Molecular Dynamics Simulations Suggest That Side-Chain Motions of Charged Amino Acids Determine Long-Range Effects in Proteins: An Egg of Coulomb

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Living systems cannot rely on random intermolecular approaches toward cell crowding, and hidden mechanisms must be present to favor only those molecular interactions required explicitly by the biological function. Electromagnetic messaging among proteins is proposed from the observation that charged amino acids located on the protein surface are mostly in adjacent sequence positions and/or in spatial proximity. Molecular dynamics (MD) simulations have been used to predict electric charge proximities arising from concerted motions of charged amino acid side chains in two protein model systems, human ubiquitin and the chitinolytic enzyme from Ostrinia furnacalis. This choice has been made for their large difference in size and sociality. Protein electrodynamics seems to emerge as the framework for a deeper understanding of the long-distance interactions of proteins with their molecular environment. Our findings will be valuable in orienting the design of proteins with specific recognition patterns.

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