ATP Can Efficiently Stabilize Protein through a Unique Mechanism.

Area of Science:

• Biochemistry
• Molecular Biophysics
• Computational Biology

Background:

• Conventional cosolvents require high concentrations to stabilize proteins and inhibit aggregation.
• Recent findings indicate Adenosine triphosphate (ATP) stabilizes proteins at significantly lower concentrations (<10 mM).
• The mechanism of ATP's stabilizing effect is poorly understood and differs from established cosolvent models.

Purpose of the Study:

• To investigate the interaction mechanism between ATP and proteins (lysozyme, ubiquitin, malate dehydrogenase).
• To elucidate how ATP binding stabilizes protein structures against thermal perturbations.
• To explore the role of cations (Mg²⁺, Na⁺) in ATP-mediated protein stabilization.

Main Methods:

• Molecular dynamics simulations were employed to model ATP-protein interactions.
• Experimental techniques were used to validate simulation findings and assess protein stability.
• Analysis focused on ATP binding sites, cluster formation, and thermal perturbation responses.

Main Results:

• ATP preferentially binds to flexible, highly hydrated protein surface regions vulnerable to thermal stress.
• Bound ATP molecules self-assemble into clusters, mediated by Mg²⁺ or, in its absence, by Na⁺.
• ATP clusters effectively reduce fluctuations in vulnerable regions, significantly enhancing protein thermal stability.

Conclusions:

• ATP stabilizes proteins through a unique clustering mechanism on flexible surface sites, distinct from conventional cosolvents.
• The formation of ATP clusters, facilitated by cations, provides substantial protection against thermal denaturation.
• Experimental validation confirms ATP binding and the resulting improvement in protein thermal stability.