Structural water stabilizes protein motifs in liquid protein phase: The folding mechanism of short β-sheets coupled to phase transition
Journal article, 2021

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.

Liquid–liquid phase separation

Quantum mechanics

Membraneless organelles

Protein folding/unfolding


Dóra Papp

University of Szeged / Szegedi Tudományegyetem

Eötvös Loránd University (ELTE)

Imola Cs Szigyártó

Hungarian Academy of Sciences

Bengt Nordén

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

András Perczel

Eötvös Loránd University (ELTE)

Tamas Beke-Somfai

Hungarian Academy of Sciences

International Journal of Molecular Sciences

16616596 (ISSN) 14220067 (eISSN)

Vol. 22 16 8595

Subject Categories

Physical Chemistry


Theoretical Chemistry





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