Precipitant ions influence on lysozyme oligomers stability investigated by molecular dynamics simulation at different temperatures

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

“…We investigated three combinations of such ions: when both of them are bound with the monomers, when only Na ions are embedded in the protein structure, and without both Na and Cl ions incorporated into the lysozyme structure (columns 2, 3, and 4 of Table 1, respectively). These precipitant conditions were chosen because, as in our previous work [9], it was found that MD results on lysozyme oligomers stability investigations are consistent with the SAXS experiments [5,6] only when accounting for all precipitant ions associated with the protein.…”

“…We investigated the same 3 types of dimer models as in [9]: with Na and Cl ions associated with the protein molecule (3 Na ions and 4 Cl ions per monomer), with lysozymebound Na ions (one ion per monomer) and without precipitant ions incorporated into the dimer structure. The protonation states of amino acid residues at pH 4.5 (in accordance with the experimental conditions [15]) were assigned by the PROPKA server [16].…”

“…The free energy of binding two monomers was computed by the molecular mechanics/generalized Born (Poisson-Boltzmann) surface area (MM/GB(PB)SA) method [9], which combines molecular mechanics and the solution of the Poisson-Boltzmann equation. The applied module gmx_MMPBSA [25] version 1.4.0, in combination with the MMPBSA.py script [26] and the AmberTools20 package [27], made it possible to use the MM/GB(PB)SA method with the generalized Born model [28] when processing the MD simulation results carried out using the GROMACS program.…”

“…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]. This technique consists of the MD modeling of isolated from the protein crystal lattice oligomers, and the subsequent analysis of the mobility of their atoms.…”

“…This technique consists of the MD modeling of isolated from the protein crystal lattice oligomers, and the subsequent analysis of the mobility of their atoms. Using the proposed method, the type of octamer formed in the pre-crystallization solution of lysozyme [8] has already been identified, and the influence of the precipitant ions built into the structure of the protein on the stability of monomer, dimer, and octamer has been determined [9]. However, it has not yet been clarified whether the change in free energy when binding two monomers correlates with the stability of dimers estimated by root mean square fluctuations (RMSF) graphs.…”