Studying the mechanism of phase separation in aqueous solutions of globular proteins via molecular dynamics computer simulations

Abstract

Proteins are the most abundant biomacromolecules in living cells, where they perform vital roles in virtually every biological process. To maintain their function, proteins need to remain in a stable...

The Effect of Arginine on the Phase Stability of Aqueous Hen Egg-White Lysozyme Solutions

“…We have therefore performed the simulation of pure arginine at the largest concentration that has been studied experimentally, namely 0.3 M. As expected, and suggested previously [ 9 ], the free arginine molecules show an extensive trend to self-associate, as seen from the arginine–arginine pair distribution function shown in Figure 2 . Clusters of two and more arginine molecules are formed (see insert of Figure 2 ), connecting to each other mostly through head-to-tail hydrogen bonding and thus aligning their hydrophobic chains, the same mechanism that was previously observed in computer simulations of globular proteins [ 13 , 15 ].…”

“…The concentration of the added free arginine molecules was kept the same as in the case of the pure arginine simulation. The simulation conditions ( T = 267 K and = 93 mg mL −1 ) were chosen in the range where the HEWL solutions in the absence of arginine undergo phase separation [ 15 ].…”

“…In the case where arginine is absent from the solution, the two protein molecules on average come much closer together (i.e., almost 1 nm) compared to the case where the 0.3 M free arginine is present in the solution. The radius of gyration for an HEWL molecule is approximately 1.38 nm [ 15 ]; this shows that in the case of no arginine, HEWL molecules come into close contact, while in the presence of free arginines no self-association of HEWL occurs.…”

“…These positions are visualized in Figure 7 . Strikingly, these amino acids are situated at the protein surface locations that were previously identified to be involved in initiating the contacts between the HEWL molecules [ 15 ]. Another interesting observation that is also consistent with our previous results is the occurrence of a particular amino acid type among these locations; while an arginine residue was previously found to be particularly instrumental in facilitating the initial contacts between two protein molecules, it is also the most common residue found to be surrounded by arginine molecules from the solution ( Figure 7 and Table 2 ).…”

“…In our previous work, the mechanism of self-association of several globular proteins was studied via a molecular dynamics (MD) simulation. By performing an extensive analysis of intermolecular residue–residue interactions, we showed that arginine is of paramount importance in the initial stage of the aggregation of the HEWL and -D crystallin [ 15 ]. The results suggest that the partial parallel and anti-parallel stacking of arginine methylene groups on different proteins occurs, stabilizing the initial protein contacts.…”