Neutron and X-ray crystallographic analysis of the human α-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex.
Research article published in Biochimica et biophysica acta (2013)
Abstract
The protonation states and hydration structures of the α-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25Å resolution. The complex represents a model of the enzyme-product (EP) complex of α-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for Dδ1 and Dε2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen Oγ of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the Oγ atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.
Abstract sourced from PubMed (NCBI) for the cited record. See the original publication for the authoritative version.
Resumen
The protonation states and hydration structures of the α-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The atomic distances were estimated by carrying out X-ray crystallographic...
Por qué esto importa para la hirudoterapia
Este estudio empleó cristalografía conjunta de rayos X y neutrones para resolver los estados de protonación y la estructura de hidratación del complejo enzima-producto de α-trombina humana y bivalirudina a resolución casi atómica. Los hallazgos clave incluyen el estado de deuteración de la histidina catalítica (H57), la aparente desprotonación del nucleófilo Oγ de la serina (S195) y la hidratación detallada en el subsitio S1 y el Exosito I — ambos fundamentales para el reconocimiento de la bivalirudina. Para ASH, esto proporciona información estructural a nivel atómico sobre cómo un derivado de la hirudina interacciona con el sitio activo y los exositos de la trombina, profundizando en la comprensión mecanística de la anticoagulación inspirada en la sanguijuela. ADVERTENCIA: Este es un estudio biofísico puramente in vitro del fármaco sintético bivalirudina; no involucra sanguijuelas, saliva completa ni aplicación terapéutica in vivo, y su pertinencia se limita a la farmacología molecular de un análogo de la hirudina.
Citación
Neutron and X-ray crystallographic analysis of the human α-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex.
Yamada et al. · Biochimica et biophysica acta, 2013
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Añadido a la biblioteca ASH: May 28, 2026 · Última actualización del sitio: June 18, 2026