EPJ D Highlight - Deeper insights into protein folding

Figure 2 (a) from the original paper Caption: “Structure of staphylococcal nuclease.” © Yakubovich et al.

Physicists have published a new theoretical foundation explaining the mechanism of protein folding and unfolding in water

Investigating the structure and dynamics of so-called Meso-Bio-Nano (MBN) systems—micron-sized biological or nanotechnology entities—is a rapidly expanding field of science. Now, scientists Alexander Yakubovich and Andrey Solov'yov from MBN Research Centre in Frankfurt, Germany, have produced a new theoretical study of a protein macromolecules changing from a coil structural conformation to a globular one. Their statistic mechanics model, just published in EPJ D, describes the thermodynamic properties of real proteins in an aqueous environment, using a minimal number of free physical parameters.

In this work, the authors confirmed the validity of their theoretical calculation of dependencies of the protein heat capacities on temperature by comparing it with the corresponding experimental measurements for two proteins, namely an enzyme called staphylococcal nuclease and an oxygen and iron carrier protein called metmyoglobin. Sudden changes in temperature could result in the loss of a protein’s three-dimensional structure and function. Thus, these findings could contribute to our understanding of high-energy ions therapy on biological cells.

The authors also focus on the folding and unfolding of globular proteins at various levels of temperature in an aqueous environment. Their statistical mechanics model is inspired by a pre-existing model of solvation of hydrophobic hydrocarbons. This leads to establishing the so-called partition function of this globular protein in water environment. In turn, this helps to determine all of the protein’s thermodynamic characteristics at equilibrium. These include its heat capacity and the average number of amino acids in an unfolded conformation.

The study validates the use of an approximation of three stages of macromolecular complexes undergoing folding and unfolding transformations, instead of using fitting parameters as previously done. These results also significantly expand the possibilities of quantitative description of the structure conformation processes for other proteins obeying simple folding kinetics and complex multi-domain proteins with peculiar folding profiles.

This was our first experience of publishing with EPJ Web of Conferences. We contacted the publisher in the middle of September, just one month prior to the Conference, but everything went through smoothly. We have had published MNPS Proceedings with different publishers in the past, and would like to tell that the EPJ Web of Conferences team was probably the best, very quick, helpful and interactive. Typically, we were getting responses from EPJ Web of Conferences team within less than an hour and have had help at every production stage.
We are very thankful to Solange Guenot, Web of Conferences Publishing Editor, and Isabelle Houlbert, Web of Conferences Production Editor, for their support. These ladies are top-level professionals, who made a great contribution to the success of this issue. We are fully satisfied with the publication of the Conference Proceedings and are looking forward to further cooperation. The publication was very fast, easy and of high quality. My colleagues and I strongly recommend EPJ Web of Conferences to anyone, who is interested in quick high-quality publication of conference proceedings.

On behalf of the Organizing and Program Committees and Editorial Team of MNPS-2019, Dr. Alexey B. Nadykto, Moscow State Technological University “STANKIN”, Moscow, Russia. EPJ Web of Conferences vol. 224 (2019)

ISSN: 2100-014X (Electronic Edition)

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