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Relajación dieléctrica en un sitio activo de la enzima: simulaciones de dinámica molecular interpretadas con un
1Department of Physics, University of Cyprus, PO 20537, CY 1678 Nicosia, Cyprus. archonti@ucy.ac.cy
Journal of the American Chemical Society
|November 1, 2001
Resumen
La relajación dieléctrica en las proteínas es crucial para los procesos químicos. Los modelos teóricos revelan que los reordenamientos de la cadena lateral de la proteína contribuyen significativamente a la carga de energía libre, lo que requiere diferentes constantes dieléctricas para los pasos estáticos y de relajación.
Área de la Ciencia:
- La biofísica es la biofísica.
- Química computacional es la química computacional.
- Mecanismos de las enzimas Mecanismos enzimáticos
Sus antecedentes:
- La relajación dieléctrica es vital para los procesos químicos de las proteínas, como la unión de ligandos y la transferencia de carga.
- La caracterización experimental de la relajación dieléctrica es un desafío, que requiere enfoques teóricos.
- La comparación de las simulaciones de dinámica molecular (DM) con los modelos de continuo ofrece valiosos conocimientos cualitativos.
Objetivo del estudio:
- Para analizar el proceso de inserción de carga, modelar la desprotonación/mutación en el sitio activo de la aspartil-tRNA sintetasa.
- Para investigar la relajación dieléctrica que involucra reorganizaciones de ligandos y cadenas laterales.
- Para comparar las simulaciones de MD con un modelo de continuo dieléctrico para obtener información sobre el comportamiento del sitio activo de la proteína.
Principales métodos:
- Simulaciones de inserción de carga en MD y modelos de continuo dieléctrico.
- Análisis de la relajación dieléctrica durante la inserción de carga.
- Complejos de modelado con sustrato de aspartato y análogo de asparagina.
Principales resultados:
- La relajación dieléctrica implica reordenamientos significativos de ligandos y cadenas laterales en el sitio activo.
- Estas reorganizaciones representan una parte sustancial de la carga total de energía gratuita.
- El modelo de continuo requiere constantes dieléctricas distintas para la estática (aprox. 1) y la relajación (3-6) pasos.
Conclusiones:
- El estudio cuantifica la contribución de la relajación dieléctrica a la carga de energía libre en los sitios activos de la enzima.
- Se necesitan diferentes constantes dieléctricas para las fases estática y de relajación en los modelos de continuo.
- La polarizabilidad local de la proteína en el sitio activo es comparable a las regiones no específicas.
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