Recent experiments
suggested that ATP can effectively stabilize
protein structure and inhibit protein aggregation when its concentration
is less than 10 mM, which is significantly lower than cosolvent concentrations
required in conventional mechanisms. The ultrahigh efficiency of ATP
suggests a unique mechanism that is fundamentally different from previous
models of cosolvents. In this work, we used molecular dynamics simulation
and experiments to study the interactions of ATPs with three proteins:
lysozyme, ubiquitin, and malate dehydrogenase. ATP tends to bind to
the surface regions with high flexibility and high degree of hydration.
These regions are also vulnerable to thermal perturbations. The bound
ATPs further assemble into ATP clusters mediated by Mg
2+
and Na
+
ions. More interestingly, in Mg
2+
-free
ATP solution, Na
+
at higher concentration (150 mM under
physiological conditions) can similarly mediate the formation of the
ATP cluster on protein. The ATP cluster can effectively reduce the
fluctuations of the vulnerable region and thus stabilize the protein
against thermal perturbations. Both ATP binding and the considerable
improvement of thermal stability of ATP-bound protein were verified
by experiments.