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Dinámica molecular y termodinámica de las interacciones proteína-ARN: la mutación de un residuo aromático conservado

D M Blakaj¹, K J McConnell, D L Beveridge

¹Chemistry Department, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, USA.

Journal of the American Chemical Society

|July 18, 2001

Resumen

La mutación del Phe56 del dominio U1A RNP a Ala desestabiliza la unión del U1 snRNA en 5.5 kcal/mol. Esto ocurre debido a la pérdida de interacciones de apilamiento y la dinámica peptídica alterada, que afecta tanto a las regiones conservadas como a las variables.

Área de la Ciencia:

La bioquímica es la bioquímica.
Biología Estructural Biología estructural.
Biología computacional Biología computacional.

Sus antecedentes:

El dominio N-terminal del RNP de U1A se une al bucle 2 del tallo del U1 snRNA.
Un residuo aromático conservado, Phe56, es crucial para esta interacción.
La mutación de Phe56 a Ala conduce a una desestabilización significativa del complejo.

Objetivo del estudio:

Para aclarar los orígenes moleculares de la desestabilización de 5,5 kcal / mol del complejo U1A-U1 snRNA sobre la mutación Phe56Ala.
Para investigar los cambios estructurales y dinámicos en los componentes de péptido y ARN.
Comprender la contribución de las regiones conservadas y variables a la afinidad vinculante.

Principales métodos:

Simulaciones de dinámica molecular (DM) de complejos de tipo salvaje y mutantes, péptidos libres y ARN libre.
Análisis del componente de energía libre para cuantificar las contribuciones a los cambios de afinidad vinculante.
Análisis de las propiedades estructurales y dinámicas, incluidas las interacciones de apilamiento y la flexibilidad del bucle.

Principales resultados:

Las simulaciones de MD revelan la pérdida de una interacción de apilamiento clave entre Phe56 y A6 del bucle del tallo 2 en el complejo mutante.
La mutación Phe56Ala causa un aumento de la dinámica en el bucle 3 del péptido dentro del complejo.
Se observaron cambios estructurales y dinámicos significativos en la hélice C y el bucle 3 en el péptido *libre* Phe56Ala, no solo en el complejo.
El análisis de energía libre confirma ~80% de desestabilización por la pérdida de apilamiento y ~20% por la adaptación alterada de U1A.

Conclusiones:

La desestabilización surge de una combinación de interacciones directas perdidas y dinámicas alteradas en el péptido libre.
La cooperación entre las regiones conservadas (Phe56) y variables (hélice C, bucle 3) contribuye significativamente a la reducción de la afinidad de unión.
Los efectos estructurales se manifiestan en el péptido libre, lo que pone de relieve la importancia de estudiar los estados complejos e individuales.

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