Small-angle X-ray scattering study of the influence of solvent replacement (from H2O to D2O) on the initial crystallization stage of tetragonal lysozyme

Бойкова, А. С.; Dyakova, Yu. A.; Ilina, Kseniia B.; Konarev, Petr V.; Kryukova, A. E.; Марченкова, М. А.; Благов, А. Е.; Pisarevskii, Yu. V.; Kovalchuk, M. V.

doi:10.1134/s1063774517060074

Cited by 24 publications

(13 citation statements)

References 16 publications

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“…Study of protein crystallization and the properties of protein crystals is undoubtedly interesting both for the development of approaches to search for protein crystallization conditions and investigate the difference between the structures of a protein molecule in the crystalline state and in a solution. It was found for several proteins that the pre-crystallization solution contains oligomers built from protein molecules, the structure of which is well-described by the structures of oligomers found in crystals of the examined proteins [1][2][3].…”

Section: Introductionmentioning

confidence: 96%

Effect of the Simulation Box Size and Precipitant Concentration on the Behavior of Tetragonal Lysozyme Dimer

et al. 2021

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The 10-nanosecond simulation of a lysozyme dimer, which is a fragment of the tetragonal lysozyme crystal structure, has been carried out by the molecular dynamics method at different simulation box sizes and precipitant concentrations in a solution. The dimer stability has been estimated by calculating the root-mean-square fluctuations of protein atoms. It is shown that the box size does not significantly affect the mobility of protein atoms on a relatively short trajectory, while the effect of the precipitant concentration on this trajectory is noticeable.

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Section: Introductionmentioning

confidence: 96%

Effect of the Simulation Box Size and Precipitant Concentration on the Behavior of Tetragonal Lysozyme Dimer

et al. 2021

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“…Dimer, tetramer, hexamer, and octamer models were prepared according to the procedure described in [4]. The fit quality of the calculated models to the experimental data obtained in the work [23] was estimated by minimizing the discrepancy χ 2 between the experimental data and the theoretical models according to the formula given in [6]. The radii of gyration and the volume fractions of the oligomeric components in solution with the addition of various precipitants, as determined by SAXS experimental data using the program OLIGOMER (Figure S1), are shown in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…In recent works [4][5][6], it has been found that before the crystallization of lysozyme, its oligomers are formed in the solution, playing the role of precursor clusters in the formation of the protein crystal.…”

Section: Introductionmentioning

confidence: 99%

The Role of Cations and Anions in the Formation of Crystallization Oligomers in Protein Solutions as Revealed by Combination of Small-Angle X-ray Scattering and Molecular Dynamics

et al. 2022

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As is known from molecular dynamics simulation, lysozyme oligomers in crystallization solutions are most stable when taking into account as many precipitant ions as possible embedded in the corresponding crystal structure. Therefore, the number of precipitant ions associated with crystallographic oligomer models can play a role during the modeling of small-angle X-ray scattering (SAXS) data. This hypothesis has been tested in the present work. As a result, it turned out that the best fit quality to the experimental SAXS data is reached when using oligomers without precipitant ions at all or with embedded chlorine ions. Molecular dynamics (MD) simulation shows that the stability of crystallization oligomers depends on the consideration of anions and cations in oligomer structure. Thus, it is chlorine ions which stabilize dimer and octamers in lysozyme crystallization solution. As SAXS is more sensitive to the role of cations and MD shows the role of anions which are “light” for X-rays, it has been shown that precipitant cations most likely do not bind to monomers, but to already-formed oligomers.

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“…Some researchers assumed that it consists only of monomers [4], but most agreed that oligomers are formed in solution. In recent works [5][6][7], it was found that, before its crystallization in solution, lysozyme's oligomers are formed, which are involved in the subsequent growth of the crystal. The authors of this study proposed to use the molecular dynamics (MD) method to assess the stability of oligomers and to study the behavior of atoms and bonds in their structure [8,9].…”

Section: Introductionmentioning

confidence: 99%

Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions

et al. 2021

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We use the MM/GBSA method to calculate the free energies of dimer formation by binding two monomers with different combinations of precipitant ions, both embedded in the structure of monomers and in the crystallization solution. It shows that the largest difference in free energy values corresponds to the most accurate dimer model, which considers all precipitant ions in their structure. In addition, it shows that in the absence of precipitant ions in the solution of lysozyme molecules, a monomer is a more energetically favorable state.

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Small-angle X-ray scattering study of the influence of solvent replacement (from H2O to D2O) on the initial crystallization stage of tetragonal lysozyme

Cited by 24 publications

References 16 publications

Effect of the Simulation Box Size and Precipitant Concentration on the Behavior of Tetragonal Lysozyme Dimer

Effect of the Simulation Box Size and Precipitant Concentration on the Behavior of Tetragonal Lysozyme Dimer

The Role of Cations and Anions in the Formation of Crystallization Oligomers in Protein Solutions as Revealed by Combination of Small-Angle X-ray Scattering and Molecular Dynamics

Free Energy Change during the Formation of Crystalline Contact between Lysozyme Monomers under Different Physical and Chemical Conditions

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