Comparative Study of Water-Mediated Interactions between Hydrophilic and Hydrophobic Nanoscale Surfaces

Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores

Phase separation of biomolecules underlies the formation and regulation of various membraneless condensates in cells. How condensates function reliably while surrounded by heterogeneous and dynamic mixtures of biomolecular components with specific and nonspecific interactions is yet to be understood. Studying multicomponent biomolecular mixtures with designer peptides has recently become an attractive avenue for learning about physicochemical principles governing cellular condensates. In this work, we employed long-timescale atomistic simulations of multicomponent tripeptide mixtures with all residue substitutions to illuminate the nature of direct and water-mediated interactions in a prototypical cellular condensate environment. We find that peptide mixtures form clusters with inverse hydrophobic order. Most multivalent and charged residues are localized in the cluster's core, with a large fraction of nonaromatic hydrophobic residues remaining on the surface. This inverse hydrophobic order in peptide clusters is partly driven by the expulsion of nonspecifically bound water molecules following peptide cluster growth. The growth of clusters is also accompanied by the formation of increasing numbers of specific water-mediated interactions between polar and charged residues. While the present study focused on the condensation of short peptide motifs, the general findings and analysis techniques should be helpful for future studies on larger peptides and protein condensation.

Effect of Hydrophobic Moieties on the Assembly of Silica Particles into Colloidal Crystals

To boost the implementation of colloidal crystals (CCs) in separation science, the effects of the most common chromatographic reversed phases, that is, butyl and octadecyl, on the assembly of silica particles into CCs and on the optical properties of CCs are investigated. Interestingly, particle surface modification can cause phase separation during sedimentation because the assembly is highly sensitive to minute changes in surface characteristics. Solvent-induced surface charge generation through acid-base interactions of acidic residual silanol groups with the solvent is enough to promote colloidal crystallization of modified silica particles. In addition, solvation forces at small interparticle distances are also involved in colloidal assembly. The characterization of CCs formed during sedimentation or via evaporative assembly revealed that C4 particles can form CCs more easily than C18 particles because of their low hydrophobicity; the latter can only form CCs in tetrahydrofuran when C18 chains with a high bonding density have extra hydroxyl side groups. These groups can only be hydrolyzed from trifunctional octadecyl silane but not from a monofunctional one. Moreover, after evaporative assembly, CCs formed from particles with different surface moieties exhibit different lattice spacings because their surface hydrophobicity and chemical heterogeneity can modulate interparticle interactions during the two main stages of assembly: the wet stage of crystal growth and the late stage of nano dewetting (evaporation of interparticle solvent bridges). Finally, short, alkyl-modified CCs were effectively assembled inside silica capillaries with a 100 μm inner diameter, laying the foundation for future chromatographic separation using capillary columns.

Different Temperature- and Pressure-Effects on the Water-Mediated Interactions between Hydrophobic, Hydrophilic, and Hydrophobic-Hydrophilic Nanoscale Surfaces

Water-mediated interactions (WMI) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic-hydrophilic) interactions have been mostly overlooked. Here we study the role of T and P of the WMI between nanoscale (i) hydrophobic-hydrophobic, (ii) hydrophilic-hydrophilic, and (iii) hydrophilic-hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic and hybrid interactions are all sensitive to P. However, while hydrophobic interactions [case (i)] are sensitive to T-variations, hydrophilic [case (ii)] and hybrid interactions [case (iii)] are practically T-independent. An analysis of the entropic and enthalpic contributions to the PMF for cases (i)-(iii) is also presented. Our results are important in understanding T- and P-induced protein denaturation, and the interactions of biomolecules in solution, including protein aggregation andphase separation processes. From the computational point of view, the results presented here are relevant in the design of implicit water models for the study of molecular and colloidal/nanoparticle systems at different thermodynamic conditions.

Supercooled liquid-like dynamics in water near a fully hydrated titania surface: Decoupling of rotational and translational diffusion

We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully hydrated surface of TiO₂ on the water dynamics. It is found that the universal relation between the rotational and translational diffusion characteristics of bulk water is broken in the water layers near the surface with the rotational diffusion demonstrating progressive retardation relative to the translational diffusion when approaching the surface. This kind of rotation-translation decoupling has so far only been observed in the supercooled liquids approaching glass transition, and its observation in water at a normal liquid temperature is of conceptual interest. This finding is also of interest for the application-significant studies of the water interaction with fully hydrated nanoparticles. We note that this is the first observation of rotation-translation decoupling in an ab initio MD simulation of water.

Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes

Water-mediated interactions (WMIs) play diverse roles in molecular biology. They are particularly relevant in geometrically confined spaces such as the interior of the chaperonin, at the interface between ligands and their binding partners, and in the ribosome tunnel. Inspired in part by the geometry of the ribosome tunnel, we consider confinement effects on the stability of peptides. We describe results from replica exchange molecular dynamics simulations of a system containing a 23-alanine or 23-serine polypeptide confined to nonpolar and polar nanotubes in the gas phase and when open to a water reservoir. We quantify the effect of water in determining the preferred conformational states of these polypeptides by calculating the difference in the solvation free energy for the helix and coil states in the open nanotube in the two phases. Our simulations reveal several possibilities. We find that nanoscopic confinement preferentially stabilizes the helical state of polypeptides with hydrophobic side chains, which is explained by the entropic stabilization mechanism proposed on the basis of polymer physics. Polypeptide chains with hydrophilic side chains can adopt helical structures within nanotubes, but helix formation is sensitive to the nature of the nanotube due to WMIs. We elaborate on the potential implications of our findings to the stability of peptides in the ribosome tunnel.