[Show abstract][Hide abstract] ABSTRACT: The use of new-generation powerful sources ("X-ray free electron lasers") in the X-ray diffraction experiment can cause substantial changes in the electronic structure of the object during the experiment. These changes may significantly complicate the solution of the direct problem of X-ray structure analysis, i.e. the prediction of the diffraction pattern, provided an atomic model of the object is available. We suggest below two simplified schemes, which allow the calculation of the diffraction pattern by means of the standard tools of biological (stationary) crystallography, with the accuracy being within the limits achieved nowdays in the study of biological objects. It was found that, at middle resolution and with X-ray pulses of a moderate photon fluence, the photoionization causes an almost simultaneous attenuation of diffracted beams for all Bragg reflections. This allows one to calculate the diffraction pattern by standard crystallographic formulae, by adapting only the general scale factor to the experiment. The use of more powerful X-ray lasers (that are unavailable yet in practice, but are under development) requires the modification of computational schemes. We suggest a modification that takes changes in atomic scattering factors during the experiment into account but retains the computational complexity inherent in standard crystallographic applications. The modification consists in replacing the standard atomic scattering factors by their "effective" counterparts, calculated on the basis of time-dependent scattering factors. The calculation of time-dependent formfactors for X-ray pulse with specified parameters is performed at the preliminary stage of the work.
The publication is in Russian and is available for open access at:
Mathematical Biology and Bioinformatics. 03/2013; 8(1):93-118.
[Show abstract][Hide abstract] ABSTRACT: The influence of three chemical chaperones: glycerol, 4-hexylresorcinol, and 5-methylresorcinol on the structure, equilibrium
fluctuations, and functional activity of the hydrophilic enzyme lysozyme and the transmembrane reaction center (RC) protein
from Rb. sphaeroides in a broad range of concentrations has been studied. The chosen chemical chaperones differ strongly in their structure and
action on hydrophilic and membrane proteins. The influence of the chemical chaperones (except methylresorcinol) on the structure,
dynamics, and functional properties of lysozyme and RC protein are well described in the framework of extended models of preferential
hydration and preferential interaction of protein with a chemical chaperone. A molecule of hexylresorcinol consists of a hydrophobic
(alkyl radical) and a hydrophilic (aromatic core) moieties; this provides for additional regulation of the functional activity
of lysozyme and RC by hexylresorcinol. The influence of methylresorcinol on proteins differs from that of glycerol and hexylresorcinol.
Methylresorcinol interacts with the surface of lysozyme directly, not via water hydrogen bonds. This leads to a decrease in
the denaturation temperature and an increase in the amplitude of equilibrium fluctuations, allowing it to be a powerful activator.
Methylresorcinol interacts with the membrane RC protein only by the condensation of hydration water, which is negligible in
this case. Therefore, methylresorcinol does not affect the functional properties of the RC protein. It is concluded that different
chaperones at the same concentration as well as one and the same chaperone at different concentrations produce protein 3D
structures differing in dynamic and functional characteristics.
Keywordslysozyme–reaction center protein–
[Show abstract][Hide abstract] ABSTRACT: In our study, we investigated the capacity of alkylhydroxybenzenes (AHB), which are microbial anabiosis autoinducers, for
alteration of the enzymatic activity of the hen egg-white lysozyme, as well as the efficiency of hydrolysis of specific (peptidoglycan)
and nonspecific (chitin) substrates catalyzed by lysozyme. AHB homologues (C7-AHB and C12-AHB), which differ in their hydrophobicity
and effects in their interaction with lysozyme, were used as modifying agents. C7-AHB stimulated enzymatic activity within
the whole range of concentrations used (10−7−10−3 M). More hydrophobic C12-AHB exhibited this ability only at low concentrations and inhibited fermentative activity at high
concentrations, acting as a mixed-type inhibitor. Both AHB homologues caused changes in the hydrophobicity of lysozyme molecules.
An increase in the affinity level between the C7-AHB-modified enzyme and the nonspecific substrate (colloidal chitin or cell
wall polymers of Saccharomyces sp.) was observed, which manifested itself in the enhancement of the hydrolysis rate by 200–500% (as compared to the native
enzyme). A significant effect on the efficiency of the lysozyme-catalyzed modifications of the substrate (peptidoglycan, colloidal
chitin) structure as a result of its complexation with AHB was demonstrated. A stabilizing effect of C7-AHB and C12-AHB was
revealed, which ensured a high level of activity of the AHB-modified enzyme (as compared to the control) after heat treatment
(functional stability), as well as at nonoptimal temperatures of catalysis (operational stability). The biological significance
of lysozyme modification with AHB and the practical aspects of its application are discussed.
[Show abstract][Hide abstract] ABSTRACT: The angular dependencies of inelastic intensities of Rayleigh scatteringof Moessbauer radiation were measured for lysozyme and myoglobin (fordifferent degrees of hydration: from h = 0.05 till h = 0.7). The treating ofthe data at h > 0.05 approves the existence of segmental motions(α-helices for myoglobin, α-helices and β-sheets forlysozyme) as well as of individual motions. Further hydration increase themean-square displacements for both types of intraglobular motions for theseproteins, while the motions of the globule as a whole remain nearlythe same as for h = 0.05. Results of the study of the radial distributionfunction deduced by Fourier - transform from the diffuse x-raymeasurements together with RSMR data allow to conclude that the waterduring hydration of proteins competes with the intramolecular hydrogenbonds, loosens the protein and increases the internal dynamics. At the sametime water arranges the ordering of macromolecule from `glassy' state ath ≈ 0.02 to the native state at h = 0.4-0.7. Differentarchitecture of proteins leads to the different structural dynamics as in thecase of lysozyme and myoglobin.
Journal of Biological Physics 06/2002; 28(2):139-45. · 0.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The angular dependencies of inelastic intensities of Rayleigh scattering of Mössbauer radiation were measured for lysozyme and myoglobin (for different degrees of hydration: from h=0.05 till h=0.7). The treating of the data at h>0.05 approves the existence of segmental motions (α-helices for myoglobin, α-helices and -sheets for lysozyme) as well as of individual motions. Further hydration increases the mean-square displacements for both types of intraglobular motions for these proteins, while the motions of the globule as a whole remain nearly the same as for h=0.05. Results of the study of the radial distribution function deduced by Fourier-transform from the diffuse X-ray measurements together with RSMR data allow to conclude that the water during hydration of proteins competes with the intramolecular hydrogen bonds, loosens the protein and increases the internal dynamics. At the same time water arranges the ordering of macromolecule from “glassy” state at h≈0.02 to the native state at h=0.4–0.7. Different architecture of proteins leads to the different structural dynamics as in the case of lysozyme and myoglobin.
[Show abstract][Hide abstract] ABSTRACT: Protein specific modes of motions are found in myoglobin crystals above 180 K. In this contribution we show that this type of motions can be analyzed by a Davidson-Cole, a Cole-Cole or a Havriliak-Negami distribution in analogy to dielectric relaxation. However, the temperature dependence of the obtained parameters is quite unusual indicating a broadening of the distributions with temperature instead of motional narrowing. This can be understood from the picture of conformational substates if one assumes that more and more substates become accessible with increasing temperature. The result shows that the analogy between glass forming organic liquids and proteins should not be exaggerated.
Chemical Physics 11/1996; 212(1):221-229. · 1.96 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Summary The classical model system poly-L-glutamic acid (poly-Glu), was investigated in a disordered coil state (at pH=7.0) and in helix state (at pH=2.0) by the RSMR technique. By considering that the coil state of poly-Glu models unfolded (random coil) state and α-helix
state models the fluctuating secondary structure (during consequent folding of protein), a comparative analysis of the dynamical
properties of poly-Glu in different states with the dynamical properties of different proteins in the native state (α-helical
myoglobin and HSA, partially β-sheet lysozyme) and in intermediate (molten globule) state (α-lactalbumin) was performed. This
comparison brings some unpredicted results: native α-helical proteins behave close to random coil, native partially β-sheet
proteins behave close to fluctuating secondary structure (α-helix) and the dynamic behaviour of molten-globule state (partially
β-sheet α-lactalbumin) is not different from the behaviour of lysozyme and much more rigid than that of native α-helical proteins.
[Show abstract][Hide abstract] ABSTRACT: The method of differential diathermic calorimetry was used to obtain the curves of release and absorption of heat in water—protein systems. The influences of the rates of cooling and heating and the influence of annealing on the state of a water—lysozyme system at different hydration degrees h = 0.1−0.7 g/g were studied. Experiments have demonstrated that at considerably large rates of cooling there are observed the effects of vitrification of water—protein systems, i.e. the stabilization of a metastable, nonequilibrium structure of system. Decrease of the cooling rate or annealing transforms more of the system into an equilibrium state, increasing the degree of globular crystallinity to more than 70%. Therefore low-temperature experiments with water—protein systems aimed at obtaining functionally important information (i.e. important also at room temperatures) should be performed with slowly cooled or with annealed systems.
Chemical Physics Letters 01/1993; 208:1-4. · 2.15 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In this survey, the scales and correlation times of the motion of iron atoms in the active site of myoglobin and hemoglobin,
in the iron containing core, in iron storage proteins, and model polymer systems, and the average fragmental motion of protein
globules of myoglobin and human serum albumin are considered. Models of intramolecular protein mobility are presented.
[Show abstract][Hide abstract] ABSTRACT: A comparative study of a native and molten globule state of α-lactalbumin and polyglutamic acid in helical and coiled states
were performed by RSMR. Molten globule state possesses the same dynamical features registrated by RSMR as the native one.
Large-scale low-frequency motions were registrated in the coiled molecule without any elements of secondary structure.
[Show abstract][Hide abstract] ABSTRACT: A critical review of recent studies of protein dynamics by the RSMR technique is given. The main approximations in quantitative analyses of RSMR data are discussed and conclusions about dynamical properties of protein and interprotein water, deduced from experiments, are described.
[Show abstract][Hide abstract] ABSTRACT: Recent experimental results on the study of intramolecular mobility of hydrated DNA by RSMR are presented. Hydrated DNA possesses
a well-developed mobility: X
2> reaches 1.2 2 at high hydration degree. RSMR spectra were measured for hydrated DNA within a temperature range of 90 K-300 K. A quasielastic
“wide” component was observed atT>260 K. Three different types of intramolecular mobility were introduced for description of experimental data.
[Show abstract][Hide abstract] ABSTRACT: In the survey, the scales and correlation times of motion on different levels are considered: iron atoms in active centre
of myoglobin and hemoglobin, iron containing core in iron storage proteins and model polymer systems, and the average fragmental
motion of a protein globule of myoglobin and human serum albumin. The models of intramolecular protein mobility have been
Applied Magnetic Resonance 01/1990; 1(3):463-481. · 0.83 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A method of Mössbauer Fourier spectroscopy is developed to determine the correlation function of coordinates of a macromolecular
system. The method does not require the use of an a priori dynamic model. The application of the method to the analysis of
RSMR data for human serum albumin has demonstrated considerable changes in the dynamic behavior of the protein globule when
the temperature is changed from 270 to 310 K. The main conclusions of the present work is the simultaneous observation of
low-frequency (τ≥10−9 sec) and high-frequency (τ≪10−9 sec) large-scaled motions, that is the two-humped distribution of correlation times of protein motions.
[Show abstract][Hide abstract] ABSTRACT: A review of recent experimental results on the study of protein dynamics by the Rayleigh scattering of Mössbauer radiation
(RSMR) method is given. Dynamical properties of protein and protein-bound water, deduced from a quantitative analysis of RSMR
data, are described.
[Show abstract][Hide abstract] ABSTRACT: Data on the electronic state of iron in active centres of heme proteins and on the dynamics of these proteins have been obtained by means of Mössbauer spectroscopy and Rayleigh scattering of Mössbauer radiation. The influence of conformational rearrangements of the protein globule on the electronic state of the iron atom is considered. Mean square displacements of the iron atom and average mean square displacements of the myoglobin globule are compared.
Journal of Molecular Catalysis. 01/1988; 47:179-186.