Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens

There have been many coarse-graining methods developed that aim to reduce the sizes of simulated systems and their computational costs. In this work, we develop a new coarse-graining method, called coarse-graining-delta (or δ-CG in short), that reduces the degrees of freedom of the potential energy surface by coarse-graining relative locations of atoms from their unit centers. Our method extends and generalizes the methods used in the coarse-grained normal mode analysis and enables us to study the roles of the individual removed atoms in a system, which have been difficult to study in molecular dynamics simulations. By applying δ-CG to coarse-grain three-point water molecules into single-point solvent particles, we successfully identify the effective hydrophilicity and hydrophobicity of all the individual protein atom types, which collectively correlate well with the known hydrophilic, hydrophobic, and amphipathic characteristics of amino acids. Moreover, our investigation shows that water's hydrogens have two roles in interacting with protein atoms. First, water molecules adjust their poses around different amino acids and their atoms, and the statistical preferences of the hydrogen poses near the atoms determine the effective hydrophilicity and hydrophobicity of the atoms, which have not been successfully addressed before. Second, the collective dynamics of the hydrogens assist the water molecules in escaping from the potential energy wells of the hydrophilic atoms. Our method also shows that coarse-graining a system mathematically leads to breaking antisymmetry of the nonbonded interactions; as a result, two interacting coarse-grained units exert different forces on each other. Our study indicates that the accuracy of coarse-grained force fields, such as the MARTINI force field and the UNRES force field, can be improved in two ways: (i) refining their potential energy functions and coefficients by analyzing the coarse-grained potential energy surface using δ-CG, and (ii) introducing non-antisymmetric interactions.

Ultra-coarse-graining modeling of liquid water

It is a great challenge to develop ultra-coarse-grained models in simulations of biological macromolecules. In this study, the original coarse-graining strategy proposed in our previous work [M. Li and J. Z. H. Zhang, Phys. Chem. Chem. Phys. 23, 8926 (2021)] is first extended to the ultra-coarse-graining (UCG) modeling of liquid water, with the N_C increasing from 4-10 to 20-500. The UCG force field is parameterized by the top-down strategy and subsequently refined on important properties of liquid water by the trial-and-error scheme. The optimal cutoffs for non-bonded interactions in the N_C = 20/100/500 UCG simulations are, respectively, determined on energy convergence. The results show that the average density at 300 K can be accurately reproduced from the well-refined UCG models while it is largely different in describing compressibility, self-diffusion coefficient, etc. The density-temperature relationships predicted by these UCG models are in good agreement with the experiment result. Besides, two polarizable states of the UCG molecules are observed after simulated systems are equilibrated. The ion-water RDFs from the ion-involved N_C = 100 UCG simulation are nearly in accord with the scaled AA ones. Furthermore, the concentration of ions can influence the ratio of two polarizable states in the N_C = 100 simulation. Finally, it is illustrated that the proposed UCG models can accelerate liquid water simulation by 114-135 times, compared with the TIP3P force field. The proposed UCG force field is simple, generic, and transferable, potentially providing valuable information for UCG simulations of large biomolecules.

Multiscale polarizable coarse-graining water models on cluster-level electrostatic dipoles

The development of a coarse-grained (CG) water model is increasingly important in CG studies of biological processes. In this work, we developed a generic CG force field of liquid water on cluster-level electrostatic dipoles. An exponential term is introduced in the non-bonded potential to adjust the well depth. The whole force field is parametrized on the AMOEBA simulation and then refined on the experimental density, dielectric permittivity and isothermal compressibility. The new CG water force field is suitable for the construction of multi-resolution water models and here the N_C = 4/5/10 systems are taken as examples. The results show that the N_C = 4/5/10 models can correctly reproduce the density and relative dielectric permittivity. The models can well predict the pressure-density/density-temperature relationships close to the all-atom or experiment results. However, the new models behave differently from other CG models in several water properties such as the air-water surface tension. Through dipole distributions, two representative polarizable configurations are captured after the N_C = 4/5/10 systems are dynamically equilibrated. Besides, the N_C = 4 model is coupled with the Martini Na⁺/Cl^- models to predict ion-relevant radial distribution functions in comparison to the Martini result. Lastly, CPU tests suggest that the new CG models can enhance simulation efficiency by factors of 20-42, compared to the TIP3P force field. The newly proposed polarizable water force field is practical and transferable and can be flexibly extended to higher coarse-graining of liquid water.