-14), a tetradecapeptide incorporating (beta-3-pyridyl-L-Ala) instead of His at position 12, have been assigned. The shift vs. temperature dependence has been analyzed at three different pD's in terms of a two-state helix (3-13) in equilibrium coil equilibrium, and the corresponding values for the thermodynamic quantities delta H degrees and delta S degrees determined. Helix populations at 0 degrees C have been measured as a function of pD, showing their dependence on two apparent pKa's at approximately 3.3 and 5.5, with a maximum at pD approximately 4.2. All the obtained results show that the new peptide has very similar folding properties to those shown by S-peptide and particularly to those of C-peptide. The 3-13 helix formed is stabilized by two interactions: a salt-bridge Glu 2-...Arg 10+ and a partial stacking between the aromatic rings of residues Phe 8 and His 12. Calculations involving ring current shifts and potential energies validate the possible existence of this latter interaction, which must present a local geometry defined by chi 81 180 degrees, chi 82 100 degrees, chi 121-60 and chi 122 80.     

Hemoglobin-membrane interaction at physiological ionic strength and temperature

The spin-label electron paramagnetic resonance (EPR) technique has been used to study the interaction between human hemoglobin and erythrocyte membranes as a function of temperature and ionic strength. We show, for the first time, experimental evidence for the existence of the interaction at physiological pH, ionic strength and temperature. In addition to the pH dependence that we have previously reported, the interactions are also temperature and ionic strength dependent. Using a simple two-state equilibrium model to analyze the EPR data, we obtain an equilibrium dissociation constant of about 8.1 +/- 5.6 X 10(-5) M for hemoglobin-membrane systems in 5 mM phosphate with 150 mM NaCl at pH 7.4 and 37 degrees C.     

Diffusion factor calculation for TIP4P model of water

A molecular dynamics study has been undertaken for a model of liquid TIP4P water. Thermal dependencies of water density and radial distribution functions were calculated for model verification. Three methods have been used for calculation of diffusion factor thermal dependencies. Their sensitivity to molecular system size and length of used trajectory has been analyzed. It has been shown that Green-Kubo formula-based approach which associates diffusion factor with speed autocorrelation function integral is preferred in case of short MD simulations. The second approach based on Einstein equation which associates mean square displacement of molecule with time is preferred in case of long simulations. It has been also demonstrated that it is possible to modify the second approach to make it more stable and reliable. This modification is to use a slope of the graph of the mean square displacement on time as the estimation of the diffusion factor instead of the ratio of molecule mean square displacement and time.     

Differences in the dynamics of oxidized and reduced cytochrome c measured by Mössbauer spectroscopy

The temperature dependence of the mean square displacement of the iron atom in reduced and oxidized cytochrome c has been studied by Mössbauer spectroscopy. The flexibility of the protein, labeled by the modes coupling to the iron, is diminished upon reduction. The differences in flexibility are sufficient to explain the differences in physicochemical properties between the oxidized and the reduced forms.     

Spectroscopic properties of fluorescein in living lymphocytes

Detailed studies have been performed on various spectroscopic properties such as time dependence and excitation wavelength dependence of the fluorescence anisotropy for fluorescein molecules introduced into rat thymus lymphocytes. Experimental results have been found to be well interpreted in terms of the coexistence of two types of dye molecules, i.e., free and bound molecules. The fluorescence spectrum of only the bound molecules has been obtained from the difference in the time-resolved spectra of fluorescence with two polarization directions. The time gate has been set at a sufficiently late time after the excitation, so that the polarization memories of the free molecules are lost. The spectrum thus determined agrees very well with that calculated from the spectral data in the stationary condition. From the above results, we come to the conclusion that the main factors which determine the fluorescence anisotropy inside the cell are the fraction and the anisotropy of the bound dye molecules. Finally, we discuss how these factors are related to biological quantities.     

Crossover from picosecond collective to single particle dynamics defines the mechanism of lateral lipid diffusion

It has been widely accepted that the thermally excited motions of the molecules in a cell membrane is the prerequisite for a cell to carry its biological functions. On the other hand, the detailed mapping of the ultrafast picosecond single-molecule and the collective lipid dynamics in a cell membrane remains rather elusive. Here, we report all-atom molecular dynamics simulations of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer over a wide range of temperature. We elucidate a molecular mechanism underlying the lateral lipid diffusion in a cell membrane across the gel, rippled, and liquid phases using an analysis of the longitudinal and transverse current correlation spectra, the velocity auto-correlation functions, and the molecules mean square displacements. The molecular mechanism is based on the anomalous ultrafast vibrational properties of lipid molecules at the viscous-to-elastic crossover. The macroscopic lipid diffusion coefficients predicted by the proposed diffusion model are in a good agreement with experimentally observed values. Furthermore, we unveil the role of water confined at the water-lipid interface in triggering collective vibrations in a lipid bilayer.