In silico assessment of S100A12 monomer and dimer structural dynamics: implications for the understanding of its metal-induced conformational changes

Abstract

Changes in the concentration of different ions modulate several cellular processes, such as Ca²⁺ and Zn²⁺ in inflammation. Upon activation of immune system effector cells, the intracellular Ca²⁺ concentration rises propagating the activation signal, leading to degranulation and generation of reactive oxygen species, which increases the Zn²⁺ intracellular concentration as a consequence of the cellular antioxidant machinery. In this context, S100A12 is of special interest because it is a pro-inflammatory protein expressed in neutrophils whose structure and function are modulated by both Ca²⁺ and Zn²⁺. The current hypothesis about its mechanism of action was built based on biochemical and crystallographic data. However, there are missing connections between molecular structure and the way in which many events are concatenated at the triggering and along the inflammatory process. In this work we use molecular dynamics simulations to describe how variations in Zn²⁺ and Ca²⁺ concentrations modulate the structural dynamics of the calcium-free S100A12 dimer and monomer, which was not considered a part of the mechanism of action before. Our results suggest that (i) Zn²⁺ have a determinant role in the dimerization step, as well as in the unbinding of the Na⁺ complexed to the N-terminal EF-hand; (ii) the N-terminal EF-hand domain is the first to bind Ca²⁺, and not the C-terminal, as usually accepted; and that (iii) Ca²⁺ modulates the structural dynamics of H-III.