nucleotidebound

Nucleotidebound is an adjective used in biochemistry and structural biology to describe a molecule, most commonly a protein, that has a nucleotide bound in a specific site. The bound nucleotide can be any cellular nucleotide, typically adenosine or guanosine triphosphates and their diphosphate forms (ATP, ADP, GTP, GDP). Nucleotide binding often induces conformational changes that regulate activity, stability, or interactions with other molecules. In many proteins the nucleotide state acts as a molecular switch, enabling transitions between different functional forms.

In proteins such as small GTPases, the nucleotide-bound state determines activity: GTP-bound forms are typically active, while GDP-bound forms are inactive. ATP binding and hydrolysis drive conformational cycles in motor proteins and various enzymes. ATPases and kinases often require an ATP-bound state for catalysis, energy transfer, or phosphate donation. Researchers frequently use non-hydrolyzable nucleotide analogs, such as GTPγS or AMP-PNP, to trap and study specific nucleotide-bound conformations.

In structural biology, nucleotidebound forms are described in crystal structures, cryo-electron microscopy reconstructions, or NMR studies to understand the relationship between binding, conformation, and function. Methods to assess nucleotide occupancy include direct observation of electron density, binding assays, and, when relevant, anomalous scattering for bound ions coordinated with the nucleotide.

The concept is also important in drug design and protein engineering, where altering nucleotide binding can modulate activity or stabilize particular functional states. The complementary state without nucleotide, the apo form, can exhibit distinct conformations and interaction patterns compared with nucleotide-bound forms.