Unveiling the entropic role of hydration water in SOD1 partitioning within FUS condensate

TL;DR

This study addresses how hydration water governs SOD1 partitioning into biomolecular condensates and crowder environments. It integrates implicit OPEP simulations with an explicit CVF water model to map hydration effects onto water-dependent coordinates, projecting free energy onto hydration-related macrostates. The analysis reveals three hydration-state macrostates for SOD1 in BSA (A,B,C) and a hydration-dominated basin for SOD1 in FUS, with hydration entropy and enthalpy contributions explaining the observed partitioning differences. The work clarifies the role of water in cellular phase separation and offers a framework to bridge microscopic solvent effects with mesoscale condensate dynamics, with potential implications for ALS-related mechanisms and larger-scale simulations.

Abstract

Biological processes like the sequestration of Superoxide Dismutase 1 (SOD1) into biomolecular condensates such as FUS and stress granules are essential to understanding disease mechanisms, including amyotrophic lateral sclerosis (ALS). Our study demonstrates that the hydration environment is crucial in these processes. Using the advanced CVF water model, which captures hydrogen-bond networks at the molecular level, we show how water greatly impacts SOD1's behavior, residency times, and transition rates between different associative states. Importantly, when water is included to hydrate an implicit solvent model (OPEP), we gain a new perspective on the free energy landscape of the system, leading to a conclusion that clarifies that suggested by OPEP alone. While the OPEP model indicated that Bovine Serum Albumin (BSA) crowders reduce SOD1's partition coefficient (PC) mainly due to nonspecific interactions with BSA, our enhanced explicit-water approach reveals that the hydration entropy behavior in BSA drives the observed decrease in PC. This highlights that explicitly modeling water is essential for accurately understanding protein-crowder interactions and their biological relevance, emphasizing water's role in cellular phase separation and disease-related processes.

Figures (13)

• Figure 1: OPEP-dis configurations for SOD1 sequestration in BSA (left) and FUS (right) crowded environments with water not shown. Blue beads represent cells occupied by SOD1, while red beads indicate cells occupied by the crowder. Water molecules (not shown) fill all the available volume left by the proteins. Blue lines mark the boundaries of the simulation box (255 Å), where pbc apply.
• Figure 2: OPEP-dis configurations for SOD1 sequestration in BSA (left) and FUS (right) crowded environments with water explicitly shown. For clarity, we represent a 2D section of the 3D system. Each volume cell is represented by a colored point: Cyan for bulk water; Blue for SOD1; Red for CWD; Magenta for water hydrating SOD1; Yellow for water hydrating CWD; Black for water hydrating both (mixed category).
• Figure 3: Free energy $\Delta G$ landscape of SOD1 into BSA (left panels) and FUS (right panels) solutions. Top panels: $\Delta G\left(\Delta E_i, {\cal C}_i\right)$, calculated from implicit solvent simulations. Bottom panels: $\Delta G \left(\Delta N_{{\rm hyd, SOD1},i}, {\cal C}_i \right)$, calculated from explicit solvent simulations. Magenta and blue lines indicate the distances of one and two hydration shells, $d_{\rm Hyd.~shell}$ and $2d_{\rm Hyd.~shell}$, respectively. Lower-left panel (SOD1-BSA in explicit solvent): Black dashed lines separate the landscape into three regions corresponding to A, B, and C states, as described in the text. The vertical dashed line, separating A from B and C, is at ${\cal C}=2d_{\rm Hyd.~shell}$. The value of $\Delta G$ is color-coded, as shown in the bars on the right of each panel.
• Figure 4: Typical configurations of associative states A, B, C for SOD1 in BSA crowders. The states are defined for individual SOD1 (in green). The other SOD1 proteins are in blue, and the BSA proteins are in red. In each configuration, water molecules (not shown) fill all the available volume left by the proteins. Blue lines mark the boundaries of the simulation box (255 Å) with pbc. Left: State A, with SOD1 in contact with BSA. Center: State B, with SOD1-SOD1 contact. Right: State C, with SOD1 away from other proteins.
• Figure 5: Kinetcs analysis of SOD1 in BSA crowders. (a): Schematic hydration free energy landscape for SOD1 in the BSA solution. The blue region corresponds to $\Delta G /k_BT\lesssim 0.5$, green to $0.5 \lesssim \Delta G/k_BT \lesssim 2$, and red to $2 \lesssim \Delta G/k_BT \lesssim 4.5$. A, B, and C labels denote the associative states described in Fig. \ref{['fig:sod1_BSA_configurations']}. (b): Time the system spends in each of the three states relative to the total simulation time. (c): Frequency of transitions among the three states, measured as the number of transitions per unit of time. (d): Probability density $\rho_P(t_R)$ of SOD1 residence time $t_R$ in states A (black circles), B (red squares), or C (green diamonds), with log-normal distribution fits (lines with matching colors; with fitting parameters in Table \ref{['table:lognorm_fit']}). Results are averages of data in Figs. (\ref{['fig:transition_residence_0_1']}--\ref{['fig:transition_residence_8_9']}).