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

Yuliya Kordonskaya,Vladimir Timofeev,Margarita Marchenkova,Yury Pisarevsky,Mikhail Kovalchuk,Yulia Dyakova

doi:10.3390/cryst11091121

Abstract

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.

Highlights

Due to its availability and ease of its crystallization, the largest number of studies on the growth of protein crystals and the effect on the conditions of the crystal structures are devoted to hen egg white lysozyme (HEWL)
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]
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]

Summary

Introduction

A.V. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 59, Leninskii Prospect, RU 119333 Moscow, Russia; Abstract: 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. Shubnikov Institute of Crystallography, Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences, 59, Leninskii Prospect, RU 119333 Moscow, Russia; Abstract: 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. Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations

Methods

Results

Conclusion