EPJ E - How do protein binding sites stay dry in water?

In a report that has just been published in EPJE, researchers from the National University of the South in Bahía Blanca, Argentina studied the condition for model cavity and tunnel structures resembling the binding sites of proteins to stay dry without losing their ability to react, a prerequisite for proteins to establish stable interactions with other proteins in water.

E.P. Schulz and colleagues used models of nanometric-scale hydrophobic cavities and tunnels to understand the influence of geometry on the ability of those structures to stay dry in solution.

The authors studied the filling tendency of cavities and tunnels carved in a system referred to as an alkane-like monolayer, chosen for its hydrophobic properties, to ensure that no factors other than geometrical constraints determine their ability to stay dry.

They determined that the minimum size of hydrophobic cavities and tunnels that can be filled with water is on the order of a nanometer. Below that scale, these structures stay dry because they provide a geometric shield; if a water molecule were to penetrate the cavity it would pay the excessive energy cost of giving up its hydrogen bonds. By comparison, water fills carbon nanotubes that are twice as small (but slightly less hydrophobic) than the alkane monolayer, making them less prone to stay dry.

The authors also showed that the filling of nanometric cavities and tunnels with water is a dynamic process that goes from dry to wet over time. They believe that water molecules inside the cavities or tunnels are arranged in a network of strong cooperative hydrogen bonds. Their disruption by means of thermal fluctuations results in the temporary drying of the holes until new bonds are re-established.

One of the many potential applications is in biophysics, to study water-exclusion sites of proteins, and understand the physical phenomenon linked to the geometry of those sites, underpinning the widespread biological process of protein-protein associations.

Behavior of water in contact with model hydrophobic cavities and tunnels and carbon nanotubes.
E.P. Schulz et al., Eur. Phys. J. E (2011) 34: 114, DOI 10.1140/epje/i2011-11114-8

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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