Immune response within multicellular organisms often requires targeted and localized action, and extra-cellular communication by production and release of signaling proteins is known to be a key component of this biomolecular process. Here, we present an atomistic level computational investigation of one such signaling protein, Monocyte Chemoattractant Protein-1 (MCP-1), and explore how simulation geometry and microscopic environmental details affect the calculated diffusion coefficient. We use this molecular dynamics work to make accurate comparisons with experiments, and we additionally perform a geometric analysis that allows us to extend the findings with MCP-1 to other proteins spanning a variety of sizes. This has enabled us to derive a series of new relationships between protein structure and dynamics that allow researchers to estimate protein diffusivity more accurately than traditional means, this using only knowledge of a protein’s molecular weight.

Signaling protein diffusion and accurate molecular weight based estimations of biomolecule dynamics

253rd National Meeting (2017)

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