How Can a Free Amino Acid Stabilize a Protein? Insights from Molecular Dynamics Simulation

Abstract

Amino acids such as proline are known as natural osmolytes that can stabilize proteins. But, there is no distinct mechanism at the molecular levels that can explain the stabilization effects of such osmolytes. In this paper, for the first time, the molecular level mechanism of protein stabilization by amino acid proline was studied using molecular dynamics simulation, which led to the following interesting points. Simulations were performed at room and high temperatures using lysozyme as a protein model. Although lysozyme was partially unfolded in the aqueous solution at high temperatures, the structure remained relatively native in the presence of 3 mol·L−1 proline. Protein residues showed slower dynamics in aqueous proline solution than that in water. These results are in agreement with experimental observations that show enhanced protein thermal stability in the presence of proline. It was also found that proline molecules are excluded from the protein surface and water molecules in the hydration shell around the protein increase, thus inducing thermodynamic stabilization of the protein. Moreover, it was shown that proline molecules form molecular aggregates in the solution, in agreement with previous experimental observations. We found that these aggregates can increase the order of water molecules and also the water–water hydrogen bond strength. This also leads to higher thermal stability of the protein in such solutions. The results of this paper shed some light on the molecular mechanism of protein stabilization by natural amino acids.