Probing Cellular Intracellular Calcium Signaling and Sensing Through Computation

Calcium signaling regulates biological function across a broad range of tissue types and species, but several factors known to control Ca2+-dependent signaling efficiency have challenged both computational and experimental inquiry. There are significant gaps in our understanding of how nuances in protein structure and dynamics, or their intracellular distribution affect fundamentally important processes including how 1) the Ca2+ accumulates within localized intracellular regions 2) proteins bind Ca2+ with high affinity 3) Ca2+ ’sensor’ proteins regulate signaling cascades. Detailed knowledge about these topics and their inter-dependencies would yield new paradigms in how we view biology, physiology and health. Computer simulations are attractive in this regard, both for describing phenomena that are difficult to directly resolve experimentally, as well as forming integrative conceptual models spanning these underlying topics. However, several prominent hurdles render such transformative simulations cost-prohibitive. Among these, reducing the intractable computational expense involved modeling in fine detail processeses like transport governed by sub-nanometer to micron scales, atomistic-scale thermodynamics factors shaping ion/protein binding, and long-range forces that promote protein/protein signaling pathways, is likely the foremost challenge in biophysics today. In this proposal, we outline several multi-scale algorithmic advances that will ease this challenge, while providing insight into important Ca2+-driven processes that orchestrate life: • Aim 1 Investigate the hypothesis that Ca2+ interactions with intracellular ’microstructure’ control the efficiency and kinetics of Ca2+-signaling using nanoporous silica as a model system. • Aim 2 Investigate the hypothesis that intrinsic factors (protein sequence, binding site volume and strain) and extrinsic factors (peptide tethering) govern apparent Ca2+ affinity and its modulation by protein-protein interactions, using parvalbumin and Troponin as model enzymes. • Aim 3 Test the hypothesis that diffusion-limited association rates for Ca2+-sensor to ’tethered’ target peptides reflect a competition between electrostatic steering and molecular tether conformational selection, using calmodulin (CaM)/calcineurin (CaN) as an example.