Multiscale Simulations and Experiments Reveal Interfacial Microenvironments within Biological Condensates Formed by Elastin-like Polypeptides

Core Concepts

Diblock elastin-like polypeptides undergo microphase separation, producing condensates with an interfacial environment that features a blend of hydrophobic and hydrophilic regions, which is crucial for their stability and organization.

Abstract

The study combines multiscale simulations and fluorescence lifetime imaging microscopy (FLIM) experiments to investigate the structural organization and solvation environment of condensates formed by diblock elastin-like polypeptides (ELPs).
Key highlights:

Multiscale simulations reveal that diblock ELPs undergo microphase separation, with the more hydrophobic blocks localizing towards the condensate interior. This results in heterogeneous microenvironments within the condensates.
The simulations show that ELP condensates form gyroid-like structures, which deviate from the weak micelle-like structures previously proposed for diblock ELPs in solution.
FLIM experiments confirm the microphase separation, demonstrating that the hydrophobic and hydrophilic ends of the ELP diblocks exhibit different physicochemical properties.
Atomistic simulations show that the condensate interior is significantly solvated, with over 75% of hydrogen bonds being between protein and water. This is due to the lack of secondary structure formation in the ELPs, which prevents them from meeting their own hydrogen bonding needs.
The stability of the ELP condensates exhibits a strong correlation with the hydrophobicity of the guest residues, as measured by the water-octanol or water-POPC-interface transfer free energies. This supports the presence of an interfacial environment within the condensates, where both hydrophobic and hydrophilic regions coexist.
The frustration between the hydrophobic and hydrophilic regions, imposed by the ELP sequence, is crucial for maintaining the interfacial environment and the high solvation within the condensates.

Stats

The transition temperature (Tt) of ELP condensates is negatively correlated with the computed surface tension (τ) of the condensates.
The radius of gyration (Rg) of ELP peptides in the condensates is comparable to that of an ideal Gaussian chain, indicating significant expansion upon phase separation.
The water hydrogen bond density is negatively correlated with the condensate transition temperature (Tt), suggesting more water molecules are engaged in hydrogen bonding in more hydrophobic condensates.

Quotes

"Surprisingly, microphase separation did not produce lamellar morphology as expected for block copolymers with equal volume fraction of the two blocks."
"Strikingly, given the importance of water molecules, the average number of hydrogen bonds per residue remained relatively constant across condensates, even when the amount of water inside the condensate varied by almost two folds."
"Therefore, we hypothesize that each water molecule in more hydrophobic condensates must engage more in hydrogen bonding than each water in hydrophilic condensates."

Key Insights Distilled From

Microphase Separation Produces Interfacial Environment within Diblock Biomolecular Condensates

by Latham,A. P.... at www.biorxiv.org 04-02-2023

https://www.biorxiv.org/content/10.1101/2023.03.30.534967v3

Deeper Inquiries

How do changes in solution conditions, such as temperature or salt concentration, affect the microphase separation and interfacial properties of ELP condensates?

Changes in solution conditions, such as temperature or salt concentration, can significantly impact the microphase separation and interfacial properties of ELP condensates. For example, variations in temperature can alter the critical temperature at which phase separation occurs, affecting the stability and organization of the condensates. Higher temperatures can promote phase separation, leading to more pronounced microphase separation and potentially different morphologies of the condensates. On the other hand, lower temperatures may hinder phase separation, resulting in less defined microenvironments within the condensates.
Similarly, changes in salt concentration can influence the electrostatic interactions and solvation environment within the condensates. Higher salt concentrations can screen electrostatic interactions between the protein molecules, potentially disrupting the phase separation process. This could lead to changes in the interfacial properties of the condensates, affecting the distribution of hydrophobic and hydrophilic residues within the microphase-separated regions. Lower salt concentrations, on the other hand, may enhance phase separation and promote the formation of well-defined interfacial environments within the condensates.
Overall, variations in solution conditions can modulate the thermodynamic stability, structural organization, and interfacial properties of ELP condensates, highlighting the sensitivity of these biomolecular assemblies to their environment.

How might higher-order effects become important in more complex protein sequences, and what are the potential limitations of the mean field interpretation of condensate stability based on individual amino acid hydrophobicity?

In more complex protein sequences, higher-order effects can become important due to the intricate interplay between multiple amino acids and their interactions within the condensates. While a mean field interpretation based on individual amino acid hydrophobicity can provide valuable insights into the stability of condensates, it may have limitations when applied to more complex sequences.
One limitation is the neglect of cooperative effects and synergistic interactions between amino acids in the sequence. In complex proteins, the combined contributions of multiple residues can lead to non-additive effects on phase behavior and condensate stability. These higher-order effects can result in emergent properties that cannot be fully captured by a simple additive model based on individual amino acid hydrophobicity.
Additionally, the mean field interpretation may overlook the influence of sequence-specific motifs, post-translational modifications, or structural features that play a crucial role in determining the organization and properties of the condensates. Complex protein sequences may exhibit non-linear relationships between amino acids, leading to deviations from the predictions of a mean field model.
Therefore, in more complex protein sequences, considering higher-order effects, sequence-specific interactions, and structural motifs is essential to fully understand the behavior of biomolecular condensates and their stability.

Could the principles of microphase separation and interfacial environment uncovered in this study for ELP condensates be generalized to other types of biomolecular condensates formed by intrinsically disordered proteins?

The principles of microphase separation and interfacial environment uncovered in the study of ELP condensates have the potential to be generalized to other types of biomolecular condensates formed by intrinsically disordered proteins (IDPs).
Intrinsically disordered proteins often exhibit similar phase separation behavior driven by multivalent interactions, such as electrostatic, π-π, and hydrophobic interactions. The interspersion of hydrophobic and hydrophilic residues within IDPs can lead to the formation of microphase-separated regions with distinct interfacial properties, similar to what was observed in ELP condensates.
The concept of frustration, where hydrophobic and hydrophilic residues cannot completely segregate due to sequence constraints, is likely to be a common feature in many IDPs, contributing to the interfacial nature of the condensates. The presence of water molecules maintaining hydrogen bonds with exposed peptide backbones, even in residues with hydrophobic side chains, may also be a prevalent characteristic in other biomolecular condensates.
Therefore, the principles of microphase separation and interfacial environment identified in ELP condensates could serve as a foundational framework for understanding the behavior of a broad range of biomolecular condensates formed by intrinsically disordered proteins. Further studies on different IDPs and their phase separation properties can help validate and extend these principles to diverse biological systems.