There cannot be only one

Is it hydrophobics or electrostatics? Is it in structure or in dynamics? Is it an enhanced rigidity or an increased flexibility of the protein matrix? Maybe the answer is in water?

Relevant scientists might not agree on what factor plays the most important role in increasing thermal stability of (hyper)thermophilic proteins, but they all agree that not only one is overall responsible. The enhanced thermal stability of a thermophilic protein is usually a result of a well-orchestrated symphony of more than one structural and/or dynamical factors. 

Even so, several experiments have demonstrated that, in some cases, single point mutations are capable of increasing the thermal stability of an enzyme. Whenever that is possible, it does come in handy, since a thermophilic enzyme with the desired properties doesn’t always exist or even if it exists it is not trivial to obtain. So we go back to studying how thermophilic proteins are mastering it. After all, it gets down to identifying trends that are immediately applicable for a rational design. 

Such a useful trend was recently presented by H. Gohlke and coworkers advocating for the importance of “qualitative” hydrophobic contacts on protein stability. By qualitative contacts the authors mean - and effectively demonstrate - that it is not the size of clusters of hydrophobic residues that distinguishes (hyper)thermophilic proteins from their mesophilic homologues. It is rather the fact that thermophilic, and even more hyperthermophilic proteins, are enriched in those hydrophobic contacts that have a low (favorable) energy. With this, they achieve in distinguishing thermophilic over mesophilic proteins with a discrimination accuracy of 80%, something that is not achieved as well when they use other energy components such as hydrogen bond energy for example. 

Finally and most importantly, the authors successfully locate weak spots on three different proteins where mutations will lead to an increased thermal stability, as well as non-weak spots that should not be mutated as they already stabilize the protein. Moreover, the computational efficiency with which this can be done makes the method a potentially very useful tool for protein design.

A droplet of water forms a spherical shape,
minimizing contact with the hydrophobic leaf.
Photo taken by tanakawho

Towards new thermostable proteins

ResearchMedia just published an highlight of the project THERMOS. The article "Towards new thermostable proteins" is in the new issue of the magazine International Innovation and can be read here (courtesy of RM). The article presents a nice overview of the project, a short description of what done so far and more importantly the lines of research we are following. Enjoy it! 

Solvation of halophilic proteins

My collaborators at the Institut of Biologie Structurale in Grenoble (FR), D. Madern and E. Girard along with the PhD student R. Tallon, just published an interesting work in Frontier (Microbiology/Extreme Microbiology), see the manuscript here. They report a detailed comparison between the structures of two homologous proteins: the halophilic tetrameric malate from the bacterium Salinibacter ruber (Sr) and the non-halophilic malate from the bacterium Chloroflexus aurantiacus (Ca). The core of the discussion concerns the role of hydration on extreme adaptation and relates to the different surface compositions of the two proteins, and the potential different coupling with the solvent layer.

First, the structures are resolved at very high-resolution. Second, the protein from Ca is resolved with a huge number of hydration molecules surrounding the protein surface and hydrating some internal locations. The presence of this well defined hydration layer around the non-halophilic protein allows to individuate precise closed structures of water, à voir pentagons, surrounding some hydrophobic patches of the surface. On the contrary the x-ray structure of the halophilic protein from the Sr bacterium lacks a well defined hydration layer and no clusters of water were visualized. Therefore the authors concluded that the chemical composition of the surface of the halophilic protein, enriched in negatively charged amino-acids, makes unfavorable for water to create extended closed networks of hydrogen bonds.

Then, and this is more speculative, the authors discuss how the enrichment in  negatively charged amino-acids could play a role for i) solubility in high-salt concentration and ii) salt-in effects observed in halophilic proteins.
Stay tuned on the blog because we are currently investigating how the life of a protein at ambient condition influences the stability of the water hydrogen bonds networks at the protein surface. For the moments, some hints from our past studies: i) role of protein surface on dynamics and structure of interfacial water (see here), ii) water networks at protein surface and protein stability (see here), iii) a molecular vision of protein hydration (see here), iv) proteins compositions and water dynamics (see here).

Halophile bacteria in Lake Natron, Tanzania