Na-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling

The monovalent sodium ion (Na+) is a critical modulator of thrombin. However, the mechanism of thrombin's activation by Na+ has been widely debated for more than twenty years. Details of the linkage between thrombin and Na+ remain vague due to limited temporal and spatial resolution in experiments. In this work, we combine microsecond scale atomic-detailed molecular dynamics simulations with correlation network analyses and hidden Markov modeling to probe the detailed thermodynamic and kinetic picture of Na+-binding events and their resulting allosteric responses in thrombin. We reveal that ASP189 and ALA190 comprise a stable Na+-binding site (referred as "inner" Na+-binding site) along with the previously known one (referred as "outer" Na+-binding site). The corresponding newly identified Na+-binding mode introduces significant allosteric responses in thrombin's regulatory regions by stabilizing selected torsion angles of residues responsive to Na+-binding. Our Markov model indicates that the bound Na+ prefers to transfer between the two Na+-binding sites when an unbinding event takes place. These results suggest a testable hypothesis of a substrate-driven Na+ migration (ΔG ∼ 1.7 kcal mol-1) from the "inner" Na+-binding site to the "outer" one during thrombin's catalytic activities. The binding of a Na+ ion at the "inner" Na+-binding site should be inferred as a prerequisite for thrombin's efficient recognition to the substrate, which opens a new angle for our understanding of Na+-binding's allosteric activation on thrombin and sheds light on detailed processes in thrombin's activation.

Resumen tomado de PubMed (NCBI) para el registro citado, en el idioma original. La versión de referencia es la de la publicación original.

El resumen se deja sin traducir para conservar la redacción original de los autores.

Combining microsecond molecular dynamics, correlation networks and hidden Markov modeling, the authors identify a second "inner" sodium-binding site in thrombin and propose that Na+ migration to the known "outer" site (ΔG ~1.7 kcal/mol) accompanies substrate recognition.

Explore cómo esta investigación se conecta con la práctica clínica

Más estudios revisados por pares en la categoría «Desarrollo de fármacos».

• Hirudoterapia en medicina y odontología — Jha K et al. (2015)
• Terapia con sanguijuelas: una historia — Hyson J (2005)
• Hirudinas de la sanguijuela medicinal asiática Hirudinaria manillensis: iguales, pero diferentes — Lukas P et al. (2019)
• Transcriptomic analysis of the salivary gland of medicinal leech Hirudo nipponia — Lu Z et al. (2018)
• Molecular dynamic and pharmacological studies on protein-engineered hirudin variants of Hirudinaria manillensis and Hirudo medicinalis — Sun Y et al. (2022)
• Síntesis acelular de la variante 1 de hirudina de la sanguijuela hematófaga Hirudo medicinalis — Wüstenhagen D et al. (2020)
• Producción de variantes de hirudina mediante fábricas microbianas modificadas genéticamente — Zhang J, Lan N (2018)
• Hirudina en la trombocitopenia inducida por heparina — Lubenow N, Greinacher A (2002)
• La hirudina mejora la nefropatía diabética al inhibir la piroptosis mediada por Gsdmd — Han J et al. (2023)
• La hirudina como anticoagulante alternativo: una revisión histórica — Markwardt F (2002)

Ver toda la investigación analizada por la ASH →