Liquid-Liquid Phase Separation Prediction of Proteins in Salt Solution by Deep Neural Network

Interaction-Based Perspective for Designing Polymer Biomaterial: A Strategic Approach to the Chitosan-Glycerophosphate System

The conventional approach for developing any polymeric biomaterial is to follow protocols available in the literature and/or perform trial-and-error runs without a scientific basis. Here, we propose an analysis of a complex overlay of molecular interactions between drugs and polymers that provides a strategic pathway for biomaterial development. First, this work provides an innovative interaction-based method for developing an ocular formulation involving in situ gelling chitosan, gelatin, and glycerophosphate systems. A systematic interaction study is conducted based on the measurement of hydrodynamic radius, zeta potential, and viscosity with the sequential addition of formulation components. The increase in the hydrodynamic radius of the polymer with the addition of drugs can be interpreted as better diffusion of the drug inside the charged polymer chains and vice versa. Based on the knowledge of these interactions, a formulation has been designed that shows better drug release results with extended and sustained release compared to literature protocols, hence accentuating the importance of this study. An in-depth analysis of interactions can lead to a better understanding of the system. Second, we demonstrate the development of two dual-drug biomaterial systems, i.e., an in situ gelling and a liquid formulation at ocular surface temperature from the same polymers, which can be used as an ocular antiglaucoma formulation. Prior knowledge of the interactions between the drug polymers can be used to design a better formulation. The demonstrated application of this interaction-based protocol development can be extended universally to any biomaterial. This would provide a comprehensive idea about the properties and interactions of polymers and drugs, which can also serve as a base/starting point for a new formulation/biomaterial development.

Elucidating the influence of electrostatic force on the re-arrangement of H-bonds of protein polymers in the presence of salts

Polyampholytes/proteins have an intriguing network of hydrogen bonds (H-bonds), especially their secondary structure, which plays a crucial role in determining the conformational stability of the polymer. The changes in protein secondary structure in the protein-salt system have been extensively deciphered by researchers, yet their pathways for breakage and recreation are unknown. Understanding the mechanism of protein conformational changes towards their biological activities, like protein folding, remains one of the main challenges and requires multiscale analysis of this strongly correlated system. Herein, salts have been used to reveal the re-arrangement behavior in the H-bond network of proteins under the influence of electrostatic interactions, as the strength of electrostatic forces is much stronger than that of H-bonds. At lower salt concentrations, there are negligible changes in the secondary structures as the electrostatic forces induced by the salt ions are less. Later, the existing H-bonds break and reconstruct new H-bonds at higher salt concentrations due to the influence of the stronger electrostatic interaction induced by the large number of salt ions. Molecular dynamics (MD) simulations and FTIR studies have been used rigorously to decipher the reason behind the re-arrangement of the H-bonds within gelatin (protein). The re-arrangement in the H-bond has also been observed with time from simulations and experiments. Thus, this study could provide a fresh perspective on the conformational changes of polyampholytes/proteins and will also influence the studies of protein folding-unfolding interaction in the presence of salt ions.

Electrostatic-Dominated Conformational Fluctuations and Transition States of Phase Separation in Charge-Balanced Protein Polymer

Hydration of the protein/polymer is the most important aspect of stability. It is well-known that salts alter the charged polymer's electrostatic forces, ultimately impacting its conformations in solution. The solvent effects lead to certain conformational fluctuations. Previous studies have shown the screening of electrostatic repulsion within the charge-imbalanced protein following charge inversion owing to counterion condensation and phase separation. This article studies conformation stability and phase separation of charge-balanced gelatin (a protein polymer at the isoelectric point) with the addition of different salts. A phenomenon has been reported where the electrostatic effect of salts results in conformational fluctuations in gelatin due to its insufficient hydrations (termed as starvation), which scales with salt concentration. This article also presents different transition states for charge-balanced proteins prior to phase separation. It is concluded that phase separation of a charge-balanced protein passes through a stable state followed by an unstable transition state, where certain unique interactions with salts occur.

Towards sequence-based principles for protein phase separation predictions

The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.

Comparison of Biomolecular Condensate Localization and Protein Phase Separation Predictors

Research in the field of biochemistry and cellular biology has entered a new phase due to the discovery of phase separation driving the formation of biomolecular condensates, or membraneless organelles, in cells. The implications of this novel principle of cellular organization are vast and can be applied at multiple scales, spawning exciting research questions in numerous directions. Of fundamental importance are the molecular mechanisms that underly biomolecular condensate formation within cells and whether insights gained into these mechanisms provide a gateway for accurate predictions of protein phase behavior. Within the last six years, a significant number of predictors for protein phase separation and condensate localization have emerged. Herein, we compare a collection of state-of-the-art predictors on different tasks related to protein phase behavior. We show that the tested methods achieve high AUCs in the identification of biomolecular condensate drivers and scaffolds, as well as in the identification of proteins able to phase separate in vitro. However, our benchmark tests reveal that their performance is poorer when used to predict protein segments that are involved in phase separation or to classify amino acid substitutions as phase-separation-promoting or -inhibiting mutations. Our results suggest that the phenomenological approach used by most predictors is insufficient to fully grasp the complexity of the phenomenon within biological contexts and make reliable predictions related to protein phase behavior at the residue level.