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 molÁL -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.

Cryopreservation of Human iPS Cell Aggregates in a DMSO-Free Solution—An Optimization and Comparative Study

“…While DSC results of the thermophysical properties of CPAs in this study showed that isoleucine did not significantly contribute to the ice inhibition effects of the CPA cocktail overall, DE algorithm results showed that post-thaw cell survival could be increased significantly (e.g., from 48.3 to 100%) by 7.5 mM isoleucine. This result is likely a "sweet spot" between the stabilizing (Brennan et al, 2003;Bozorgmehr and Monhemi, 2015) and destabilizing (Taneja and Ahmad, 1994) effects of a hydrophobic amino acid on protein molecules in the cells. While albumin may not have a significant effect on ice formation as shown by DSC, it can act as a scavenger of free radicals alleviating oxidative stress and a carrier of waste produced from any cell damage and stress in freezing and thawing (Boldt, 2010).…”

Structure of the Cyclic, Cationic Antimicrobial Peptide (KKWWKF) in Octanol Solution: <i>in silico</i> Approach

“…4, the calculated RMSF values for c-AMP residues in simulated systems have been reported. RMSF is a measure of the flexibility of the peptide residues [27][28]. In Fig.…”

Molecular computations of preferential interactions of proline, arginine.HCl, and NaCl with IgG1 antibodies and their impact on aggregation and viscosity

“…The preferential interaction coefficient of antibodyexcipient mixtures can be measured experimentally via vapor pressure osmometry, 15 and is also accessible via simulation. 11 Numerous experimental [16][17][18][19] and simulation 6,7,[20][21][22][23] studies have been performed on the effects of amino acid and ionic excipients on proteins. However, many of the studies that have been performed focus on how excipients interact with only one or two proteins.…”