Proteins form complex biological
machineries whose functions in
the cell are highly regulated at both the cellular and molecular levels.
Cellular regulation of protein functions involves differential gene
expressions, post-translation modifications, and signaling cascades.
Molecular regulation, on the other hand, involves tuning an optimal
local protein environment for the functional site. Precisely how a
protein achieves such an optimal environment around a given functional
site is not well understood. Herein, by surveying the literature,
we first summarize the various reported strategies used by certain
proteins to ensure their correct functioning. We then formulate three
key physicochemical factors for regulating a protein’s functional
site, namely, (i) its immediate interactions, (ii) its solvent accessibility,
and (iii) its conformational flexibility. We illustrate how these
factors are applied to regulate the functions of free/metal-bound
Cys and Zn sites in proteins.