Interacting Ions in Biophysics: Real is not Ideal

Abstract

Ions in water are important in biology, from molecules to organs. Classically, ions in water are treated as ideal noninteracting particles in a perfect gas. Excess free energy of ion was zero. Mathematics was not available to deal consistently with flows, or interactions with ions or boundaries. Non-classical approaches are needed because ions in biological conditions flow and interact. The concentration gradient of one ion can drive the flow of another, even in a bulk solution. A variational multiscale approach is needed to deal with interactions and flow. The recently developed energetic variational approach to dissipative systems allows mathematically consistent treatment of bio-ions Na, K, Ca and Cl as they interact and flow. Interactions produce large excess free energy that dominate the properties of the high concentration of ions in and near protein active sites, channels, and nucleic acids: the number density of ions is often more than 10 M. Ions in such crowded quarters interact strongly with each other as well as with the surrounding protein. Non-ideal behavior has classically been ascribed to allosteric interactions mediated by protein conformation changes. Ion-ion interactions present in crowded solutions--independent of conformation changes of proteins--are likely to change interpretations of allosteric phenomena. Computation of all atoms is a popular alternative to the multiscale approach. Such computations involve formidable challenges. Biological systems exist on very different scales from atomic motion. Biological systems exist in ionic mixtures (extracellular/intracellular solutions), and usually involve flow and trace concentrations of messenger ions (e.g., 10-7 M Ca2+). Energetic variational methods can deal with these characteristic properties of biological systems while we await the maturation and calibration of all atom simulations of ionic mixtures and divalents.

References in corpus (8)

• Tuning ion coordination preferences to enable selective permeation
• Ion specificity and the theory of stability of colloidal suspensions
• A transferable ab-initio based force field for aqueous ions
• Multiple Scales in the Simulation of Ion Channels and Proteins
• Binary non-additive hard sphere mixtures: Fluid demixing, asymptotic decay of correlations and free fluid interfaces
• Multi-ion conduction bands in a simple model of calcium ion channels
• Permeation as a Diffusion Process
• Ionic Interactions in Biological and Physical Systems: a Variational Treatment

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