ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections.

ABSTRACT: In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP·Mg²⁺. In aqueous solution, two chelation geometries predominate, distinguished by bidentate and tridentate Mg²⁺-phosphate coordination. These are approximately isoenergetic but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP·Mg²⁺ coordination. Applying an enhanced sampling scheme to circumvent prohibitively slow sampling of transitions between coordination modes, we observed striking contradictions between Amber and CHARMM fo

SUBMITTER: Buelens FP 

PROVIDER: S-EPMC8023659 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature