Ion-dependent protein–surface interactions from intrinsic solvent response

Abstract

The phyllosilicate mineral muscovite mica is widely used as a surface template for the patterning of macromolecules, yet a molecular understanding of its surface chemistry under varying solution conditions, required to predict and control the self-assembly of adsorbed species, is lacking. We utilize all-atom molecular dynamics simulations in conjunction with an electrostatic analysis based in local molecular field theory that affords a clean separation of long-range and short-range electrostatics. Using water polarization response as a measure of the electric fields that arise from patterned, surface-bound ions that direct the adsorption of charged macromolecules, we apply a Landau theory of forces induced by asymmetrically polarized surfaces to compute protein–surface interactions for two muscovite-binding proteins (DHR10-mica6 and C98RhuA). Comparison of the pressure between surface and protein in high-concentration KCl and NaCl aqueous solutions reveals ion-specific differences in far-field protein–surface interactions, neatly capturing the ability of ions to modulate the surface charge of muscovite that in turn selectively attracts one binding face of each protein over all others.

A deterministic code for transcription factor-DNA recognition through computation of binding interfaces

“…Electrostatic interactions are long-range forces ( 55 ), that follow the Coulomb’s law, whereby the potential bond energy varies inversely versus the distance between opposite charges. Hydrophobic interactions can occur between any residue depending on the increase in entropy gained by the removal of hydrophobic surface area from ordered solvating water.…”

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

“…Except when heavy metals are present, most large-scale molecular simulations employ nonpolarizable force fields for computational efficiency, meaning that the only contributor to solvent polarization between semirigid bodies is the induced polarization of water molecules (although see ref for recent advances and applications of polarizable force fields in biology). This polarization is precisely measurable in simulations of modest length, and the far-field component of the polarization can be extracted by convoluting the resulting signal with a Gaussian of characteristic width as in local molecular field (LMF) theory . The boundary surface fields needed for Landau theory are therefore much more accessible than the surface potential needed for the Poisson–Boltzmann theory, which must be zeroed appropriately and is nontrivial to compute …”

“…472 Applying the Landau-LMF framework to the early stages of assembly of muscovite-binding proteins, Prelesnik et al found that the far-field polarization over muscovite mica changes dramatically when aqueous potassium was replaced with sodium. 294 This seemingly benign change to solution conditions resulted in mineral-protein interaction pressures of opposite signs, highlighting the importance of obtaining mean-field model parameters carefully. Such an effect is experimentally visible for proteins like C98 RhuA (see section 2.1.5), which binds to muscovite with one dipolar face or the other depending on the identity of the ions that pattern the surface.…”

“…Furthermore, the magnitude of the macromolecular interaction is exquisitely sensitive to model input values, with pressures varying by orders of magnitude when parameters are tweaked by factors of two. 294 Thus, while mean-field theories are attractive due to the length scales accessible, their utility is contingent on the appropriateness of the parameters used. Even when it is possible to acquire these parameters with great reliability in bulk, there is often spatial nonuniformity.…”

Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins

“…In this study, we extend our previous work using all-atom molecular dynamics (MD) to interrogate the intrinsic response of the electrolyte solution at both mica–water and protein–water interfaces, now with specific focus on the physicochemical properties of two different, but closely related, types of mica. In that previous study, we were able to rigorously isolate the long-range polarization response between the front and back faces of two designed proteins in concentrated electrolyte solutions (3 M KCl and NaCl). Although these results provided a rationale for the observed specific ion effects that switch the binding face of these proteins, this long-range polarization was not a useful descriptor of the pronounced epitaxial alignment observed for lattices of both designed proteins.…”