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Bioinformatics, Computational and Systems Biology

Bioinformatics, Computational and Systems Biology - Poster Session A

Poster A10 - Charge Asymmetry and Sequence Effects on Self-Coacervation of Intrinsically Disordered Proteins

Thursday, October 24, 2024

10:00 AM - 11:00 AM EST

Location: Exhibit Hall E, F & G

Presenting Author(s)

Kelsey K. Fu

Student
UCLA BMES
Los Angeles, California, United States

Primary Investigator(s)

ZW

Zhen-Gang Wang, PhD

Dick and Barbara Dickinson Professor of Chemical Engineering
California Institute of Technology
Pasadena, California, United States

Co-Author(s)

PW

Pierre Walker

PhD Candidate
California Institute of Technology, United States
SC

Shensheng Chen

Postdoctoral Fellow
California Institute of Technology, United States

Introduction: In aqueous environments, intrinsically disordered proteins (IDP) can often undergo liquid–liquid phase separation (LLPS), with the formation of a protein-rich liquid phase (coacervate) coexisted with a dilute supernatant phase. LLPS of IDP is a ubiquitous phenomenon underlying the formation of membraneless organelles that relates to myriads of essential cellular processes. The physiological function of the IDP coacervates is largely determined by their structure evolution and phase behavior. Significant progress has been made on the computational and experimental fronts in understanding the charge sequence effects on phase behavior, and structure-function relationship in self-coacervations of IDPs. However, most simulation studies assume that each protein has equal amount of positive and negative charges, while in nature typical IDPs always almost have some degree of charge asymmetry. It remains unclear how sequence effects under charge asymmetric conditions can regulate the thermodynamics and dynamics of self-coacervation in IDPs. This study explores the effects of varying sequence, charge asymmetry, and salt concentration on the self-coacervation of IDP using molecular dynamic (MD) simulations.

Materials and

Methods: We employed a coarse-grained model using LAMMPS on a HPC cluster to perform molecular dynamics (MD) simulations. The force fields utilized in the simulations, as detailed in Figure 1, include finite extensible nonlinear elastic (FENE) bonds for bonded interactions, Weeks-Chandler-Andersen potential for non-bonded interactions, and Coulombic interactions. The IDP model comprised of 50 monomers with simulations conducted using varying extents of disorder: 0.0 represents an ordered deblock and 1.0 represents a completely disordered chain. To investigate the role of charge in self-coacervation, polymer with different charge states were tested: 0, +2, +4, +8, and +12.
Three types of MD simulations were conducted. First, single-chain simulations were performed to estimate the radius of gyration so that we may determine which sequence disorder and net charges were most likely to self-coacervate. Second, from this set of IDPs, we then perform two-chain simulations to obtain the potential mean force (PMF) between chains with varying salt to further isolate those systems which should coacervate (Figure 3). Finally, with the identified systems, we performed large-scale simulations with 200 chains to obtain the interfacial density profile (Figure 5), from which the phase diagram could then be traced.
In parallel to these simulations, a mean-field liquid state theory was implemented to trace both the single-and multi-component phase diagrams with varying sequence disorders and net charges (Figure 4). These helped corroborate the simulation results and provide an efficient way to predict self-coacervation of IDPs.

Results, Conclusions, and Discussions: The study demonstrates that specific alpha values and charge densities significantly influence the self-coacervation behavior of polymer chains. Our results find that only IDPs with moderate disorder (0.0, 0.2, 0.4 alpha values) are capable of self-coacervation (Figure 2 and 3). Among these, with an introduction of charge asymmetry, polymer chains with net charges of +2 and +4 are still capable of self-coacervation, while higher charges weakly or do not self-coacervate. This behavior can be attributed to the balance between electrostatic attractions and entropic effects. At moderate charge densities, the electrostatic attractions are still strong enough to overcome the entropic penalties associated with polymer chain collapse and entanglement, leading to self-coacervation. However, at higher charge densities, the increased repulsive electrostatic forces among similarly charged groups weaken the overall interaction, disfavoring self-coacervation. These findings are consistent with our liquid-state theory up to the critical point of the solution.
When examining the effect of salt addition, our findings indicate that, for neutral IDP, the addition of salt results in a screening of the attractions between the chains and therefore inhibit self-coacervation. Inversely, in the case of charged IDP, the screening of electrostatic repulsions initially enhances self-coacervation, even enabling it in the case of IDPs which could not coacervate by themselves. However, once a high enough salt-concentration is reached, the favorable electrostatic interactions become screened instead and begin to inhibit coacervation. This re-entrant behavior of IDPs is successfully captured by our liquid-state theory, thus highlighting the reliability of this approach to reproduce the phase diagram of IDP.
In summary, our study highlights the delicate interplay between net charge, sequence disorder and salt concentration in determining the self-coacervation behavior of IDP. We have successfully traced the entire phase space described by these variables, thus providing a powerful map for the prediction of IDP self-coacervation. These findings provide valuable insights for the design and optimization systems for various applications, emphasizing the need to carefully tune these parameters to achieve desires coacervation properties.

Acknowledgements (Optional):