Molecular mechanisms behind protein halo tolerance
Final Report Abstract
Halophilic organisms (halophiles), unlike most life on Earth, have the uncanny ability to survive at molar external NaCl concentrations. To counterbalance the high osmotic stress induced by their environment, some halophiles accumulate equivalent concentrations of KCl in their cytoplasm. Proteins of halophiles have adapted to this condition by changing their amino acid composition, the most dramatic feature being that halophilic proteins are on average richer in acidic amino acids than mesophilic ones. In this project we used molecular dynamics simulations with classical potential energy functions (force fields) to investigate molecular scale mechanisms that can explain this difference in amino acid composition. To do so, we required force fields for proteins, water, and ions with the correct balance of interactions between all the species, both at low and high (up to several molal) KCl concentrations. The force fields we used met this requirement for most interactions. The exception was the interaction potential between potassium and carboxylate ions, which was of very poor quality and which we optimized to reproduce reliable experimental observables. Our next step was to identify 5 pairs of halophilic and mesophilic proteins. Atomistic molecular dynamics simulations of these 10 proteins revealed that proteins with a larger fraction of acidic amino acids indeed have higher hydration levels, as measured by the concentration of water in their hydration shell and the number of water/protein hydrogen bonds. However, the hydration level of each protein is identical at low and high KCl concentrations, indicating that excess acidic amino acids are not necessary to maintain proteins hydrated at high salt concentration as suggested in the literature. It has also been proposed that cooperative interactions between acidic amino acids in halophilic proteins and hydrated cations could stabilize the folded protein structure and would lead to slower dynamics of the solvation shell. We found that translational dynamics of solvation shells is barely distinguishable between halophilic and mesophilic proteins, but that nevertheless such a cooperative effect exists, although it is weak. We quantified the magnitude of the cooperative effect through free energy calculations, which also revealed that this mechanism has an electrostatic origin and depends on subtle interactions between two acidic amino acids and their neighbors. Importantly, this study revealed that the cooperative effect does not stem from rigid orientations of neighboring acid amino acids, as previously believed. This research revealed that some commonly believed mechanisms believed to explain the abundance of acidic amino acids in halophiles do not hold, whereas others do.
Publications
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Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids. Biophysical Journal, 120(13), 2746-2762.
Geraili, Daronkola Hosein & Vila, Verde Ana
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The Role of Acidic Amino Acids in the Hydration and Stabilization of ¨ Halophilic Proteins; Die Rolle Saurer Amino Sauren Bei Der Hydratation Und Stabilisierung Von Halophilen Proteinen. PhD Thesis, University of Potsdam, Germany, 2021
H. Geraili Daronkola
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Prevalence and mechanism of synergistic carboxylate-cation-water interactions in halophilic proteins. Biophysical Journal, 122(12), 2577-2589.
Geraili, Daronkola Hosein & Vila, Verde Ana
