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Ratchet electrostático para la síntesis de péptidos sucesivos en una máquina molecular no ribosómica
Jun Ohnuki1, Yasuhiro Arimura2, Tomonori Kono3
1Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo 169-8555, Japan.
Journal of the American Chemical Society
|July 15, 2023
Resumen
La enzima RimK utiliza un mecanismo de trinquete electrostático, impulsado por ATP, para agregar secuencialmente moléculas de glutamato. Esta máquina molecular
Área de la Ciencia:
- La bioquímica
- Biología molecular
- Biología estructural
Sus antecedentes:
- RimK es una máquina de síntesis de péptidos no ribosómicos.
- Añade ácidos L-glutámicos a la proteína ribosómica S6 (RpsF) y sintetiza poli-α-glutamatos.
- El mecanismo de adición sucesiva de glutamato, impulsado por ATP, no está claro.
Objetivo del estudio:
- Investigar el mecanismo de síntesis de péptidos sucesivos de RimK.
- Elucidar el papel del ATP en la adición de glutamato.
- Determinar el mecanismo de unión y ligadura del glutamato.
Principales métodos:
- Simulación de la dinámica molecular (DM) de la unión del glutamato con RimK.
- Análisis de los estados estructurales de RimK.
- Determinación del paisaje de la energía de unión.
- Obtención de la estructura cristalina de RimK en presencia de RpsF.
Principales resultados:
- RimK adopta tres estados estructurales estables relacionados con la unión al ATP.
- El glutamato se une a una región cargada positivamente en RimK y se mueve a lo largo de ella.
- Los cambios conformacionales dependientes del ATP actúan como un ratillo electrostático, guiando al glutamato hacia el sitio activo.
- Se identificó el sitio de unión para el segundo glutamato, lo que sugiere un mecanismo de ligadura.
- La estructura cristalina reveló una densidad de electrones consistente con el extremo C de RpsF.
Conclusiones:
- Se propone un mecanismo para la síntesis de péptidos sucesivos por RimK.
- Los hallazgos revelan el intrincado funcionamiento de esta máquina molecular.
- El mecanismo comparte similitudes con otras máquinas moleculares de síntesis de péptidos.
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