The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme

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

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.

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

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.

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

Abstract

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.