Effects of Conformational Constraint on Peptide Solubility Limits

Abstract

Liquid-liquid phase separation of proteins preferentially involves intrinsically disordered proteins or disordered regions. Understanding the solution chemistry of these phase separations is key to learning how to quantify and manipulate systems that involve such processes. Here, we investigate the effect of cyclization on the liquid-liquid phase separation of short polyglycine peptides. We simulated separate aqueous systems of supersaturated cyclic and linear GGGGG and observed spontaneous liquid-liquid phase separation in each of the solutions. The cyclic GGGGG phase separates less robustly than linear GGGGG and has a higher aqueous solubility, even though linear GGGGG has a more favorable single molecule solvation free energy. The versatile and abundant interpeptide contacts formed by the linear GGGGG stabilize the condensed droplet phase, driving the phase separation in this system. In particular, we find that van der Waals close contact interactions are enriched in the droplet phase as opposed to electrostatic interactions. An analysis of the change in backbone conformational entropy that accompanies the phase transition revealed that cyclic peptides lose significantly less entropy in this process as expected. However, we find that the enhanced interaction enthalpy of linear GGGGG in the droplet phase is enough to compensate for a larger decrease in conformational entropy.

Figure 1.

Snapshots from MD simulations showing the peptide droplet (red/purple) and aqueous (blue/cyan) phases in the cGGGGG (A) and GGGGG (B) systems at 0, 10, and 350 ns of the MD simulation. Peptides shown in gray are nondroplet clusters, i.e., peptides with <4 Å interpeptide contacts but not connected to the main droplet. The abundance of this state in the 10 ns cGGGGG system demonstrates the slower phase separation.

Figure 2.

Plot of the number of aqueous peptides vs time for each simulated system.

Figure 3.

Molecular image of the cyclic peptide stacking H-bond interactions present abundantly in the droplet phase.

Figure 4.

Average conformational entropy values for aqueous (blue) and liquid droplet (red) phase peptides for the linear and cyclic peptide systems.

Figure 5.

Average interaction enthalpy values for aqueous (blue) and liquid droplet (red) phase peptides. Error bars represent the standard error of the H_int distribution.

Figure 6.

Electrostatic and van der Waals interaction enthalpy values for aqueous (blue) and liquid droplet (red) phase peptides. Error bars represent the standard error of the H_int distribution.