Role of entropy in determining the phase behavior of protein solutions induced by multivalent ions

Quantitative Prediction of Protein-Polyelectrolyte Binding Thermodynamics: Adsorption of Heparin-Analog Polysulfates to the SARS-CoV-2 Spike Protein RBD

Interactions of polyelectrolytes (PEs) with proteins play a crucial role in numerous biological processes, such as the internalization of virus particles into host cells. Although docking, machine learning methods, and molecular dynamics (MD) simulations are utilized to estimate binding poses and binding free energies of small-molecule drugs to proteins, quantitative prediction of the binding thermodynamics of PE-based drugs presents a significant obstacle in computer-aided drug design. This is due to the sluggish dynamics of PEs caused by their size and strong charge-charge correlations. In this paper, we introduce advanced sampling methods based on a force-spectroscopy setup and theoretical modeling to overcome this barrier. We exemplify our method with explicit solvent all-atom MD simulations of the interactions between anionic PEs that show antiviral properties, namely heparin and linear polyglycerol sulfate (LPGS), and the SARS-CoV-2 spike protein receptor binding domain (RBD). Our prediction for the binding free-energy of LPGS to the wild-type RBD matches experimentally measured dissociation constants within thermal energy, k B T, and correctly reproduces the experimental PE-length dependence. We find that LPGS binds to the Delta-variant RBD with an additional free-energy gain of 2.4 k B T, compared to the wild-type RBD, due to the additional presence of two mutated cationic residues contributing to the electrostatic energy gain. We show that the LPGS-RBD binding is solvent dominated and enthalpy driven, though with a large entropy-enthalpy compensation. Our method is applicable to general polymer adsorption phenomena and predicts precise binding free energies and reconfigurational friction as needed for drug and drug-delivery design.

From structure and dynamics to biomolecular functions: The ubiquitous role of solvent in biology

Biological activity requires a solvent that can provide a suitable environment, which satisfies the twin need for stability and the ability to change. Among all the solvents water plays the most important role. We review, analyze, and comment on recent works on the structure and dynamics of water around biomolecules and their role in specific biological functions. While studies in the past have focused on understanding the biomolecule-water interactions through a hydration layer; recently the attention has shifted towards understanding functions at a molecular level. Such a microscopic understanding clearly requires elucidation of detailed dynamical processes where solvent molecules play an important role. Finally, we comment on the advances made in understanding the role of water inside a biological cell.

Surfactancy in a tadpole model of proteins

We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with 'tadpole' constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.

Trivalent cation-induced phase separation in proteins: ion specific contribution in hydration also counts

Multivalent (specifically trivalent) metal ions are known to induce microscopic phase separation (commonly termed as liquid-liquid phase separation (LLPS)) in negatively charged globular proteins even at ambient temperatures, the process being mostly driven by protein charge neutralization followed by aggregation. Recent simulation studies have revealed that such self-aggregation of proteins is entropy driven; however, it is associated with a solvation effect, which could as well be different from the usual notion of hydrophobic hydration. In this contribution we have experimentally probed the explicit change in hydration associated with ion-induced LLPS formation of a globular protein bovine serum albumin (BSA) at ambient temperature using FIR-THz FTIR spectroscopy (50-750 cm^-1; 1.5-22.5 THz). We have used ions of different charges: Na⁺, K⁺, Ca²⁺, Mg²⁺, La³⁺, Y³⁺, Ho³⁺ and Al³⁺. We found that all the trivalent ions induce LLPS; the formation of large aggregates has been evidenced from dynamic light scattering (DLS) measurements, but without perturbing the protein structure as confirmed from circular dichroism (CD) measurements. From the frequency dependent absorption coefficient (α(ν)) measurements in the THz frequency domain we estimate the various stretching/vibrational modes of water and we found that ions, forming LLPS, produce definite perturbation in the overall hydration, the extent of which is ion specific, invoking the definite role of hydrophilic (electrostatic) hydration of ions in the observed LLPS process.