@phdthesis{GerailiDaronkola2021,
  author    = {Geraili Daronkola, Hosein},
  title     = {The role of acidic amino acids in the hydration and stabilization of halophilic proteins},
  doi       = {10.25932/publishup-51671},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516713},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xx, 111},
  year      = {2021},
  abstract  = {Proteins of halophilic organisms that accumulate molar concentrations of KCl in their cytoplasm have much higher content in acidic amino acids than proteins of mesophilic organisms. It has been proposed that this excess is necessary to maintain proteins hydrated in an environment with low water activity: either via direct interactions between water and the carboxylate groups of acidic amino acids or via cooperative interactions between acidic amino acids and hydrated cations, which would stabilize the folded protein. In the course of this Ph.D. study, we investigated these possibilities using atomistic molecular dynamics simulations and classical force fields. High quality parameters describing the interaction between K+ and carboxylate groups present in acidic amino acids are indispensable for this study. We first evaluated the quality of the default parameters for these ions within the widely used AMBER ff14SB force field for proteins and found that they perform poorly. We propose new parameters, which reproduce solution activity derivatives of potassium acetate solutions up to 2 mol/kg and the distances between potassium ions and carboxylate groups observed in x-ray structures of proteins. To understand the role of acidic amino acids in protein hydration, we investigated this aspect for 5 halophilic proteins in comparison with 5 mesophilic ones. Our results do not support the necessity of acidic amino acids to keep folded proteins hydrated. Proteins with a larger fraction of acidic amino acids indeed have higher hydration levels. However, the hydration level of each protein is identical at low (b_KCl = 0.15 mol/kg) and high (b_KCl = 2 mol/kg) KCl concentration. It has also been proposed that cooperative interactions between acidic amino acids with nearby hydrated cations stabilize the folded protein and slow down its solvation shell; according to this theory, the cations would be preferentially excluded from the unfolded structure. We investigate this possibility through extensive free energy calculation simulations. We find that cooperative interactions between neighboring acidic amino acids exist and are mediated by the ions in solution but are present in both folded and unfolded structures of halophilic proteins. The translational dynamics of the solvation shell is barely distinguishable between halophilic and mesophilic proteins; therefore, such a cooperative effect does not result in unusually slow solvent dynamics as has been suggested.},
  language  = {en}
}